bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential biomarkers or therapeutic targets of mesenchymal stem cells in multiple myeloma by bioinformatics analysis
Authors: Li Zhi-Ran , Cai Wen-Ke , Yang Qin , Shen Ming-Li , Zhang Hua-Zhu , Huang Qian , Zhao Gui-Xin , Chen Ke-Yan , He Gong-Hao 
Published: June 2020

AbstractObjectivesMesenchymal stem cells (MSCs) play important roles in multiple myeloma (MM) pathogenesis. Previous studies have discovered a group of MM-associated potential biomarkers in MSCs derived from bone marrow (BM-MSCs). However, no study of the bioinformatics analysis was conducted to explore the key genes and pathways of MSCs derived from adipose (AD-MSCs) in MM. The aim of this study was to screen potential biomarkers or therapeutic targets of AD-MSCs and BM-MSCs in MM.MethodsThe gene expression profiles of AD-MSCs (GSE133346) and BM-MSCs (GSE36474) were downloaded from Gene Expression Omnibus (GEO) database. Gene Oncology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network of differentially expressed genes (DEGs) were performed.ResultsA total of 456 common downregulated DEGs in two datasets were identified and the remaining DEGs in GSE133346 were further identified as specific DEGs of AD-MSCs. Furthermore, a PPI network of common downregulated DEGs was constructed and seven hub genes were identified. Importantly, cell cycle was the most significantly enrichment pathway both in AD-MSCs and BM-MSCs from MM patients.ConclusionWe identified key genes and pathways closely related with MM progression, which may act as potential biomarkers or therapeutic targets of MM.
Immobilization, Direct Electrochemistry and Electrocatalysis of Hemoglobin on Peptide-Carbon Nanotube Modified Electrode
Authors: Sheikholeslam Mohammadali , Nanda Piyush , Pritzker Mark , Chen P. 
Published: June 2020

ABSTRACTThe direct electrochemistry of hemoglobin (Hb) immobilized on a glassy carbon electrode (GCE) by mixing with a hybrid dispersion of self-assembling peptide EFK8 and single-walled carbon nanotubes (SWNT) was investigated and shown to have effective properties as a biosensor for hydrogen peroxide (H2O2). Preliminary experiments involving cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) showed that the presence of SWNTs in the modifying peptide layer on GCE significantly enhanced the electrochemical response of the electrode for the ferricyanide/ferrocyanide redox couple. Also, when more layers of the peptide-SWNT dispersion were applied to the surface, the electrochemical response of the GCE was further increased. This behavior was then exploited to fabricate a biosensor for H2O2by mixing hemoglobin with the hybrid peptide-SWNT dispersion and casting this mixture on a glassy carbon electrode. AFM imaging, CV and EIS analysis revealed successful immobilization of Hb on the electrode and the ability of the electrode to enable direct electron transfer from Hb to the electrode surface. In particular, CVs obtained in 0.1M PBS (pH 7.0) showed that the immobilized Hb retained its bio-catalytic activity for Fe ions, indicating that it had not denatured and the hybrid layer remained biocompatible with Hb. Furthermore, this electrode was found to accurately measure the H2O2concentration over the range from 20 to 9.6×102μM in 0.1M PBS (pH 7.0) under mediatorless conditions using both CV and amperometry techniques. In this way, the EFK8-SWNT hybrid layer shows promise as a biocompatible layer for simple non-covalent enzyme immobilization and the basis of a mediatorless biosensor.
Impact of transposable elements on methylation and gene expression across natural accessions ofBrachypodium distachyon
Authors: Wyler Michele , Stritt Christoph , Walser Jean-Claude , Baroux Célia , Roulin Anne C. 
Published: June 2020

AbstractTransposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grassBrachypodium distachyonas a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed inArabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns inB. distachyon.Significance statementTransposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.
Wheat blast caused byMagnaporthe oryzaepv.Triticumis efficiently controlled by the plant defence inducer isotianil
Authors: Portz Katharina , Casanova Florencia , Jordine Angelina , Bohnert Stefan , Mehl Andreas , Portz Daniela , Schaffrath Ulrich 
Published: June 2020

