bluuebunny/crossref_metadata_2025_split huggingface dataset:
Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages
Authors: Miclot Tom , Hognon Cécilia , Bignon Emmanuelle , Terenzi Alessio , Grandemange Stéphanie , Barone Giampaolo , Monari Antonio 
Published: December 2021

AbstractDNA integrity is an important factor to assure genome stability and, more generally, cells and organisms’ viability. In presence of DNA damage, the normal cell cycle is perturbed while cells activate their repair processes. Although efficient, the repair system is not always able to ensure the complete restoration of gene integrity. In these cases, not only mutations may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold which induces apoptosis and the programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiations are the most toxic, due to their inherently difficult repair, which may lead to genomic instability. In this article we show, by using classical molecular simulations techniques, that differently from the canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show a remarkable structural stability, even in presence of two strand breaks. Since G4-DNA are recognized for their regulatory roles in cell senescence and gene expression, also involving oncogene, their stability can be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.
A 3D printable device allowing fast and reproducible longitudinal preparation of mouse intestines
Authors: DeLucia Beckey , Samorezov Sergey , Zangara Megan T , Markley Rachel L , Osborn Lucas J , Schultz Karlee B , McDonald Christine , Claesen Jan 
Published: December 2021

AbstractAccurate and reproducible analysis of mouse small and large intestinal lumen is key for research involving intestinal pathology in preclinical models. Currently, there is no easily accessible, standardized method that allows researchers of different skill levels to consistently dissect intestines in a time-efficient manner. Here, we describe the design and use of the 3D printed “Mouse Intestinal Slicing Tool” (MIST), which can be used to longitudinally prepare murine intestines for further analysis. We benchmarked the MIST against a commonly used procedure involving scissors to make a longitudinal cut along the intestines. Use of the MIST halved the time per mouse to prepare the intestines and outperformed alternative methods in smoothness of the cutting edge and general reproducibility. By sharing the plans for printing the MIST, we hope to contribute a uniformly applicable method for saving time and increasing consistency in studies of the mouse gastrointestinal tract.
Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases
Authors: Le Nguyen Thanh Thanh , Gao Huanyao , Liu Duan , Ye Zhenqing , Lee Jeong-Heon , Shi Geng-xian , Copenhaver Kaleigh , Zhang Lingxin , Wei Lixuan , Yu Jia , Zhang Cheng , Li Hu , Wang Liewei , Ordog Tamas , Weinshilboum Richard M. 
Published: December 2021

AbstractUnderstanding the function of non-coding genetic variants represents a formidable challenge for biomedicine. We previously identified genetic variants that influence gene expression only after exposure to a hormone or drug. Using glucocorticoid signaling as a model system, we have now demonstrated, in a genome-wide manner, that exposure to glucocorticoids triggered disease risk variants with previously unclear function to influence the expression of genes involved in autoimmunity, metabolic and mood disorders, osteoporosis and cancer. Integrating a series of pharmacogenomic and pharmacoepigenomic datasets, we identified the cis-regulatory elements and 3-dimensional interactions underlying the ligand-dependent associations between those genetic variants and distant risk genes. These observations increase our understanding of mechanisms of non-coding genetic variant-chemical environment interactions and advance the fine-mapping of disease risk and pharmacogenomic loci.
Thermal Analysis of Protein Stability and Ligand Binding in Complex Media
Authors: Eskew Matthew W. , Benight Albert S. 
Published: December 2021

ABSTRACTScreening of ligands that can bind to biologic products of in vitro expression systems typically requires some purification of the expressed biologic target. Such purification is often laborious and time consuming and a limiting challenge. What is required, that could represent an enormous advantage, is the ability to screen expressed proteins in the crude lysate stage without purification. For that purpose, we explore here the utility of differential scanning calorimetry (DSC) measurements for detecting the presence of specific proteins and their interactions with ligands in the complex media where they were prepared, i.e. crude lysates. Model systems were designed to mimic analogous conditions comparable to those that might be encountered in actual in vitro expression systems. Results are reported for several examples where DSC measurements distinctly showed differences in the thermal denaturation behaviors of the crude lysate alone, proteins and proteins plus binding ligands added to the crude lysate. Results were obtained for Streptavidin/Biotin binding in E. coli lysate, and binding of Angiotensin Converting Enzyme 2 (ACE2) by captopril or lisinopril in the lysate supernatant derived from cultured Human Kidney cells (HEK293). ACE2 binding by the reactive binding domain (RBC) of SARS-CoV-2 was also examined. Binding of ACE2 by RBC and lisinopril were similar and consistent with the reported ACE2 inhibitory activity of lisinopril.
Dioxin Disrupts Thyroid Hormone and Glucocorticoid Induction of klf9, a Master Regulator of Frog Metamorphosis
Authors: Han David T. , Zhao Weichen , Powell Wade H. 
Published: December 2021

