bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro Antibacterial effect ofCommiphora myrrhaOil against Dental Pathogens
Authors: Izzeldien Reem , Abdulaziz Sondos , Ahmed Ayat , Noma Mounkaila 
Published: October 2020

AbstractDental caries is a chronic disease caused by the interaction of oral microorganisms, diet and host factors over time.Streptococcus mutansis considered as the main bacteria involve in dental decay, while the level ofLactobacillus spp. is directly related to the presence or onset of caries.Commiphora myrrhais an ancient plant which extracts are used as antiseptic and anti-inflammatory for mouth and throat due to it is antimicrobial activity. This study assessed the impact ofCommiphora myrrhaon two bacteriaStreptococcus mutansandLactobacillus spp. involved in dental caries. Three samples ofStreptococcus mutansbacteria were collected randomly from patients with dental caries in Khartoum dental teaching hospital, whileLactobacillus spp. were obtained from fermented milk. Disk and well diffusion methods were used to test the effect of four concentration (100,50,25 and 12.5 mg/ml) of Myrrha volatile oil, extracted by hydro-distillation technique. The biochemical analysis ofCommiphora myrrhaoil was carried out using Gas Chromatography/Mass Spectrophotometric technique. The finding revealed that the four concentrations of oil were effective onStreptococcus mutanswith the largest inhibition zone (18.7± 0.6 mm) through the well diffusion method and inhibition zone of (14.00 mm) with disc diffusion method regardless the two methods these inhibition zones were recorded at 100 mg/ml, with Minimum Bactericidal Concentration (MBC) at 3.125 mg/ml. WhileLactobacillus spp. bacteria sensitive to three concentrations (100,50 and 25 mg/ml) and resistance to concentration 12.5 mg/ml, it is MBC found to be 25 mg/ml. In conclusion, this research revealed that Myrrh oil is effective on bothS.mutansandLactobacillus spp. Hence, Myrrha oil is a potential antibacterial product of interest in dental caries.
Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex inArabidopsis
Authors: Zhang Yi-Zhe , Yuan Jianlong , Zhang Lingrui , Chen Chunxiang , Wang Yuhua , Zhang Guiping , Peng Li , Xie Si-Si , Jiang Jing , Zhu Jian-Kang , Du Jiamu , Duan Cheng-Guo 
Published: October 2020

SUMMARYHistone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a new mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, inArabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector geneARGONAUTE 5(AGO5) and We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
Assessment of Heterogeneity of Cytochrome P450 Activity in Cancer-Cell Population by Cytometry of Reaction Rate Constant is Robust to Variation in Substrate Concentration
Authors: Oliveira Mariana Bleker de , Koshkin Vasilij , Perry Christopher G. R. , Krylov Sergey N. 
Published: October 2020

ABSTRACTEnzymes of the cytochrome P450 (CYP) family catalyze the metabolism of chemotherapeutic agents and are among the key players in primary and acquired chemoresistance of cancer. The activity of CYP is heterogeneous in tumor tissues, and the quantitative characteristics of this heterogeneity can be used to predict chemoresistance. Cytometry of reaction rate constant (CRRC) is a kinetic approach to assess cell population heterogeneity by measuring rates of processes at the single-cell levelviatime-lapse imaging. CRRC was shown to be an accurate and robust method for assessing the heterogeneity of drug-extrusion activity catalyzed by ABC transporters, which are also key players in cancer chemoresistance. We hypothesized that CRRC is also a reliable method for assessing the heterogeneity of CYP activity. Here, we evaluated the robustness of assessing the heterogeneity of CYP activity by CRRC with respect to controlled variation in the concentration of a CYP substrate by comparing CRRC with non-kinetic approaches. We found that changing the substrate concentration by 20% resulted only in minimal changes in the position, width, and asymmetry of the peak in the CRRC histogram, while these parameters varied greatly in the non-kinetic histograms. Moreover, the Kolmogorov-Smirnov statistical test showed that the distribution of the cell population in CRRC histograms was not significantly different; the result was opposite for non-kinetic histograms. In conclusion, we were able to demonstrate the robustness of CRRC with respect to changes in substrate concentration when evaluating CYP activity at the single-cell level.
Extinctions have strongly reduced the mammalian consumption of primary productivity
Authors: Pedersen Rasmus Østergaard , Faurby Søren , Svenning Jens-Christian 
Published: October 2020

