bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creation of X-linked Alport Syndrome Rat Model withCol4a5Deficiency
Authors: Namba Masumi , Kobayashi Tomoe , Kohno Mayumi , Koyano Takayuki , Hirose Takuo , Fukushima Masaki , Matsuyama Makoto 
Published: April 2021

SummaryAlport syndrome is an inherited chronic human kidney disease, characterized by glomerular basement membrane abnormalities. This disease is caused by mutations inCOL4A3, COL4A4, orCOL4A5gene. The knockout mice forCol4α3, Col4α4, andCol4α5are developed and well characterized for the study of Alport syndrome. However, disease progression and effects of pharmacological therapy depend on the genetic variability. This model is reliable only to mice. Therefore in this study, we created a novel Alport syndrome rat model utilizing rGONAD technology.Col4α5deficient rats showed hematuria, proteinuria, high levels of BUN, Cre, and then died at 18 to 28 weeks of age (Hemizygous mutant males). Histological and ultrastructural analyses displayed the abnormalities including parietal cell hyperplasia, mesangial sclerosis, and interstitial fibrosis. Then, we demonstrated that α3/α4/α5 (IV) and α5/α5/α6 (IV) chains of type IV collagen disrupted in theCol4α5deficient rats. Moreover, immunofluorescence analyses revealed that some glomeruli ofCol4α5mutant rats were found to be disrupted from postnatal day 0. Thus,Col4α5mutant rat is a reliable candidate for Alport syndrome model for underlying the mechanism of renal diseases and further identifying potential therapeutic targets for human renal diseases.
Genome-wide comprehensive analysis of miRNAs and their target genes expressed in resistant and susceptibleCapsicum annuumlandrace duringPhytophthora capsiciinfection
Authors: Rabuma Tilahun , Gupta Om Prakash , Chhokar Vinod 
Published: April 2021

AbstractMiRNAs regulate plants responses to fungal infection and immunity by modulating the gene expression. Despite extensive works on miRNA’s role during plant-fungus interaction, work inCapsicum annuum-Phytophthora capsicipathosystem is limited. Therefore, in the current study, genome-wide known and novel miRNAs were identified in two contrasting chilli pepper landraces,i.e.GojamMecha_9086 (resistant) and Dabat_80045 (susceptible) duringP. capsiciinfection. The small RNA deep sequencing resulted in 79 known miRNAs corresponding to 24 miRNAs families and 477 novel miRNAs along with 22,895 potential targets, including 30 defence-related genes againstP. capsiciinfection. The expression analysis of ∼29 known & 157 novel miRNAs in resistant and 30 known and 176 novel miRNAs in susceptible landrace revealed differential accumulation pattern. RT-qPCR of a set of 8 defence related miRNAs representing 4 novel (Pz-novel-miR428-1, Pz-novel-miR160-1, Pz-novel-miR1028-1, Pz-novel-miR204-1) and 4 known (Pz-known-miR803-1, Pz-known-miR2059-1, Pz-known-miR2560-1, Pz-known-miR1872-1) revealed differential accumulation pattern in both resistant and susceptible landrace. Additionally, validation of 8 target genes of corresponding miRNAs using RA-PCR, which as good as 5’ RLM-RACE, revealed an inverse relation with their corresponding miRNAs suggesting their key role during disease response. This study provides comprehensive genome-wide information about the repertoire of miRNAs and their target genes expressed in resistant and susceptible chilli pepper landrace, which can serve as a valuable resource for better understanding the post-transcriptional regulatory mechanism duringC. annuum-P. capsicipathosystem.
CRTC2 regulates plasma cell metabolism and survival
Authors: Hong Jason S , Ahsan Fasih M , Montecino-Rodriguez Encarnacion , Pioli Peter D , Lee Min-sub , Nguyen Thang L , Brooks David G , Golovato Justin , Niazi Kayvan R , Dorshkind Kenneth , Teitell Michael A 
Published: April 2021

