bluuebunny/crossref_metadata_2025_split huggingface dataset:
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
Authors: Sharma Deepti , De Falco Louis , Padavattan Sivaraman , Rao Chang , Geifman-Shochat Susana , Liu Chuan-Fa , Davey Curt A. 
Published: December 2019

AbstractThe poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.
HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge
Authors: Wang Huarong , Cai Han , Wang Xiao , Zhang Meiling , Liu Bingying , Chen Ziqi , Yang Tingting , Fang Junshun , Zhang Yanhao , Liu Wei , Han Jun , Guo Qirui , Zhang Hua , Wang Haibin , Xia Guoliang , Wang Chao 
Published: December 2019

AbstractIt is known that granulosa cells (GCs) mediate gonadotropin-induced oocyte meiosis resumption by releasing EGF-like factors in mammals, however, the detailed molecular mechanisms remain unclear. Here, we demonstrate that luteinizing hormone (LH) surge-induced histone deacetylase 3 (HDAC3) downregulation in GCs is essential for oocyte maturation. Before the LH surge, HDAC3 is highly expressed in GCs. Transcription factors, such as FOXO1, mediate recruitment of HDAC3 to the amphiregulin (Areg) promoter, which suppresses AREG expression. With the LH surge, decreased HDAC3 in GCs enables histone H3K14 acetylation and binding of the SP1 transcription factor to the Areg promoter to initiate AREG transcription and oocyte maturation. Conditional knockout of Hdac3 in granulosa cells in vivo or inhibition of HDAC3 activity in vitro promotes the maturation of oocytes independent of LH. Taking together, HDAC3 in GCs within ovarian follicles acts as a negative regulator of EGF-like growth factor expression before the LH surge.
Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA
Authors: Caldas Paulo , López-Pelegrín Mar , Pearce Daniel J. G. , Budanur Nazmi Burak , Brugués Jan , Loose Martin 
Published: December 2019

AbstractDuring bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.
IL-17+ CD8+ T cell suppression by dimethyl fumarate associates with clinical response in multiple sclerosis
Authors: Lückel Christina , Picard Felix , Raifer Hartmann , Campos Carrascosa Lucia , Guralnik Anna , Zhang Yajuan , Klein Matthias , Bittner Stefan , Steffen Falk , Moos Sonja , Marini Federico , Gloury Renee , Kurschus Florian C. , Chao Ying-Yin , Bertrams Wilhelm , Sexl Veronika , Schmeck Bernd , Bonetti Lynn , Grusdat Melanie , Lohoff Michael , Zielinski Christina E. , Zipp Frauke , Kallies Axel , Brenner Dirk , Berger Michael , Bopp Tobias , Tackenberg Björn , Huber Magdalena 
Published: December 2019

AbstractIL-17-producing CD8+ (Tc17) cells are enriched in active lesions of patients with multiple sclerosis (MS), suggesting a role in the pathogenesis of autoimmunity. Here we show that amelioration of MS by dimethyl fumarate (DMF), a mechanistically elusive drug, associates with suppression of Tc17 cells. DMF treatment results in reduced frequency of Tc17, contrary to Th17 cells, and in a decreased ratio of the regulators RORC-to-TBX21, along with a shift towards cytotoxic T lymphocyte gene expression signature in CD8+ T cells from MS patients. Mechanistically, DMF potentiates the PI3K-AKT-FOXO1-T-BET pathway, thereby limiting IL-17 and RORγt expression as well as STAT5-signaling in a glutathione-dependent manner. This results in chromatin remodeling at the Il17 locus. Consequently, T-BET-deficiency in mice or inhibition of PI3K-AKT, STAT5 or reactive oxygen species prevents DMF-mediated Tc17 suppression. Overall, our data disclose a DMF-AKT-T-BET driven immune modulation and suggest putative therapy targets in MS and beyond.
Slow recombination of spontaneously dissociated organic fluorophore excitons
Authors: Yamanaka Takahiko , Nakanotani Hajime , Adachi Chihaya 
Published: December 2019