AbstractHerbivorous mammals are important for natural ecosystems even today, but how much stronger would there effects be without human-linked extinctions and extirpations? The ranges of many mammal species have contracted and numerous species have gone extinct due to human pressures, so herbivore impacts in even seemingly natural ecosystems likely deviate from their pre-anthropogenic state. However, such effects remain poorly understood and often unrecognized. To address this issue, we here quantified and mapped plant consumption by all terrestrial mammals in natural areas based on both current and estimated natural ranges. We then compared the estimated consumption rates to current plant net primary productivity, and summarised the results for global ecosystem types both broadly and in the wildest remaining natural areas around the world (the Last of the Wild). We found that wild mammals consume 7.3% (95% interquantile range: 0.85% - 26%) of net primary productivity in current natural areas, and that this would be much higher in the absence of extinctions and extirpations, namely 13% (95% interquantile range: 1.7% - 40%), i.e., a >50% higher consumption rate. Marked human-linked declines in herbivory were seen even in the wildest remaining natural areas, where mammals now consume a mean of 9% (95% interquantile range: 2.2% - 26%) of plant primary productivity, which is only 60% of no-extinction level. Our results show that mammalian herbivores naturally play an important part in ecosystems at a global scale, but that this effect has been strongly reduced by extinctions and extirpations.
Clustered Rapid Induction of Apoptosis Limits ZIKV and DENV-2 Proliferation in the Midguts ofAedes aegypti
Authors: Ayers Jasmine B. , Coatsworth Heather G. , Kang Seokyoung , Dinglasan Rhoel R. , Zhou Lei 
Published: October 2020

ABSTRACTInter-host transmission of pathogenic arboviruses such as dengue virus (DENV) and Zika virus (ZIKV) requires systemic infection of the mosquito vector. Successful systemic infection requires initial viral entry and proliferation in the midgut cells of the mosquito followed by dissemination to secondary tissues and eventual entry into salivary glands1. Lack of arbovirus proliferation in midgut cells has been observed in severalAedes aegyptistrains2, but the midgut antiviral responses underlying this phenomenon are not yet fully understood. We report here that there is a rapid induction of apoptosis (RIA) in theAedes aegyptimidgut epithelium within 2 hours of infection with DENV-2 or ZIKV in bothin vivoblood-feeding andex vivomidgut infection models. Inhibition of RIA led to increased virus proliferation in the midgut, implicating RIA as an innate immune mechanism mediating midgut infection in this mosquito vector.
Removing independent noise in systems neuroscience data using DeepInterpolation
Authors: Lecoq Jérôme , Oliver Michael , Siegle Joshua H. , Orlova Natalia , Koch Christof 
Published: October 2020

Progress in nearly every scientific discipline is hindered by the presence of independent noise in spatiotemporally structured datasets. Three widespread technologies for measuring neural activity—calcium imaging, extracellular electrophysiology, and fMRI—all operate in domains in which shot noise and/or thermal noise deteriorate the quality of measured physiological signals. Current denoising approaches sacrifice spatial and/or temporal resolution to increase the Signal-to-Noise Ratio of weak neuronal events, leading to missed opportunities for scientific discovery.Here, we introduceDeepInterpolation, a general-purpose denoising algorithm that trains a spatio-temporal nonlinear interpolation model using only noisy samples from the original raw data. Applying DeepInterpolation toin vivotwo-photon Ca2+imaging yields up to 6 times more segmented neuronal segments with a 15 fold increase in single pixel SNR, uncovering network dynamics at the single-trial level. In extracellular electrophysiology recordings, DeepInterpolation recovered 25% more high-quality spiking units compared to a standard data analysis pipeline. On fMRI datasets, DeepInterpolation increased the SNR of individual voxels 1.6-fold. All these improvements were attained without sacrificing spatial or temporal resolution.DeepInterpolation could well have a similar impact in other domains for which independent noise is present in experimental data.
K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle
Authors: Yu Yuanyuan , Zheng Qingyun , Erramilli Satchal K. , Pan Man , Park Seongjin , Xie Yuan , Li Jingxian , Fei Jingyi , Kossiakoff Anthony A. , Liu Lei , Zhao Minglei 
Published: October 2020