AbstractWheat blast caused byMagnaporthe oryzaepv.Triticum(MoT) is an upcoming threat to wheat cultivation worldwide. The disease crossing over to wheat first gained attention in South America, with increasing interest coming from its more recent appearance in the big wheat growing areas of Asia. The increasing economic relevance of the disease and the lack of genetic resistance in current wheat breading material, besides fungicide resistance already present in fungal pathogen populations, highlighted the need to evaluate the potential of isotianil as an alternative plant protection measure. Isotianil is already registered in Asia for the protection of rice againstM. oryzaebut because the agronomic practices and disease development of blast differ between rice and wheat, the efficacy of isotianil against wheat blast was hard to predict. Testing isotianil in the currently available formulations, applied either as seed treatment or soil drench, resulted in a significant reduction of disease severity. The efficacy was comparably high, on different wheat cultivars and using several fungal isolates with different degrees of virulence. Microscopic analyses revealed that isotianil treatment can prevent invasive growth of the pathogen. No phytotoxicity from isotianil treatment was observed on wheat plants up to the stage of heading. Importantly, isotianil not only protects wheat plants at the seedling stage but also on spikes thereby preventing losses due to this most severe disease syndrome. In summary, the results showed the high potential of isotianil to protect against wheat blast.
Targeted control of pneumolysin production by a mobile genetic element inStreptococcus pneumoniae
Authors: Stevens Emily J. , Morse Daniel J. , Bonini Dora , Duggan Seána , Brignoli Tarcisio , Recker Mario , Lees John A. , Croucher Nicholas J. , Bentley Stephen , Wilson Daniel J. , Earle Sarah G. , Dixon Robert , Nobbs Angela , Jenkinson Howard , van Opijnen Tim , Thibault Derek , Wilkinson Oliver J. , Dillingham Mark S. , Carlile Simon , McLoughlin Rachel M. , Massey Ruth C. 
Published: June 2020

AbstractStreptococcus pneumoniaeis a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis. Young children are at a particularly high risk, with an estimated half a million deaths worldwide in those under five attributable to invasive pneumococcal disease each year. The cytolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, yet despite its key role in pathogenesis, immune evasion, and transmission, the regulation of Ply production is not well defined. Using a genome-wide association approach we identified a large number of potential affectors of Ply activity, including a gene acquired horizontally on the antibiotic resistance conferring Integrative and Conjugative Element (ICE) ICESp23FST81. This gene encodes a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like domains with potent ATP-dependent nuclease activity. We found the regulatory effect of ZomB to be specific for theplyoperon, potentially mediated by its high affinity for the BOX repeats encoded therein. Using a murine model of pneumococcal colonisation, we further demonstrate that a ZomB mutant strain colonises both the upper respiratory tract and lungs at higher levels when compared to the wild type strain. While the antibiotic resistance conferring aspects of ICESp23FST81 is often credited with contributing to the success of theS. pneumoniaelineages that acquire it, its ability to control the expression of a major virulence factor implicated in bacterial transmission is also likely to have played an important role.
Towards a new treatment against polymicrobial infections: high antibacterial activity of lemon IntegroPectin againstPseudomonas aeruginosaandEscherichia coli
Authors: Presentato Alessandro , Scurria Antonino , Albanese Lorenzo , Picone Pasquale , Pagliaro Mario , Zabini Federica , Meneguzzo Francesco , Alduina Rosa , Nuzzo Domenico , Ciriminna Rosaria 
Published: June 2020

