bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perturbations in 3D genome organization can promote acquired drug resistance
Authors: Manjón Anna G , Hupkes Daan Peric , Liu Ning Qing , Friskes Anoek , Joosten Stacey , Teunissen Hans , Aarts Marleen , Prekovic Stefan , Zwart Wilbert , de Wit Elzo , van Steensel Bas , Medema René H 
Published: February 2021

AbstractAcquired drug resistance is a major problem in the treatment of cancer. hTERT-immortalized, untransformed RPE-1 (RPE) cells can acquire resistance to taxol by derepressing the ABCB1 gene, encoding for the multidrug transporter P-gP. Here we have investigated how the ABCB1 gene is derepressed. We show that activation of the ABCB1 gene is associated with reduced DNA methylation, reduced H3K9 trimethylation and increased H3K27 acetylation at the ABCB1 promoter. In addition, we find that the ABCB1 locus has moved away from the nuclear lamina in the taxol-resistant cells. This raises the question which of these alterations were causal to derepression. Directly modifying DNA methylation or H3K27 methylation had neither significant effect on ABCB1 expression, nor did it promote drug resistance. In contrast, the disruption of Lamin B Receptor (LBR), a component of the nuclear lamina involved in genome organization, did promote the acquisition of a taxol-resistant phenotype in a subset of cells. Using CRISPRa-mediated gene activation, we could further substantiate a model in which disruption of lamina association renders the ABCB1 gene permissive to derepression. Based on these data we propose a model in which nuclear lamina dissociation of a repressed gene allows for its activation, implying that deregulation of the 3D genome topology could play an important role in tumor evolution and the acquisition of drug resistance.
Endothelial cell senescence exacerbates pulmonary hypertension through Notch-mediated juxtacrine signaling
Authors: Ramadhiani Risa , Ikeda Koji , Miyagawa Kazuya , Ryanto Gusty Rizky Teguh , Tamada Naoki , Suzuki Yoko , Hirata Ken-ichi , Emoto Noriaki 
Published: February 2021

AbstractPulmonary arterial hypertension (PAH) is a fatal disease characterized by pathological pulmonary artery remodeling. Endothelial cells (EC) injury including DNA damage is critically involved in the vascular remodeling in PAH, and persistent injury leads to cellular senescence in ECs. Here, we show that EC senescence exacerbates pulmonary hypertension through Notch-mediated juxtacrine signaling. EC-specific progeroid mice that we recently generated showed exacerbated pulmonary hypertension after chronic hypoxia exposure, accompanied by the enhanced pulmonary arterial smooth muscle cells (PASMCs) proliferation in the distal pulmonary arteries. Mechanistically, we identified that senescent ECs highly expressed Notch ligands, and thus activated Notch signaling in PASMCs, leading to enhanced PASMCs proliferation and migration capacities. Consistently, pharmacological inhibition of Notch signaling attenuated the effects of senescent ECs on SMCs functions in vitro, and on the pulmonary hypertension in EC-specific progeroid mice in vivo. These data establish EC senescence as a crucial disease-modifying facor in PAH.
Establishing regulated unconventional secretion for production of heterologous proteins
Authors: Hussnaetter Kai P. , Philipp Magnus , Müntjes Kira , Feldbrügge Michael , Schipper Kerstin 
Published: February 2021

AbstractHeterologous protein production is a highly demanded biotechnological process. Secretion of the product to the culture broth is advantageous because it drastically reduces downstream pro-cessing costs. We exploit unconventional secretion for heterologous protein expression in the fungal model microorganism Ustilago maydis. Proteins of interest are fused to carrier chitinase Cts1 for export via the fragmentation zone of dividing yeast cells in a lock-type mechanism. Here, we are first to develop regulatory systems for unconventional protein secretion. This enables uncoupling the accumulation of biomass and protein synthesis of a product of choice from its export. Regulation was successfully established at two different levels using transcriptional and post-translational induction strategies. As a proof-of-principle, we applied autoinduction based on transcriptional regulation for the production and secretion of functional anti-Gfp nanobodies. The presented developments comprise tailored solutions for differentially prized products and thus constitute another important step towards a competitive protein production platform.
ChIPflow: from raw data to epigenomic dynamics
Authors: Daunesse Maëlle , Legendre Rachel , Varet Hugo , Pain Adrien , Chica Claudia 
Published: February 2021