AbstractThe harvesting of excitons as luminescence by organic fluorophores forms the basis of light-emitting applications. Although high photoluminescence quantum yield is essential for efficient light emission, concentration-dependent quenching of the emissive exciton is generally observed. Here we demonstrate generation and accumulation of concentration-dependent “long-lived” (i.e., over 1 h) photo-generated carriers and the successive release of their energy as electroluminescence in a solid-state film containing a polar fluorophore. While fluorophore excitons are generally believed to be stable because of their high exciton binding energies, our observations show that some of the excitons undergo spontaneous exciton dissociation in a solid-state film by spontaneous orientation polarization even without an external electric field. These results lead to the reconsideration of the meaning of “luminescence quantum yield” for the solid films containing polar organic molecules because it can differ for optical and electrical excitation.
Guanidinocalix[5]arene for sensitive fluorescence detection and magnetic removal of perfluorinated pollutants
Authors: Zheng Zhe , Yu Huijuan , Geng Wen-Chao , Hu Xin-Yue , Wang Yu-Ying , Li Zhihao , Wang Yuefei , Guo Dong-Sheng 
Published: December 2019

AbstractPerfluorinated alkyl substances, such as perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA), are toxic materials that are known to globally contaminate water, air, and soil resources. Strategies for the simultaneous detection and removal of these compounds are desired to address this emerging health and environmental issue. Herein, we develop a type of guanidinocalix[5]arene that can selectively and strongly bind to PFOS and PFOA, which we use to demonstrate the sensitive and quantitative detection of these compounds in contaminated water through a fluorescent indicator displacement assay. Moreover, by co-assembling iron oxide nanoparticle with the amphiphilic guanidinocalix[5]arene, we are able to use simple magnetic absorption and filtration to efficiently remove PFOS and PFOA from contaminated water. This supramolecular approach that uses both molecular recognition and self-assembly of macrocyclic amphiphiles is promising for the detection and remediation of water pollution.
Super-resolution provided by the arbitrarily strong superlinearity of the blackbody radiation
Authors: Graciani Guillaume , Amblard François 
Published: December 2019

AbstractBlackbody radiation is a fundamental phenomenon in nature, and its explanation by Planck marks a cornerstone in the history of Physics. In this theoretical work, we show that the spectral radiance given by Planck’s law is strongly superlinear with temperature, with an arbitrarily large local exponent for decreasing wavelengths. From that scaling analysis, we propose a new concept of super-resolved detection and imaging: if a focused beam of energy is scanned over an object that absorbs and linearly converts that energy into heat, a highly nonlinear thermal radiation response is generated, and its point spread function can be made arbitrarily smaller than the excitation beam focus. Based on a few practical scenarios, we propose to extend the notion of super-resolution beyond its current niche in microscopy to various kinds of excitation beams, a wide range of spatial scales, and a broader diversity of target objects.
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization
Authors: Wang Sibo , Li Linzhou , Li Haoyuan , Sahu Sunil Kumar , Wang Hongli , Xu Yan , Xian Wenfei , Song Bo , Liang Hongping , Cheng Shifeng , Chang Yue , Song Yue , Çebi Zehra , Wittek Sebastian , Reder Tanja , Peterson Morten , Yang Huanming , Wang Jian , Melkonian Barbara , Van de Peer Yves , Xu Xun , Wong Gane Ka-Shu , Melkonian Michael , Liu Huan , Liu Xin 
Published: December 2019

AbstractMounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens
Authors: Leggett Richard M. , Alcon-Giner Cristina , Heavens Darren , Caim Shabhonam , Brook Thomas C. , Kujawska Magdalena , Martin Samuel , Peel Ned , Acford-Palmer Holly , Hoyles Lesley , Clarke Paul , Hall Lindsay J. , Clark Matthew D. 
Published: December 2019

AbstractThe MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is,Klebsiella pneumoniaeandEnterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.
Corticosterone-mediated physiological stress modulates hepatic lipid metabolism, metabolite profiles, and systemic responses in chickens
Authors: Zaytsoff Sarah J. M. , Brown Catherine L. J. , Montina Tony , Metz Gerlinde A. S. , Abbott D. Wade , Uwiera Richard R. E. , Inglis G. Douglas 
Published: December 2019