AbstractAntibody secreting cell (ASC) function and longevity determines the strength and durability of a humoral immune response. Previously, we identified the inactivation of the CREB-regulated transcriptional coactivator-2 (CRTC2) in anin vitroB cell differentiation assay that produced functional ASCs. However, the requirement for CRTC2 inactivation in ASC physiologyin vivoremains unknown. Using transgenic (TG) mice that express a constitutively active form of CRTC2 (Crtc2-AA) as an experimental tool, we demonstrate thatCrtc2repression in plasma cells (PCs) is an intrinsic requirement for ASC metabolic fitness. Sustained CRTC2 activity shortens the survival of splenic and bone marrow PCs, resulting in reduced numbers of long-lived PCs and antibody deficits against T cell dependent and independent antigens, and an acute viral infection. TG PCs resemble short-lived PCs with reductions in glycolysis, oxidative metabolism, spare respiratory capacity, and antibody secretion. Mechanistically,Crtc2repression is necessary for the fidelity of PC gene expression and mRNA alternative-splicing programs. Combined,Crtc2repression in PCs must occur to support PC metabolism and extend ASC survival during a humoral immune response.
ARickettsiellaendosymbiont is a potential source of essential B-vitamins for the poultry red mite,Dermanyssus gallinae
Authors: Price Daniel R. G. , Bartley Kathryn , Blake Damer P. , Karp-Tatham Eleanor , Nunn Francesca , Burgess Stewart T. G. , Nisbet Alasdair J. 
Published: April 2021

AbstractObligate blood-sucking arthropods rely on symbiotic bacteria to provision essential B vitamins that are either missing or at sub-optimal amounts in their nutritionally challenging blood diet. The poultry red miteDermanyssus gallinae, an obligate blood-feeding ectoparasite, is primarily associated with poultry and a serious threat to the hen egg industry. Thus far, the identity and biological role of nutrient provisioning bacterial mutualists fromD. gallinaeare little understood. Here, we demonstrate that aRickettsiellaGammaproteobacteria in maternally transmitted inD. gallinaeand universally present inD. gallinaemites collected at different sites throughout Europe. In addition, we report the genome sequence of uncultivable endosymbiont “CandidatusRickettsiella rubrum” fromD. gallinaeeggs. The endosymbiont has a circular 1. 89 Mbp genome that encodes 1973 protein. Phylogenetic analysis confirms the placementR. rubrumwithin theRickettsiellagenus, closely related to a facultative endosymbiont from the pea aphid andCoxiella-like endosymbionts from blood feeding ticks. Analysis of theR. rubrumgenome reveals many protein-coding sequences are either pseudogenized or lost, butR. rubrumhas retained several B vitamin biosynthesis pathways, confirming the importance of these pathways in evolution of its nutritional symbiosis withD. gallinae. In silicometabolic pathway reconstruction revealed thatR. rubrumis unable to synthesise protein amino acids and therefore these nutrients are likely provisioned by the host. In contrastR. rubrumretains biosynthetic pathways for B vitamins: thiamine (vitamin B1) via the salvage pathway; riboflavin (vitamin B2) and pyridoxine (vitamin B6) and the cofactors: flavin adenine dinucleotide (FAD) and coenzyme A (CoA) that likely provision these nutrients to the host. We propose that bacterial symbionts which are essential to blood-feeding arthropod survival provide attractive targets for the development of novel control methods.
Transcriptomic analysis of quinoa reveals a group of germin-like proteins induced byTrichoderma
Authors: Rollano-Peñaloza Oscar M. , Mollinedo Patricia A. , Widell Susanne , Rasmusson Allan G. 
Published: April 2021