AbstractProtein ubiquitination shows remarkable topological and functional diversity through the polymerization of ubiquitin via different linkages. Deciphering the cellular ubiquitin code is of central importance to understand the physiology of the cell. Among the eight possible linkages, K29-linked polyubiquitin is a relatively abundant type of polyubiquitin in both human and yeast cells. However, our understanding of its function is rather limited due to the lack of specific binders as tools to detect K29-linked polyubiquitin. In this study, we screened and characterized a synthetic antigen-binding fragment, termed sAB-K29, that can specifically recognize K29-linked polyubiquitin using chemically synthesized K29-linked diubiquitin. We further determined the crystal structure of this fragment bound to the K29-linked diubiquitin, which revealed the molecular basis of specificity. Using sAB-K29 as a tool, we uncovered that K29-linked ubiquitination is involved in different kinds of cellular proteotoxic stress response as well as cell cycle regulation. In particular, we showed that K29-linked ubiquitination is enriched in the midbody and downregulation of the K29-linked ubiquitination signal arrests cells in G1/S phase.
Noise correlations for faster and more robust learning
Authors: Nassar Matthew R. , Scott Daniel , Bhandari Apoorva 
Published: October 2020

AbstractDistributed population codes are ubiquitous in the brain and pose a challenge to downstream neurons that must learn an appropriate readout. Here we explore the possibility that this learning problem is simplified through inductive biases implemented by stimulus-independent noise correlations that constrain learning to task-relevant dimensions. We test this idea in a set of neural networks that learn to perform a perceptual discrimination task. Correlations among similarly tuned units were manipulated independently of overall population signal-to-noise ratio in order to test how the format of stored information affects learning. Higher noise correlations among similarly tuned units led to faster and more robust learning, favoring homogenous weights assigned to neurons within a functionally similar pool, and could emerge through Hebbian learning. When multiple discriminations were learned simultaneously, noise correlations across relevant feature dimensions sped learning whereas those across irrelevant feature dimensions slowed it. Our results complement existing theory on noise correlations by demonstrating that when such correlations are produced without significant degradation of the signal-to-noise ratio, they can improve the speed of readout learning by constraining it to appropriate dimensions.Significance statementPositive noise correlations between similarly tuned neurons theoretically reduce the representational capacity of the brain, yet they are commonly observed, emerge dynamically in complex tasks, and persist even in well-trained animals. Here we show that such correlations, when embedded in a neural population with a fixed signal to noise ratio, can improve the speed and robustness with which an appropriate readout is learned. In a simple discrimination task such correlations can emerge naturally through Hebbian learning. In more complex tasks that require multiple discriminations, correlations between neurons that similarly encode the task-relevant feature improve learning by constraining it to the appropriate task dimension.
Tau protein in smooth muscle cells and tissues
Authors: Shults Nataliia V. , Seeherman Sarah , Sariipek Nurefsan E. , Rybka Vladyslava , Marcocci Lucia , Gychka Sergiy G. , Ibrahim Yasmine F. , Suzuki Yuichiro J. 
Published: October 2020

AbstractTau is a microtubule-associated protein and plays a critical role in the pathophysiology of neurons. However, whether tau protein is expressed in smooth muscle cells is unknown. Here, we report that tau protein is expressed and is constitutively phosphorylated at threonine 181 in various smooth muscle cell types, including human cerebral artery smooth muscle cells, human pulmonary artery smooth muscle cells, and human bronchial airway smooth muscle cells. We also detected the expression of tau protein in the vascular smooth muscle of brain tissues from patients with systemic hypertension who died of ischemic stroke. Immunofluorescence staining revealed that phosphorylated tau at threonine 181 is more organized in the cell than does total tau protein. A protein phosphatase inhibitor, calyculin A induced the formation of higher molecular weight species of phosphorylated tau as visualized by Western blotting, indicating the occurrence of tau aggregation. Immunofluorescence also showed that calyculin A caused the aggregation of phosphorylated tau and disrupted the cytoskeletal organization. These results demonstrate the existence of tau protein in smooth muscle cells and tissues and that smooth muscle tau is susceptible to protein phosphorylation and aggregation.
A wildCucurbitagenome reveals the role of structural variants and introgression in domestication
Authors: Barrera-Redondo Josué , Sánchez-de la Vega Guillermo , Aguirre-Liguori Jonás A. , Castellanos-Morales Gabriela , Gutiérrez-Guerrero Yocelyn T. , Aguirre-Dugua Xitlali , Aguirre-Planter Erika , Tenaillon Maud I. , Lira-Saade Rafael , Eguiarte Luis E. 
Published: October 2020