AbstractLemon IntegroPectin obtained via hydrodynamic cavitation of waste lemon peel in water only shows high antibacterial activity against two Gram-negative bacteria,Pseudomonas aeruginosaandEscherichia coli. The antibacterial effect against the ubiquitous pathogenP. aeruginosawas evaluated in terms of the minimal bactericidal (MBC) and minimal inhibitory concentration (MIC). Preliminary insight on the antibacterial mechanism of IntegroPectin originates from investigating its inhibitory activity againstE. coli. Given the non-cytotoxic nature of citrus IntegroPectin and the ease of its reproducible production in large amounts, the route is open to the industrial development of a new antimicrobial treatment against polymicrobial infections unlikely to develop drug resistance.
Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform
Authors: Batty Elizabeth M. , Kochakarn Theerarat , Wangwiwatsin Arporn , Joonlasak Khajohn , Huang Angkana T. , Panthan Bhakbhoom , Jiaranai Poramate , Kümpornsin Krittikorn , Kotanan Namfon , Manasatienkij Wudtichai , Watthanachockchai Treewat , Rakmanee Kingkan , Jones Anthony R. , Fernandez Stefan , Sensorn Insee , Sungkanuparph Somnuek , Pasomsub Ekawat , Klungthong Chonticha , Chookajorn Thanat , Chantratita Wasun 
Published: June 2020

AbstractGenomic surveillance has a key role in tracking the ongoing COVID-19 pandemic, but information on how different sequencing library preparation approaches affect the data produced are lacking. We compared three library preparation methods using both tagmentation (Nextera XT and Nextera Flex) and ligation-based (KAPA HyperPrep) approaches on both positive and negative samples to provide insights into any methodological differences between the methods, and validate their use in SARS-CoV-2 amplicon sequencing. We show that all three library preparation methods allow us to recover near-complete SARS-CoV-2 genomes with identical SNP calls. The Nextera Flex and KAPA library preparation methods gave better coverage than libraries prepared with Nextera XT, which required more reads to call the same number of genomic positions. The KAPA ligation-based approach shows the lowest levels of human contamination, but contaminating reads had no effect on the downstream analysis. We found some examples of library preparation-specific differences in minority variant calling. Overall our data shows that the choice of Illumina library preparation method has minimal effects on consensus base calling and downstream phylogenetic analysis, and suggests that all methods would be suitable for use if specific reagents are difficult to obtain.
Stage-specific muscle wasting mechanisms in a novel cancer cachexia mouse model for ovarian granulosa cell tumor
Authors: Zhang Yaqi , Zhu Jie , Kim So-Youn , Romero Megan M , Even Kelly A , Kurita Takeshi , Woodruff Teresa K 
Published: June 2020

AbstractCachexia is a progressive muscle wasting syndrome that increases mortality risk in cancer patients, while there are still no effective treatment due to the complexity of syndrome and the lack of preclinical models. We identified a transgenic mice model with ovarian granulosa cell tumors mimic the progression of cachexia seen in humans, including drastic weight loss, skeletal muscle wasting and increased serum cachexia biomarker activin A and GDF15. Hypercatabolism was detected in skeletal muscle, having upregulation of E3 ligasesAtrogin-1andMurf-1. Our cachexia model exhibited stage-specific muscle wasting mechanisms. At precachexia stage, elevation of activin A activates p38 MAPK. Inhibition of activin A with Follistatin reversed weight loss at precachexia stage. At cachexia stage, energy stress in skeletal muscle activates AMPKα and leads to upregulation ofFoxO3. Our results indicate this novel preclinical cancer cachexia model is exploitable for studying pathophysiological mechanisms and testing therapeutic agents of cachexia.
Peripheral Natural Killer cells from chronic hepatitis B patients display molecular hallmarks of T cell exhaustion
Authors: Marotel M. , Villard M. , Tout I. , Besson L. , Allatif O. , Pujol M. , Rocca Y. , Ainouze M. , Roblot G. , Viel S. , Gomez M. , Loustaud V. , Alain S. , Durantel D. , Walzer T. , Hasan U. , Marçais A. 
Published: June 2020