AbstractWe present ChIPflow, a Snakemake-based pipeline for epigenomic data from the raw fastq files to the differential analysis. It can be applied to any chromatin factor, e.g. histone modification or transcription factor, which can be profiled with ChIP-seq. ChIPflow streamlines critical steps like the quality assessment of the immunoprecipitation using cross-correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ChIPflow provides linear and nonlinear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed binding/marking differences.ChIPflow can process in parallel multiple chromatin factors with different experimental designs, number of biological replicates and/or conditions. It also facilitates the specific parametrisation of each dataset allowing both narrow or broad peak calling, as well as comparisons between the conditions using multiple statistical settings. Finally, complete reports are produced at the end of the bioinformatic and the statistical part of the analysis, which facilitate the data quality control and the interpretation of the results.We explored the discriminative power of the statistical settings for the differential analysis, using a published dataset of three histone marks (H3K4me3, H3K27ac and H3K4me1) and two transcription factors (Oct4 and Klf4) profiled with ChIP-seq in two biological conditions (shControl and shUbc9). We show that distinct results are obtained depending on the sources of ChIP-seq variability and the dynamics of the chromatin factor under study. We propose that ChIPflow can be used to measure the richness of the epigenomic landscape underlying a biological process by identifying diverse regulatory regimes and the associated genes sets.
Transmission of pre-XDR and XDR-TB in the Mumbai Metropolitan Region, India
Authors: Dreyer Viola , Mandal Ayan , Dev Prachi , Merker Matthias , Barilar Ivan , Utpatel Christian , Nilgiriwala Kayzad , Rodrigues Camilla , Crook Derrick W. ,   the CRyPTIC Consortium, Mistry Nerges , Niemann Stefan 
Published: February 2021

AbstractMultidrug-resistant (MDR) and extensively drug resistant (XDR)Mycobacterium tuberculosiscomplex (MTBC) strains are a great challenge for tuberculosis (TB) control in India. Still, factors driving the MDR/XDR epidemic in India are not well defined.To address this, whole genome sequencing (WGS) data from 1 852 MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai were used for phylogenetic strain classification, resistance prediction, and cluster analysis (12 allele distance threshold). Factors associated with pre-XDR/XDR-TB were defined by odds ratios and a multivariate logistic regression model.Overall, 1 017 MTBC strains were MDR, out of which 57.8 % (n=591) were pre-XDR, and 17.9 % (n=183) were XDR. Lineage 2 (L2) strains represented 41.7 % of the MDR, 77.2 % of the pre-XDR, and 86.3 % of the XDR strains, and were significantly associated with pre-XDR/XDR-TB (P < 0.001). Cluster rates were high among MDR (78 %) and pre-XDR/XDR (85 %) strains with three dominant L2 strain clusters (Cl 1-3) representing half of the pre-XDR and two thirds of the XDR-TB cases. Cl 1 strains accounted for 52.5 % of the XDR MTBC strains. Transmission could be confirmed by identical mutation patterns of particular pre-XDR/XDR strains.As a conclusion high rates of pre-XDR/XDR strains among MDR-TB patients require rapid changes in treatment and control strategies. Transmission of particular pre-XDR/XDR L2 strains is the main driver of the pre-XDR/XDR-TB epidemic. Accordingly, control of the epidemic in the region requires measures with stopping transmission especially of pre-XDR/XDR L2 strains.
A variant selection framework for genome graphs
Authors: Jain Chirag , Tavakoli Neda , Aluru Srinivas 
Published: February 2021

AbstractMotivationVariation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias. Vast catalogues of genetic variants for many species now exist, and it is natural to ask which among these are crucial to circumvent reference bias during read mapping.ResultsIn this work, we propose a novel mathematical framework for variant selection, by casting it in terms of minimizing variation graph size subject to preserving paths of lengthαwith at mostδdifferences. This framework leads to a rich set of problems based on the types of variants (SNPs, indels), and whether the goal is to minimize the number of positions at which variants are listed or to minimize the total number of variants listed. We classify the computational complexity of these problems and provide efficient algorithms along with their software implementation when feasible. We empirically evaluate the magnitude of graph reduction achieved in human chromosome variation graphs using multipleαandδparameter values corresponding to short and long-read resequencing characteristics. When our algorithm is run with parameter settings amenable to long-read mapping (α= 10 kbp,δ= 1000), 99.99% SNPs and 73% indel structural variants can be safely excluded from human chromosome 1 variation graph. The graph size reduction can benefit downstream pan-genome analysis.Implementationhttps://github.com/at-cg/VFContactchirag@iisc.ac.in,neda.tavakoli@gatech.edu,aluru@cc.gatech.edu
Evidence that standard metabolic rate and risk-taking to breathe air are linked to boldness, activity level and exploratory behaviour in a catfish
Authors: McKenzie David J. , Belão Thiago C. , Killen Shaun S. , Blasco Felipe R. , Svendsen Morten B.S. , Rantin F. Tadeu 
Published: February 2021