AbstractFrog metamorphosis, the development of an air-breathing froglet from an aquatic tadpole, is controlled by thyroid hormone (TH) and glucocorticoids (GC). Metamorphosis is susceptible to disruption by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AHR) agonist. Krüppel-Like Factor 9 (klf9), an immediate early gene in the endocrine-controlled cascade of expression changes governing metamorphosis, can be synergistically induced by both hormones. This process is mediated by an upstream enhancer cluster, the klf9 synergy module (KSM). klf9 is also an AHR target. We measured klf9 mRNA following exposures to triiodothyronine (T3), corticosterone (CORT), and TCDD in the Xenopus laevis cell line XLK-WG. klf9 was induced 6-fold by 50 nM T3, 4-fold by 100 nM CORT, and 3-fold by 175 nM TCDD. Co- treatments of CORT and TCDD or T3 and TCDD induced klf9 7- and 11-fold, respectively, while treatment with all 3 agents induced a 15-fold increase. Transactivation assays examined enhancers from the Xenopus tropicalis klf9 upstream region. KSM-containing segments mediated a strong T3 response and a larger T3/CORT response, while induction by TCDD was mediated by a region ∼1 kb farther upstream containing 5 AHR response elements (AHREs). This region also supported a CORT response in the absence of readily-identifiable glucocorticoid responsive elements, suggesting mediation by protein-protein interactions. A functional AHRE cluster is positionally conserved in the human genome, and klf9 was induced by TCDD and TH in HepG2 cells. These results indicate that AHR binding to upstream AHREs represents an early key event in TCDD’s disruption of endocrine-regulated klf9 expression and metamorphosis.
Lifelong Cytomegalovirus and Early-Life Irradiation Synergistically Potentiate Age-Related Defects in Response to Vaccination and Infection
Authors: Pugh Jason L. , Coplen Christopher P. , Sukhina Alona S. , Uhrlaub Jennifer L. , Padilla-Torres Jose , Hayashi Tomonori , Nikolich-Zugich Janko 
Published: December 2021

ABSTRACTA popular “DNA-damage theory” of aging posits that unrepaired DNA damage leads to cellular (and organismal) senescence. Indeed, some hallmarks of immune aging are more prevalent in individuals exposed to Whole-Body Irradiation (WBI). To test this hypothesis in a model relevant to human immune aging, we examined separate and joint effects of lifelong latent Murine Cytomegalovirus (MCMV) and early-life WBI (i) over the course of the lifespan; (ii) in response to a West Nile virus (WNV) live attenuated vaccine; and (iii) following lethal WNV challenge subsequent to vaccination. We recently published that a single dose of non-lethal WBI in youth, on its own, was not sufficient to accelerate aging of the murine immune system despite causing widespread DNA damage and repopulation stress in hematopoietic cells. However, 4Gy sub-lethal WBI caused manifest reactivation of MCMV. Following vaccination and challenge with WNV in the old age, MCMV-infected animals experiencing 4Gy, but not lower, dose of sub-lethal WBI in youth had reduced survival. By contrast, old irradiated mice lacking MCMV and MCMV-infected, but not irradiated, mice were both protected to the same high level as the old non-irradiated, uninfected controls. Analysis of the quality and quantity of anti-WNV immunity showed that higher mortality in MCMV-positive WBI mice correlated with increased levels of MCMV-specific immune activation during WNV challenge. Moreover, we demonstrate that infection, including that by WNV, led to MCMV reactivation. Our data suggest that MCMV reactivation may be an important determinant of increased late-life mortality following early-life irradiation and late-life acute infection.
Single-molecule biophysics experiments in silico: Towards a physical model of a replisome
Authors: Maffeo Christopher , Chou Han-Yi , Aksimentiev Aleksei 
Published: December 2021

AbstractThe interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments out-right with computational mimics. Here we offer a blueprint for performing single-molecule studies in silico using a DNA binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic experimental assays. We show that, after initially correcting excess attraction between the DNA and protein, qualitative consistency between several experiments and their computational equivalents is achieved, while additionally providing a detailed portrait of the underlying mechanics. Finally the model is used to simulate the trombone loop of a replication fork, a large complex of proteins and DNA.
The functional evolution of termite gut microbiota
Authors: Arora Jigyasa , Kinjo Yukihiro , Šobotník Jan , Buček Aleš , Clitheroe Crystal , Stiblik Petr , Roisin Yves , Žifčáková Lucia , Park Yung Chul , Kim Ki Yoon , Sillam-Dussès David , Hervé Vincent , Lo Nathan , Tokuda Gaku , Brune Andreas , Bourguignon Thomas 
Published: December 2021