AbstractA significant proportion of individuals infected by HBV develops chronic infection. Antiviral effectors such as Natural Killer (NK) cells have impaired functions in these patients, but the molecular mechanism responsible for this dysfunction remains poorly characterized. Here, we show that peripheral NK cells from chronic hepatitis B (CHB) patients have a defective capacity to produce IFN-γ, MIP1-β and TNF-α but retain an intact killing capacity. This functional phenotype was associated with a decrease in the expression of NKp30 and CD16, combined with defects in IL-15 stimulation of the mTOR pathway. Transcriptome analysis of NK cells in CHB patients further revealed a strong enrichment for transcripts typically expressed in exhausted T cells suggesting that NK cell dysfunction and T cell exhaustion rely on common molecular mechanisms. In particular, the transcription factor thymocyte selection-associated HMG box protein (TOX) and several of its targets, including immune checkpoints, were over-expressed in NK cells of CHB patients. This T cell exhaustion signature was predicted to be dependent on the calcium (Ca2+)-associated transcription factor NFAT. In line with this, when stimulating the Ca2+-dependent pathway in isolation, we recapitulated the dysfunctional phenotype. Thus, deregulated Ca2+signalling could be a central event in both T cell exhaustion and NK cell dysfunction that occur during chronic infections.
Fast EEG-based decoding of the directional focus of auditory attention using common spatial patterns
Authors: Geirnaert Simon , Francart Tom , Bertrand Alexander 
Published: June 2020

AbstractObjectiveNoise reduction algorithms in current hearing devices lack information about the sound source a user attends to when multiple sources are present. To resolve this issue, they can be complemented with auditory attention decoding (AAD) algorithms, which decode the attention using electroencephalography (EEG) sensors. State-of-the-art AAD algorithms employ a stimulus reconstruction approach, in which the envelope of the attended source is reconstructed from the EEG and correlated with the envelopes of the individual sources. This approach, however, performs poorly on short signal segments, while longer segments yield impractically long detection delays when the user switches attention.MethodsWe propose decoding the directional focus of attention using filterbank common spatial pattern filters (FB-CSP) as an alternative AAD paradigm, which does not require access to the clean source envelopes.ResultsThe proposed FB-CSP approach outperforms both the stimulus reconstruction approach on short signal segments, as well as a convolutional neural network approach on the same task. We achieve a high accuracy (80% for 1 s windows and 70% for quasi-instantaneous decisions), which is sufficient to reach minimal expected switch durations below 4 s. We also demonstrate that the decoder can adapt to unlabeled data from an unseen subject and works with only a subset of EEG channels located around the ear to emulate a wearable EEG setup.ConclusionThe proposed FB-CSP method provides fast and accurate decoding of the directional focus of auditory attention.SignificanceThe high accuracy on very short data segments is a major step forward towards practical neuro-steered hearing devices.
Estrogen withdrawal alters oxytocin signaling in the paraventricular hypothalamus and dorsal raphe nucleus to increase postpartum anxiety
Authors: Hedges Valerie L. , Heaton Elizabeth C. , Amaral Claudia , Benedetto Lauren E. , Bodie Clio L. , D’Antonio Breanna I. , Davila Portillo Dayana R. , Lee Rachel H. , Levine M. Taylor , O’Sullivan Emily C. , Pisch Natalie P. , Taveras Shantal , Wild Hannah R. , Ross Amy P. , Albers H. Elliott , Been Laura E. 
Published: June 2020