AbstractWe used an air-breathing catfish,Clarias gariepinus,to investigate the hypothesis that individual variation in metabolic rate, and the propensity to take risks to obtain a resource (oxygen from air), would be correlated with behavioural tendencies such as boldness, activity level and exploratory behaviour. The standard metabolic rate (SMR) of 58 juvenile catfish was positively correlated with their rates of aerial respiration in daylight when surfacing was inherently risky. SMR was positively correlated with boldness measured in two contexts, namely the time-lag to resume air-breathing in a potentially dangerous environment (T-res, measured in a respirometer), and the timelag to enter the centre of a novel environment (T-centre, measured in an open field test (OFT)). These two measures of boldness were very highly correlated. Thus, these data support the hypothesis that high SMR and an associated tendency to take risks to acquire resources are linked to increased boldness in animals. Individual SMR was positively correlated with the proportion of time the fish spent moving in the OFT, but was negatively correlated with movement speed. The data confirmed previous observations that these catfish may exhibit a bimodal distribution of T-res phenotypes, whereby individuals either resumed air-breathing relatively rapidly (< 85 min, bold n = 26) or more slowly (> 115 min, shy n = 31) after a startle stimulus. Bold T-res phenotypes had significantly higher SMR than shy; breathed more air during the day, and showed greater boldness but less activity and exploration in the OFT. No parallel bold/shy dichotomy was observed, however, in any measure of boldness in the OFT. Therefore, the data support propositions regarding how SMR and risk-taking should relate to boldness, but provide mixed results about how SMR relates to activity and exploration, and whether bold/shy is a dichotomy or spectrum.
Pluripotent stem cell SOX9 and INS reporters facilitate differentiation into insulin-producing cells
Authors: Dettmer Rabea , Niwolik Isabell , Mehmeti Ilir , Jörns Anne , Naujok Ortwin 
Published: February 2021

AbstractDifferentiation of human pluripotent stem cells into insulin-producing stem cell-derived beta cells harbors great potential for research and therapy of diabetes. The SOX9 gene plays a crucial role during development of the pancreas and particularly in the development of insulin-producing cells as SOX9+ cells form the source for NEUROG3+ endocrine progenitor cells. For the purpose of easy monitoring of differentiation efficiencies into pancreatic progenitors and insulin-producing cells, we generated new reporter lines by knocking in a P2A-H-2Kk-F2A-GFP2 reporter genes into theSOX9locus and a P2A-mCherry reporter gene into theINSlocus mediated by CRISPR/CAS9-technology. The knock-ins enable co-expression of the endogenous genes and reporter genes, report the endogenous gene expression and enable the purification of pancreatic progenitors and insulin-producing cells using FACS or MACS. Using these cell lines we established a new differentiation protocol geared towards SOX9+ cells to efficiently drive human pluripotent stem cells into glucose-responsive beta cells.
“A feed-forward Ca2+-dependent mechanism boosting glycolysis and OXPHOS by activating Aralar-malate-aspartate shuttle, upon neuronal stimulation”
Authors: Pérez-Liébana Irene , Juaristi Inés , González-Sánchez Paloma , González-Moreno Luis , Rial Eduardo , Podunavac Maša , Zakarian Armen , Molgó Jordi , Pardo Beatriz , Satrústegui Jorgina , del Arco Araceli 
Published: February 2021