SUMMARYTermites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa. We intend to feel this gap and provide a global understanding of the functional evolution of termite gut microbiota. We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that key nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ∼150 million years ago. Therefore, the “world smallest bioreactor” has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.
MgrB dependent colistin resistance in Klebsiella pneumoniae is associated with an increase in host-to-host transmission
Authors: Bray Andrew S. , Smith Richard D. , Hudson Andrew W. , Hernandez Giovanna E. , Young Taylor M. , Ernst Robert K. , Zafar M. Ammar 
Published: December 2021

AbstractDue to its high transmissibility, Klebsiella pneumoniae (Kpn) is one of the leading causes of nosocomial infections. Here, we studied the biological cost of colistin resistance, an antibiotic of last resort, of this opportunistic pathogen using a murine model of gut colonization and transmission. Colistin resistance in Kpn is commonly the result of inactivation of the small regulatory protein MgrB. Without a functional MgrB, the two-component system PhoPQ is constitutively active, leading to increased lipid A modifications and subsequent colistin resistance. Using an engineered MgrB mutant, we observed that MgrB-dependent colistin resistance is not associated with a fitness defect during in vitro growth conditions. However, colistin-resistant Kpn colonizes the murine gut poorly, which may be due to the decreased production of capsular polysaccharide by the mutant. The colistin-resistant mutant of Kpn had increased survival outside the host when compared to the parental colistin-sensitive strain. We attribute this enhanced survivability to dysregulation of the PhoPQ two-component system and accumulation of the master stress regulator RpoS. The enhanced survival of the colistin resistant strain may be a key factor in the observed rapid host-to-host transmission in our model. Together, our data demonstrate that colistin-resistant Kpn experiences a biological cost in gastrointestinal colonization. However, this cost is mitigated by enhanced survival outside the host, increasing the risk of transmission. Additionally, it underscores the importance of considering the entire life cycle of a pathogen to truly determine the biological cost associated with antibiotic resistance.ImportanceThe biological cost associated with colistin resistance in Klebsiella pneumoniae (Kpn) was examined using a murine model of Kpn gut colonization and fecal-oral transmission. A common mutation resulting in colistin resistance in Kpn is a loss-of-function mutation of the small regulatory protein MgrB that regulates the two-component system PhoPQ. Even though colistin resistance in Kpn comes with a fitness defect in gut colonization, it increases bacterial survival outside the host enabling it to more effectively transmit to a new host. The enhanced survival is dependent upon the accumulation of RpoS and dysregulation of the PhoPQ. Hence, our study expands our understanding of the underlying molecular mechanism contributing to the transmission of colistin-resistant Kpn.
CTP synthase does not form cytoophidia in Drosophila interfollicular stalks
Authors: Wu Zheng , Liu Ji-Long 
Published: December 2021

ABSTRACTCTP synthase (CTPS) catalyzes the final step of de novo synthesis of the nucleotide CTP. In 2010, CTPS has been found to form filamentous structures termed cytoophidia in Drosophila follicle cells and germline cells. Subsequently, cytoophidia have been reported in many species across three domains of life: bacteria, eukaryotes and archaea. Forming cytoophidia appears to be a highly conserved and ancient property of CTPS. To our surprise, here we find that polar cells and stalk cells, two specialized types of cells composing Drosophila interfollicular stalks, do not possess obvious cytoophidia. Moreover, we show that Myc level is low in these two types of cells, supporting the idea that Myc regulates cytoophidium assembly. Treatment with a glutamine analog, 6-diazo-5-oxo-l-norleucine (DON), increases cytoophidium assembly in main follicle cells, but not in polar cells or stalk cells. Our findings provide an interesting paradigm for the in vivo study of cytoophidium assembly and disassembly among different populations of follicle cells.
Rapid genomic evolution inBrassica rapawith bumblebee selection in experimental evolution
Authors: Frachon Léa , Schiestl Florian P. 
Published: December 2021