AbstractSymbiotic strains of fungi in the genusTrichodermaaffect growth and pathogen resistance of many plant species, but the interaction is not known in molecular detail. Here we describe the transcriptomic response of two cultivars of the cropChenopodium quinoato axenic co-cultivation withTrichoderma harzianumBOL-12 andTrichoderma afroharzianumT22. The response ofC. quinoaroots to BOL-12 and T22 in the early phases of interaction was studied by RNA sequencing and RT-qPCR verification. Interaction with the two fungal strains induced partially overlapping gene expression responses. Comparing the two plant genotypes, a broad spectrum of putative quinoa defense genes were found activated in the cultivar Kurmi but not in the Real cultivar. In cultivar Kurmi, relatively small effects were observed for classical pathogen response pathways but instead aC. quinoa-specific clade of germin-like genes were activated. Germin-like genes were found to be more rapidly induced in cultivar Kurmi as compared to Real. The same germin-like genes were found to also be upregulated systemically in the leaves. No strong correlation was observed between any of the known hormone-mediated defense response pathways and any of the quinoa-Trichodermainteractions. The differences in responses are relevant for the capabilities of applyingTrichodermaagents for crop protection of different cultivars ofC. quinoa.
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae
Authors: Schön Max E. , Zlatogursky Vasily V. , Singh Rohan P. , Poirier Camille , Wilken Susanne , Mathur Varsha , Strassert Jürgen F. H. , Pinhassi Jarone , Worden Alexandra Z. , Keeling Patrick J. , Ettema Thijs J. G. , Wideman Jeremy G. , Burki Fabien 
Published: April 2021

AbstractThe endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.
A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis
Authors: Alvelos Maria Inês , Szymczak Florian , Castela Ângela , Marín-Cañas Sandra , de Souza Bianca Marmontel , Gkantounas Ioannis , Colli Maikel , Fantuzzi Federica , Cosentino Cristina , Igoillo-Esteve Mariana , Marselli Lorella , Marchetti Piero , Cnop Miriam , Eizirik Décio L. 
Published: April 2021

AbstractExposure of human pancreatic beta cells to pro-inflammatory cytokines or metabolic stressors is used to model events related to type 1 and type 2 diabetes, respectively. Quantitative real-time PCR is commonly used to quantify changes in gene expression. The selection of the most adequate reference gene(s) for gene expression normalization is an important pre-requisite to obtain accurate and reliable results. There are no universally applicable reference genes, and the human beta cell expression of commonly used reference genes can be altered by different stressors. Here we aimed to identify the most stably expressed genes in human beta cells to normalize quantitative real-time PCR gene expression.We used comprehensive RNA-sequencing data from the human pancreatic beta cell line EndoC-βH1, human islets exposed to cytokines or the free fatty acid palmitate in order to identify the most stably expressed genes. Genes were filtered based on their level of significance (adjusted P-value >0.05), fold-change (|fold-change| <1.5) and a coefficient of variation <10%. Candidate reference genes were validated by quantitative real-time PCR in independent samples.We identified a total of 264 genes stably expressed in EndoC-βH1 cells and human islets following cytokine- or palmitate-induced stress, displaying a low coefficient of variation. Validation by quantitative real-time PCR of the top five genesARF1,CWC15,RAB7A,SIAH1andVAPAcorroborated their expression stability under most of the tested conditions. Further validation in independent samples indicated that the geometric mean ofACTBandVAPAexpression can be used as a reliable normalizing factor in human beta cells.
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer
Authors: Ankill Jørgen , Aure Miriam Ragle , Bjørklund Sunniva , Langberg Severin ,   Oslo Breast Cancer Research Consortium (OSBREAC), Kristensen Vessela N. , Vitelli Valeria , Tekpli Xavier , Fleischer Thomas 
Published: April 2021

AbstractBreast cancer is a highly heterogeneous disease driven by multiple factors including genetic and epigenetic alterations. DNA methylation patterns have been shown to be altered on a genome-wide scale and previous studies have highlighted the critical role of aberrant DNA methylation on gene expression and breast cancer pathogenesis. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL), a method for integration of CpG methylation and gene expression to identify disease-driving genes under epigenetic control. By grouping these emQTLs by biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis such as proliferation and tumor infiltrating fibroblasts. We report hypomethylation at enhancers carrying transcription factor binding sites of key proliferation-driving transcription factors such as CEBP-β, FOSL1, and FOSL2, with concomitant high expression of cell cycle- and proliferation-related genes in aggressive breast tumors. The identified CpGs and genes were found to be connected through chromatin loops, together indicating that proliferation in aggressive breast tumors is under epigenetic regulation by DNA methylation. Interestingly, there was a significant correlation between proliferation-related DNA methylation and gene expression also within subtypes of breast cancer, thereby showing that varying proliferation may be explained by epigenetic profiles across breast cancer subtypes. Indeed, the identified proliferation gene signature was prognostic both in the Luminal A and Luminal B subtypes. Taken together, we show that proliferation in breast cancer is linked to hypomethylation at specific enhancers and transcription factor binding mediated through chromatin loops.
DENTATE GRANULE CELLS ARE HYPEREXCITABLE IN THE TGF344-AD RAT MODEL OF ALZHEIMER’S DISEASE
Authors: Smith Lindsey A. , Goodman Anthoni M. , McMahon Lori L. 
Published: April 2021