SummaryCalcium is an important second messenger regulating a bioenergetic response to the workloads triggered by neuronal activation. In cortical neurons using glucose as only fuel, activation by NMDA, which elicits a strong workload dependent on Na+entry, stimulates glucose uptake, glycolysis, pyruvate and lactate production, and OXPHOS in a Ca2+-dependent way. We find that Ca2+-upregulation of glycolysis, pyruvate levels and respiration, but not glucose uptake, all depend on Aralar/AGC1/Slc25a12, the Ca2+regulated mitochondrial aspartate-glutamate carrier, component of the malate-aspartate shuttle (MAS). Ca2+-activation of MAS increases pyruvate production, which directly fuels workload-stimulated respiration. Also it stimulates glycolysis. MCU silencing had no effect indicating that none of these processes required mitochondrial Ca2+. The neuronal respiratory response to carbachol was also dependent on Aralar, but not on MCU. We also find that cortical neurons are endowed with a constitutive ER-to-mitochondria Ca2+flow maintaining basal cell bioenergetics in which Ryanodine receptors, RyR2, rather than InsP3R, are responsible for Ca2+release, and in which MCU does not participate. The results reveal that in neurons using glucose MCU does not participate in OXPHOS regulation under basal or stimulated conditions, while Aralar-MAS appears as the major Ca2+-dependent pathway tuning simultaneously glycolysis and OXPHOS to neuronal activation.
Latent gammaherpesvirus exacerbates arthritis and requires age-associated B cells
Authors: Mouat Isobel C. , Morse Zach J. , Shanina Iryna , Brown Kelly L. , Horwitz Marc S. 
Published: February 2021

AbstractEpstein-Barr virus (EBV) infection is associated with rheumatoid arthritis (RA) in adults, though the nature of the relationship remains unknown. Herein, we examine the contribution of viral infection to the severity of arthritis in mice. We provide the first evidence that latent gammaherpesvirus infection enhances clinical arthritis, modeling EBV’s role in RA. Mice latently infected with a murine analog of EBV, gammaherpesvirus 68 (γHV68), develop more severe collagen-induced arthritis and a Th1-skewed immune profile reminiscent of human disease. We demonstrate that disease enhancement requires viral latency and is not due to active virus stimulation of the immune response. Age-associated B cells (ABCs) are associated with several human autoimmune diseases, including arthritis, though their contribution to disease is not well understood. Using ABC knockout mice, we provide the first evidence that ABCs are mechanistically required for viral enhancement of disease, thereby establishing that latent gammaherpesvirus infection stimulates ABCs to provoke arthritis.Conflict of interest statementThe authors have declared that no conflict of interest exists.
Sleeping at the Switch
Authors: Bouchard Maude , Lina Jean-Marc , Gaudreault Pierre-Olivier , Lafrenière Alexandre , Dubé Jonathan , Gosselin Nadia , Carrier Julie 
Published: February 2021

ABSTRACTSleep slow waves are studied for their role in brain plasticity, homeostatic regulation and their changes during aging. Here, we address the possibility that two types of slow waves co-exist in humans. Thirty young and 29 older adults underwent a night of polysomnographic recordings. Using theTransition frequency, slow waves with a slow transition (slow switchers) and with a fast transition (fast switchers) were discovered. Slow switchers had a high EEG connectivity along their depolarization transition while fast switchers had a lower connectivity dynamic and dissipated faster during the night. Aging was associated with lower temporal dissipation of sleep pressure in slow and fast switchers and lower EEG connectivity at the microscale of the oscillations, suggesting a decreased flexibility in the connectivity network of older individuals. Our findings show that two different types of slow waves with possible distinct underlying functions, coexist in the slow wave spectrum.
AN INULIN-TYPE FRUCTAN ENRICHED EXCLUSIVE ENTERAL NUTRITION FORMULA SUPPRESSES COLITIS THROUGH GUT MICROBIOME MODULATION AND PROMOTING EXPANSION OF ANTI-INFLAMMATORY T CELL SUBSETS
Authors: Healey Genelle R. , Tsai Kevin , Lisko Daniel J. , Cook Laura , Vallance Bruce A. , Jacobson Kevan 
Published: February 2021