AbstractThe impact of physiological stress on lipid metabolism, the metabolome, and systemic responses was examined in chickens. To incite a stress response, birds were continuously administered corticosterone (CORT) in their drinking water at three doses (0 mg/L, 10 mg/L, and 30 mg/L), and they were sampled 1, 5, and 12 days after commencement of CORT administration. Corticosterone administration to birds differentially regulated lipogenesis genes (i.e. FAS, ACC, ME, and SREBF1), and histopathological examination indicated lipid deposition in hepatocytes. In addition, CORT affected water-soluble metabolite profiles in the liver, as well as in kidney tissue and breast muscle; thirteen unique metabolites were distinguished in CORT-treated birds and this was consistent with the dysregulation of lipid metabolism due to physiological stress. Acute phase responses (APRs) were also altered by CORT, and in particular, expression of SAA1 was decreased and expression of CP was increased. Furthermore, CORT administration caused lymphoid depletion in the bursa of Fabricius and elevated IL6 and TGFβ2 mRNA expression after 5 and 12 days of CORT administration. Collectively, incitement of physiological stress via administration of CORT in chickens modulated host metabolism and systemic responses, which indicated that energy potentials are diverted from muscle anabolism during periods of stress.
Mutation signature analysis identifies increased mutation caused by tobacco smoke associated DNA adducts in larynx squamous cell carcinoma compared with oral cavity and oropharynx
Authors: South Andrew P. , den Breems Nicoline Y. , Richa Tony , Nwagu Uche , Zhan Tingting , Poojan Shiv , Martinez-Outschoorn Ubaldo , Johnson Jennifer M. , Luginbuhl Adam J. , Curry Joseph M. 
Published: December 2019

AbstractSquamous cell carcinomas of the head and neck (HNSCC) arise from mucosal keratinocytes of the upper aero-digestive tract. Despite a common cell of origin and similar driver-gene mutations which divert cell fate from differentiation to proliferation, HNSCC are considered a heterogeneous group of tumors categorized by site of origin within the aero-digestive mucosa, and the presence or absence of HPV infection. Tobacco use is a major driver of carcinogenesis in HNSCC and is a poor prognosticator that has previously been associated with poor immune cell infiltration and higher mutation numbers. Here, we study patterns of mutations in HNSCC that are derived from the specific nucleotide changes and their surrounding nucleotide context (also known as mutation signatures). We identify that mutations linked to DNA adducts associated with tobacco smoke exposure are predominantly found in the larynx. Presence of this class of mutation, termed COSMIC signature 4, is responsible for the increased burden of mutation in this anatomical sub-site. In addition, we show that another mutation pattern, COSMIC signature 5, is positively associated with age in HNSCC from non-smokers and that larynx SCC from non-smokers have a greater number of signature 5 mutations compared with other HNSCC sub-sites. Immunohistochemistry demonstrates a significantly lower Ki-67 proliferation index in size matched larynx SCC compared with oral cavity SCC and oropharynx SCC. Collectively, these observations support a model where larynx SCC are characterized by slower growth and increased susceptibility to mutations from tobacco carcinogen DNA adducts.
The DNA topoisomerase II inhibitor amsacrine as a novel candidate adjuvant in a model of glaucoma filtration surgery
Authors: Yamamoto Kotaro , Kokubun Taiki , Sato Kota , Akaishi Takahiro , Shimazaki Atsushi , Nakamura Masatsugu , Shiga Yukihiro , Tsuda Satoru , Omodaka Kazuko , Saya Hideyuki , Nakazawa Toru 
Published: December 2019

AbstractTreatments for refractory glaucoma include trabeculectomy, in which a filtering bleb is created to reduce aqueous pressure. Mitomycin C (MMC) is often used as an adjuvant to reduce post-trabeculectomy bleb scarring and consequent failure. However, scarring sometimes still occurs. Thus, we searched for more effective trabeculectomy adjuvants with high-throughput screening (HTS) of a library of 1,165 off-patent drug compounds. This revealed that amsacrine (AMSA), a DNA topoisomerase II (TOP2) inhibitor, was the top candidate. Compared to MMC, rabbits that underwent trabeculectomy with 10% AMSA had lower IOP at 42, 56, and 70 days (P < 0.01 at all measurement points) and a higher bleb score at 28, 42, 56, and 70 days (P =  < 0.01, 0.04, 0.04, and < 0.01, respectively). Compared to saline, rabbits that received 1% AMSA also had lower IOP and better bleb score at all time points, without a sharp drop in IOP just after surgery (all P < 0.01). Both effects were milder than MMC at 7 days (P = 0.02 and <0.01, respectively). Thus, this study showed that HTS may help identify new, promising uses for off-patent drugs. Furthermore, trabeculectomy with AMSA at a suitable concentration may improve the prognosis after trabeculectomy compared to MMC.
How dietary patterns affect left ventricular structure, function and remodelling: evidence from the Kardiovize Brno 2030 study
Authors: Maugeri Andrea , Hruskova Jana , Jakubik Juraj , Hlinomaz Ota , Medina-Inojosa Jose R. , Barchitta Martina , Agodi Antonella , Vinciguerra Manlio 
Published: December 2019