AbstractThe dentate gyrus is both a critical gatekeeper for hippocampal signal processing and one of the first regions to dysfunction in Alzheimer’s disease (AD). Accordingly, the appropriate balance of excitation and inhibition through the dentate is a compelling target for mechanistic investigation and therapeutic intervention of early AD. Previously, we reported increased LTP magnitude at medial perforant path-dentate granule cell (MPP-DGC) synapses in slices from TgF344-AD rats compared to Wt as early as 6 months. We next determined that the enhanced LTP magnitude was due to heightened function of β-ARs leading us to ask if dentate granule cells (DGCs) also have modified passive or active membrane properties which may also contribute to hyperexcitability or aberrant hippocampal processing. Although there was no detectable difference in spine density and presynaptic release probability, dentate granule cells (DGCs) themselves might have increased electrical response to synaptic input during LTP induction, which was measured as a significant increase in charge transfer during high-frequency stimulation. In this study, we found passive membrane properties and active membrane properties are altered, leading to increased TgF344-AD DGC excitability. Specifically, TgF344-AD DGCs have an increased input resistance and decreased rheobase, decreased sag, and increased action potential (AP) spike accommodation. Importantly, we find that the voltage response increased in DGCs from TgF344-AD compared to Wt accompanied by decreased delay to fire the first AP, indicating that for the same amount of depolarizing current injection TgF344-AD DGCs membranes are more excitable. Taken together, DGCs of TgF344-AD rats are more excitable, but due to heightened accommodation, may be unable to discharge at high frequency for longer durations of time, compared to their Wt littermates.
Thiophenesulfonamides are specific inhibitors of quorum sensing in pathogenic Vibrios
Authors: Newman Jane D. , Shah Priyanka , Chopra Jay , Shi Eda , McFadden Molly E. , Horness Rachel E. , Brown Laura C. , van Kessel Julia C. 
Published: April 2021

AbstractVibriobacteria are pathogens of fish, shellfish, coral, and humans due to contaminated seafood consumption.Vibriovirulence factors are controlled by the cell-to-cell communication called quorum sensing, thus this signaling system is a promising target for therapeutic design. We screened a compound library and identified nine compounds, including several 2-thiophenesulfonamides, that inhibit the master quorum sensing transcription factor LuxR inVibrio campbelliibut do not affect cell growth. We synthesized a panel of 50 thiophenesulfonamide compounds to examine the structure-activity relationship effects on quorum sensingin vivo.The most potent molecule identified, PTSP (3-phenyl-1-(thiophen-2-ylsulfonyl)-1H-pyrazole), specifically inhibits LuxR homologs in multiple strains ofVibrio vulnificus,Vibrio parahaemolyticus, andV. campbelliiwith sub-micromolar concentrations. PTSP efficacy is driven by amino acid conservation in the binding pocket, which is accurately predicted usingin silicomodeling of inhibitors. Our results underscore the potential for developing thiophenesulfonamides as specific quorum sensing-directed treatments forVibrioinfections.
Recurrent connectivity underlies lateralized temporal processing differences in Auditory Cortex
Authors: Neophytou Demetrios , Arribas Diego , Levy Robert B. , Park Memming , Oviedo Hysell V. 
Published: April 2021