AbstractBackgroundInsect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes remain largely unknown despite their importance in predicting adaptive responses to natural or to artificial selection. Based on a nine-generation experimental evolution study with fast cyclingBrassica rapaplants adapting to bumblebees, we investigate the genomic evolution associated with the previously observed parallel phenotypic evolution. In this current evolve and resequencing (E&R) study, we conduct a genomic scan of the allele frequency changes along the genome in bumblebee-pollinated and hand-pollinated plants and perform a genomic principal component analysis (PCA).ResultsWe highlight rapid genomic evolution associated with the observed phenotypic evolution mediated by bumblebees. Controlling for genetic drift, we observe significant changes in allelic frequencies at multiple loci. However, this pattern differs according to the replicate of bumblebee-pollinated plants, suggesting putative non-parallel genomic evolution. Finally, our study underlines an increase in genomic differentiation implying the putative involvement of multiple loci in short-term pollinator adaptation.ConclusionsOverall, our study enhances our understanding of the complex interactions between pollinator and plants, providing a steppingstone towards unravelling the genetic basis of plant genomic adaptation to biotic factors in the environment.
Layer 1 NDNF+ Interneurons Control Bilateral Sensory Processing in a Layer-dependent Manner
Authors: Vighagen Rasmus , Gesuita Lorenzo , Damilou Angeliki , Cavaccini Anna , Banterle Lila , Steenhuis Veerle , Karayannis Theofanis 
Published: December 2021

ABSTRACTBilateral sensory information is indispensable for navigating the world. In most mammals, signals sensed by either side of the midline will ultimately reach the cortex where they will be integrated for perception and appropriate action selection. Even though information transferred across the hemispheres is routed through the corpus callosum, how and which microcircuits are key in integrating it is not well understood. Here we identify an essential role for layer 1 NDNF+ inhibitory cells of mice in integrating bilateral whisker-evoked information in an NMDA receptor-dependent manner. Direct connections from the contralateral cortex and the ipsilateral side activate NDNF+ neurons, which subsequently inhibit the late spiking activity of underlying layer 2/3 neurons, but not layer 5. Our results identify a feed-forward regulatory pathway for bilateral cortical sensory processing of upper layer cortical neurons actuated via layer 1 NDNF+ interneurons.
Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development
Authors: Kim Junil , Rothová Michaela Mrugala , Madan Esha , Rhee Siyeon , Weng Guangzheng , Palma António M. , Liao Linbu , David Eyal , Amit Ido , Hajkarim Morteza Chalabi , Gutiérrez-García Andrés , Fisher Paul B. , Brickman Joshua M. , Gogna Rajan , Won Kyoung Jae 
Published: December 2021

SummaryDevelopment of multicellular organisms is orchestrated by persistent cell-cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single cell RNAseq (scRNAseq) technology cannot adequately analyze cell-cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell-cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified novel gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells overexpress Lhx5 and Nkx2-1 genes, when exclusively interacting with the definitive endoderm (DE) cell. Moreover, there was a reciprocal impact on the transcriptome of the DE cells, as they tend to overexpress Rax and Gsc genes when in contact with the NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-tSNE to display the pseudo-spatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis with potential broader implication in other physiologically relevant processes.SignificancePhysical contact between neighboring cells is known to induce transcriptional changes in the interacting partners. Accurate measurement of these cell-cell contact based influences on the transcriptome is a very difficult experimental task. However, determining such transcriptional changes will highly enhance our understanding for the developmental processes. Current scRNAseq technology isolates the tissue into individual cells, making it hard to determine the potential transcriptomic changes due to its interacting partners. Here, we combined PIC-seq and computational algorithms to identify cell-type contact dependent transcriptional profiles focusing on endoderm development. We have computationally identified and experimentally validated specific gene expression patterns depending upon the presence of specific neighboring cell types. Our study suggests a new way to study cell-cell interactions for embryogenesis.
Glucose-1,6-bisphosphate, a key metabolic regulator, is synthesized by a distinct family of α-phosphohexomutases widely distributed in prokaryotes
Authors: Neumann Niels , Friz Simon , Forchhammer Karl 
Published: December 2021

AbstractThe reactions of α-D-phosphohexomutases (αPHM) are ubiquitous, key to primary metabolism and essential for several processes in all domains of life. The functionality of these enzymes relies on an initial auto-phosphorylation step which requires the presence of α-D-glucose-1,6-bisphosphate (Glc-1,6-BP). While well investigated in vertebrates, the origin of this activator compound in bacteria is unknown. Here we show that the Slr1334 protein from the unicellular cyanobacterium Synechocysitis sp. PCC 6803 is a Glc-1,6-BP-synthase. Biochemical analysis revealed that Slr1334 efficiently converts fructose-1,6-bisphosphate (Frc-1,6-BP) and α-D-glucose-1-phosphate/α-D-glucose-6-phosphate into Glc-1,6-BP and also catalyzes the reverse reaction. As inferred from phylogenetic analysis, the slr1334 product belongs to a primordial subfamily of αPHMs that is present especially in deeply branching bacteria and also includes human commensals and pathogens. Remarkably, the homologue of Slr1334 in the human gut bacterium Bacteroides salyersiae catalyzes the same reaction, suggesting a conserved and essential role for the members of this αPHM subfamily.