AbstractBackground & AimsExclusive enteral nutrition (EEN) is used to treat pediatric Crohn’s disease (CD), but therapeutic benefits are not long lasting. Due to reported lower efficacy EEN is not routinely used to treat pediatric ulcerative colitis (UC). Inulin-type fructans (IN) beneficially modulate the gut microbiome and promote expansion of anti-inflammatory immune cells. We hypothesized that enriching EEN with IN (EENIN) would enhance treatment efficacy. To test this, we examined the effects of EEN-IN on colitis development, the gut microbiome and CD4+T cells using an adoptive T cell transfer model of colitis.MethodsTCR-ß deficient mice were randomized to one of four groups: 1) Control, 2) Chow, 3) EEN and 4) EEN-IN, and naïve CD4+T cells were adoptively transferred into groups 2-4, after which mice were monitored for 5-weeks prior to experimental endpoint.ResultsMice fed EEN-IN showed greater colitis protection, with colonic shortening, goblet cell and crypt density loss reduced over that of EEN fed mice and reduced disease activity and immune cell infiltration compared to chow fed mice, and less crypt hyperplasia and higher survival compared to both groups. EENIN mice maintained colonic mucus layer thickness and had increased levels of Foxp3+IL-10+and Rorγt+IL- 22+and reduced levels of Tbet+IFNγ+and Tbet+TNF+CD4+T cells. EEN-IN also lead to higher butyrate,Bifidobacteriumspp. andBacteroidesspp. concentrations.ConclusionThe EEN-IN group showed reduced colitis development as compared to the chow and EEN groups. This highlights the potential benefits of EEN-IN as a novel induction therapy for pediatric CD and UC patients.SynopsisWe demonstrated that inulin-type fructan enriched exclusive enteral nutrition formula reduced colitis development likely due to butyrate-dependent pathways that helped preserve the mucus layer and promote an anti-inflammatory intestinal environment via expansion of regulatory T cells.
Dynamic modulation of spleen germinal center reactions by gut bacteria duringPlasmodiuminfection
Authors: Mandal Rabindra K. , Denny Joshua E. , Namazzi Ruth , Opoka Robert O. , Datta Dibyadyuti , John Chandy C. , Schmidt Nathan W. 
Published: February 2021

AbstractGut microbiota educate the local and distal immune system in early life to imprint long-term immunological outcomes while maintaining the capacity to dynamically modulate the local mucosal immune system throughout life. It is unknown if gut microbiota provide signals that dynamically regulate distal immune responses following an extra-gastrointestinal infection. Using the murine model of malaria, we show that existing spleen germinal center reactions are malleable to dynamic cues provided by gut bacteria that impact parasite burden. Gut bacteria composition was also shown to correlate with the severity of malaria in humans. Whereas antibiotic-induced changes in gut bacteria has been associated with immunopathology or impairment of immunity, our data demonstrate antibiotic-induced changes in gut bacteria can enhance humoral immunity toPlasmodium. This effect is not universal, but depends on baseline gut bacteria composition. These data demonstrate the dynamic communications that exist between gut bacteria and the systemic immune system as well as the plasticity of an ongoing humoral immune response.SummaryThe study by Mandal R, et al. provides new insight into the dynamic communications that exist between gut bacteria, the systemic immune system and the plasticity of spleen germinal center reactions duringPlasmodiuminfection.
Deficits of Hippocampal RNA Editing and Social Interaction Resulting from Prenatal Stress are Mitigated by Clozapine
Authors: Bristow Greg C. , Dong Erbo , Nwabuisi-Heath Evelyn , Gentile Saverio , Guidotti Alessandro , Sodhi Monsheel 
Published: February 2021

AbstractBackgroundNeurodevelopmental deficits resulting from prenatal stress are associated with neurological disorders that include deficits of social behavior, such as schizophrenia1and autism2–7. Studies of human brain and animal models indicate that an epitranscriptomic process known as ‘RNA editing’ contributes to the pathophysiology of these disorders, which occur more frequently in males than in females8–20. RNA editing plays an important role in brain development through its modification of excitatory and inhibitory neurotransmission21.MethodsWe exposed pregnant mice to restraint stress three times daily during gestational weeks 2 and 3. We treated the adult male offspring with haloperidol (1mg/kg), clozapine (5mg/kg) or saline twice daily for 5 days. Subsequently we measured social interaction behavior (SI) and locomotor activity, followed by next-generation sequencing analyses of hippocampal RNA editing.ResultsMice exposed to PRS exhibited reduced SI, which correlated with hippocampal RNA editing of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunits GluA2, GluA3 and GluA4, the potassium channel Kv1.1, the calcium channel subunit Cav1.3, calcium-dependent secretion activator (CAPS-1) and the calcium-dependent cell adhesion protein, cadherin 22 (CDH22). Treatment with clozapine, but not haloperidol, normalized SI behavior, and selectively reduced the deficits in GluA2 RNA editing in PRS mice.ConclusionsRNA editing may contribute to impaired hippocampal function after exposure to PRS. The efficacy of clozapine in improving SI behavior may include indirect stimulation of GluA2 RNA editing in the hippocampus. Although these data are from male mice and not humans, the results suggest a new molecular pathway by which PRS leads to life-long impairments of hippocampal function.