AbstractBackgroundEstrogen increases dramatically during pregnancy, but quickly drops below pre-pregnancy levels at birth and remains suppressed during the postpartum period. Clinical and rodent work suggests that this postpartum drop in estrogen results in an “estrogen withdrawal” state that is related to changes in affect, mood, and behavior. Most studies examining the effect of estrogen withdrawal on the brain have focused solely on the hippocampus.MethodsWe used a hormone-simulated pseudopregnancy model in Syrian hamsters, a first for this species. Ovariectomized females were given daily injections to approximate hormone levels during gestation and then withdrawn from estrogen to simulate postpartum estrogen withdrawal. Subjects were tested for behavioral assays of anxiety and anhedonia during estrogen withdrawal. Following sacrifice, neuroplasticity in oxytocin-producing neurons in the paraventricular nucleus of the hypothalamus (PVH) and its efferent targets was measured.ResultsEstrogen-withdrawn females had increased anxiety-like behaviors in the elevated plus and open field, but did not differ from controls in sucrose preference. Furthermore, estrogen-withdrawn females had more oxytocin-immunoreactive cells and oxytocin mRNA in the PVH, as well as an increase in oxytocin receptor density in the dorsal raphe nucleus (DRN). Finally, blocking oxytocin receptors in the DRN during estrogen withdrawal prevented the high-anxiety behavioral phenotype in estrogen-withdrawn females.ConclusionsEstrogen withdrawal alters oxytocin signaling in the PVH and DRN to increase anxiety-like behavior during the postpartum period. More broadly, these experiments suggest Syrian hamsters as a novel organism in which to model the effects of postpartum estrogen withdrawal on the brain and anxiety-like behavior.
Metagenome-assembled genomes of phytoplankton communities across the Arctic Circle
Authors: Duncan A. , Barry K. , Daum C. , Eloe-Fadrosh E. , Roux S. , Tringe S. G. , Schmidt K. , Valentin K. U. , Varghese N. , Grigoriev I. V. , Leggett R. , Moulton V. , Mock T. 
Published: June 2020

AbstractPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genetic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for eukaryote-enriched polar and non-polar phytoplankton communities. Here, we have assembled draft prokaryotic and eukaryotic MAGs from environmental DNA extracted from chlorophyll a maximum layers in the surface ocean across the Arctic Circle in the Atlantic. From 679 Gbp and estimated 50 million genes in total, we recovered 140 MAGs of medium to high quality. Although there was a strict demarcation between polar and non-polar MAGs, adjacent sampling stations in each environment on either side of the Arctic Circle had MAGs in common. Furthermore, phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic south of the Arctic Circle. Approximately 60% of protein families were shared between polar and non-polar MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to south of the Arctic circle. Thus, our study enabled us to place differences in functional plankton diversity in a genomic context to reveal that the evolution of these MAGs likely was driven by significant differences in the seascape on either side of an ecosystem boundary that separates polar from non-polar surface ocean waters in the North Atlantic.
Comparative genomics ofVerticillium dahliaeisolates reveals thein planta-secreted effector protein recognized inV2tomato plants
Authors: Chavarro-Carrero Edgar A. , Vermeulen Jasper P. , Torres David E. , Usami Toshiyuki , Schouten Henk J. , Bai Yuling , Seidl Michael F. , Thomma Bart P.H.J. 
Published: June 2020

SUMMARYPlant pathogens secrete effector molecules during host invasion to promote host colonization. However, some of these effectors become recognized by host receptors, encoded by resistance genes, to mount defense response and establish immunity. Recently, a novel resistance was identified in tomato, mediated by the single dominantV2locus, to control strains of the soil-borne vascular wilt fungusVerticillium dahliaethat belong to race 2. We performed comparative genomics between race 2 strains and resistance-breaking race 3 strains to identify the avirulence effector that activatesV2resistance, termed Av2. We identified 277 kb of race 2-specific sequence comprising only two genes that encode predicted secreted proteins, both of which are expressed byV. dahliaeduring tomato colonization. Subsequent functional analysis based on genetic complementation into race 3 isolates confirmed that one of the two candidates encodes the avirulence effector Av2 that is recognized inV2tomato plants. The identification of Av2 will not only be helpful to select tomato cultivars that are resistant to race 2 strains ofV. dahliae, as the correspondingV2resistance gene has not yet been mapped, but also to monitor adaptations in theV. dahliaepopulation to deployment ofV2-containing tomato cultivars in agriculture.