AbstractBrain asymmetry in the sensitivity to spectrotemporal modulation is an established functional feature that underlies the perception of speech and music. Recent studies in humans suggest separable neural mechanisms must underlie these cognitively complex functions. The left Auditory Cortex (ACx) is believed to specialize in processing fast temporal components of speech sounds, and the right ACx slower components. However, the circuit features and neural computations behind these lateralized spectrotemporal processes are poorly understood. To answer these mechanistic questions we use mice, an animal model that captures some relevant features of human communication systems. In this study, we screened for circuit features that could subserve temporal integration differences between the left and right ACx. We mapped excitatory input to principal neurons in all cortical layers and found significantly stronger recurrent connections in the superficial layers of the right ACx compared to the left. We hypothesized that the underlying recurrent neural dynamics would exhibit differential characteristic timescales corresponding to their hemispheric specialization. To investigate, we recorded spike trains from awake mice and estimated the network time constants using a quasi-Bayesian method to combine evidence from multiple weak signal-to-noise ratio neurons. We found longer temporal integration windows in the right ACx compared to the left as predicted by stronger recurrent excitation. Our study shows direct evidence that stronger recurrent synaptic connections lead to longer network time scales. These findings support speech processing theories that purport asymmetric integration time constants is a crucial feature of lateralization in auditory processing.
The Instability of Functional Connectomes Across the First Year of Life
Authors: Dufford Alexander J. , Noble Stephanie , Gao Siyuan , Scheinost Dustin 
Published: April 2021

AbstractThe uniqueness and stability of the adolescent and adult functional connectome has been demonstrated to be high (80–95% identification) using connectome-based identification (ID) or “fingerprinting”. However, it is unclear to what extent individuals exhibit similar distinctiveness and stability in infancy, a developmental period of rapid and unparalleled brain development. In this study, we examined connectome-based ID rates within and across the first year of life using a longitudinal infant dataset at 1 month and 9 months of age. We also calculated the test–retest reliability of individual connections across the first year of life using the intraclass correlation coefficient (ICC). Overall, we found substantially lower infant ID rates than have been reported in adult and adolescent populations. Within-session ID rates were moderate and significant (ID = 48.94–70.83%). Between-session ID rates were very low and not significant, with task-to-task connectomes resulting in the highest between-session ID rate (ID = 26.6%). Similarly, average edge-level test-retest reliability was higher within-session than between-session (mean within-session ICC = 0.17, mean between-session ICC = 0.10). These findings suggest a lack of uniqueness and stability in functional connectomes across the first year of life consistent with the unparalleled changes in brain functional organization during this critical period.
Transcriptome profiling reveals CD73 and age-driven changes in neutrophil responses againstStreptococcus pneumoniae
Authors: Bhalla Manmeet , Heinzinger Lauren R. , Morenikeji Olanrewaju B. , Marzullo Brandon , Thomas Bolaji N. , Bou Ghanem Elsa N. 
Published: April 2021

AbstractNeutrophils are required for host resistance againstStreptococcus pneumoniaebut their function declines with age. We previously found that CD73, an enzyme required for antimicrobial activity, is down-regulated in neutrophils from aged mice. This study explored transcriptional changes in neutrophils induced byS. pneumoniaeto identify pathways controlled by CD73 and dysregulated with age. Ultrapure bone marrow-derived neutrophils isolated from wild type (WT) young, old, and CD73KO young mice were mock-challenged or infected withS. pneumoniae ex vivo. RNA sequencing was performed to identify differentially expressed genes (DEGs). We found that infection triggered distinct global transcriptional changes across hosts, that were strongest in CD73KO neutrophils. Surprisingly, there were more down-regulated than up-regulated genes in all groups upon infection. Down-regulated DEGs indicated a dampening of immune responses in old and CD73KO hosts. Further analysis revealed that CD73KO neutrophils expressed higher numbers of long non-coding RNAs (lncRNAs) compared to WT controls. Predicted network analysis indicated that CD73KO specific lncRNAs control several signaling pathways. We found that genes in the JNK-MAPK-pathway were up-regulated upon infection in CD73KO and WT old but not in young mice. This corresponded to functional differences, as phosphorylation of the downstream AP-1 transcription factor component c-Jun was significantly higher in infected CD73KO and old mice neutrophils. Importantly, inhibiting JNK/AP-1 rescued the ability of these neutrophils to killS. pneumoniae. Altogether, our findings revealed that neutrophils modify their gene expression to better adapt to bacterial infection and that this capacity declines with age and is regulated by CD73.