AbstractLittle is still known about the effect of dietary patterns on left ventricular hypertrophy (LVH). Here, we derived dietary patterns by principal component analysis (PCA) and evaluated their association with LV structure, function, and remodelling. Our cross-sectional study included 438 members (aged 25–65 years; 59.1% women) of the Kardiovize Brno 2030 with no history of cardiovascular disease. Two dietary patterns were derived using PCA, namely prudent and western. Primary outcomes were echocardiographic parameters and LV geometric patterns, such as concentric LV remodelling (cLVR), concentric LVH (cLVH), and eccentric LVH (eLVH). Interestingly, participants with high adherence to the prudent dietary pattern had decreased odds of cLVH after adjustment for socio-demographic, clinical and behavioral covariates (OR = 0.24, 95% CI = 0.08–0.88; p = 0.031). By contrast, several echocardiographic parameters increased with increasing adherence to the western dietary pattern, which resulted in higher odds of cLVH among participants with high adherence (OR = 5.38, 95% CI = 1.17–23.58; p = 0.035). Although our findings may have an immediate relevance for public-health strategies, further large-size prospective studies should be encouraged to better understand the observed association and their causality.
Prediction and final temporal errors are used for trial-to-trial motor corrections
Authors: López-Moliner Joan , Vullings Cécile , Madelain Laurent , van Beers Robert J. 
Published: December 2019

AbstractMany daily life situations (e.g. dodging an approaching object or hitting a moving target) require people to correct planning of future movements based on previous temporal errors. However, the actual temporal error can be difficult to perceive: imagine a baseball batter that swings and misses a fastball. Here we show that in such situations people can use an internal error signal to make corrections in the next trial. This signal is based on the discrepancy between the actual and the planned action onset time: the prediction error. In this study, we used three interception tasks: reaching movements, saccadic eye movements and a button press that released a cursor moving ballistically for a fixed time. We found that action onset depended on the previous temporal error in the arm movement experiment only and not in the saccadic and button press experiments. However, this dependency was modulated by the movement time: faster arm movements depended less on the previous actual temporal error. An analysis using a Kalman filter confirmed that people used the prediction error rather than the previous temporal error for trial-by-trial corrections in fast arm movements, saccades and button press.
Characterization of multi-channel intraneural stimulation in transradial amputees
Authors: Strauss I. , Valle G. , Artoni F. , D’Anna E. , Granata G. , Di Iorio R. , Guiraud D. , Stieglitz T. , Rossini P. M. , Raspopovic S. , Petrini F. M. , Micera S. 
Published: December 2019

AbstractAlthough peripheral nerve stimulation using intraneural electrodes has been shown to be an effective and reliable solution to restore sensory feedback after hand loss, there have been no reports on the characterization of multi-channel stimulation. A deeper understanding of how the simultaneous stimulation of multiple electrode channels affects the evoked sensations should help in improving the definition of encoding strategies for bidirectional prostheses. We characterized the sensations evoked by simultaneous stimulation of median and ulnar nerves (multi-channel configuration) in four transradial amputees who had been implanted with four TIMEs (Transverse Intrafascicular Multichannel Electrodes). The results were compared with the characterization of single-channel stimulation. The sensations were characterized in terms of location, extent, type, and intensity. Combining two or more single-channel configurations caused a linear combination of the sensation locations and types perceived with such single-channel stimulations. Interestingly, this was also true when two active sites from the same nerve were stimulated. When stimulating in multi-channel configuration, the charge needed from each electrode channel to evoke a sensation was significantly lower than the one needed in single-channel configuration (sensory facilitation). This result was also supported by electroencephalography (EEG) recordings during nerve stimulation. Somatosensory potentials evoked by multi-channel stimulation confirmed that sensations in the amputated hand were perceived by the subjects and that a perceptual sensory facilitation occurred. Our results should help the future development of more efficient bidirectional prostheses by providing guidelines for the development of more complex stimulation approaches to effectively restore multiple sensations at the same time.