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits inCucurbitaspecies (pumpkins and squashes) is currently lacking.Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to studyCucurbitadomestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies ofC. argyrospermaacross Mexico. We also assembled the first wildCucurbitagenome at a chromosome level. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We uncovered candidate domestication genes that are involved in the synthesis and regulation of growth hormones, plant defense mechanisms, flowering time and seed development. The presence of shared selected alleles with the closely related speciesCucurbita moschatasuggests domestication-related introgression between both taxa.
Anatomical identification of the neuroendocrine system in theNothobranchius furzeribrain
Authors: Do Eunjeong , Kim Yumi 
Published: October 2020

AbstractThe hypophysis functions as a central gland of the neuroendocrine system for regulating fundamental body physiology. Upon aging, several hormones produced by the endocrine system are dramatically altered. Recently,Nothobranchius furzeri(the turquoise killifish) has become a popular model for aging studies because of its short lifespan and highly conserved aging phenotypes. However, the anatomical details of the major neuroendocrine system of the killifish have not been investigated so far. In this study, we have identified the pituitary and pineal glands of the turquoise killifish, which are critical components of the brain endocrine system. These two neuroendocrine glands were weakly attached to the main body of the killifish brain. The pineal gland was located on the dorsal part of the brain, while the pituitary gland was located on the ventral part. Brain sections containing pineal and pituitary glands were performed and revealed that cells in both the pituitary and pineal glands are densely placed than any other regions of brain. Further, three-dimensional images both in pineal and pituitary glands were uncovered their distinctive cellular arrangements. Vasopressin intestinal peptide (VIP) was strongly expressed in the neurohypophysis of the pituitary gland. Glial cells were found inside the pineal gland, while astrocytes covered the outside. These findings illustrate basic features of the neuroendocrine system ofNothobranchius furzeri.
Male brain processing of the body odor of ovulating women compared to that of pregnant women
Authors: Habel Ute , Regenbogen Christina , Kammann Catharina , Stickel Susanne , Chechko Natalia 
Published: October 2020

AbstractFemale chemical signals underlie the advertising of sexual receptivity and fertility. Whether the body odor of a pregnant woman also has a signaling function with respect to male behavior is yet to be conclusively established. This study examines how the body odors of ovulating and pregnant women differentially affect the behavior of heterosexual men.Body odor samples were collected from 5 pregnant women and 5 matched controls during ovulation. In a double-blind functional magnetic resonance imaging design, 18 heterosexual men were exposed to female body odors during ovulation (OV) and pregnancy (PRG) while being required to indicate the attractiveness of concurrently presented female portrait images. The participants were also required to indicate whether they assumed a depicted woman was pregnant.While neither OV nor PRG altered the perceived attractiveness of a presented face, the men tended to identify the women as pregnant while exposed to a PRG body odor. On the neural level, OV activated a network of the frontotemporal and limbic regions, while PRG activated the superior medial frontal gyrus.The results suggest that the detection of sexual availability activates the male brain regions associated with face processing and reward/motivation, whereas sensing pregnancy activates a region responsible for empathy and prosocial behavior. Thus, the female body odor during pregnancy likely helps foster circumstances conducive to the future care of offspring while the body odor advertising sexual availability promotes mating behavior. The brains of heterosexual men may be capable of unconsciously discriminating between these two types of olfactory stimuli.
Spike-timing-dependent plasticity can account for connectivity aftereffects of dual-site transcranial alternating current stimulation
Authors: Schwab Bettina C. , König Peter , Engel Andreas K. 
Published: October 2020

AbstractTranscranial alternating current stimulation (tACS), applied to two brain sites with different phase lags, has been shown to modulate stimulation-outlasting functional EEG connectivity between the targeted regions. Given the lack of knowledge on mechanisms of tACS aftereffects, it is difficult to further enhance effect sizes and reduce variability in experiments. In this computational study, we tested if spike-timing-dependent plasticity (STDP) can explain stimulation-outlasting connectivity modulation by dual-site tACS and explored the effects of tACS parameter choices. Two populations of spiking neurons were coupled with synapses subject to STDP, and results were validated via a re-analysis of EEG data. Our simulations showed stimulation-outlasting connectivity changes between in- and anti-phase tACS, dependent on both tACS frequency and synaptic conduction delays. Importantly, both a simple network entraining to a wide range of tACS frequencies as well as a more realistic network that spontaneously oscillated at alpha frequency predicted that the largest effects would occur for short conduction delays between the stimulated regions. This finding agreed with experimental EEG connectivity modulation by 10 Hz tACS, showing a clear negative correlation of tACS effects with estimated conduction delays between regions. In conclusion, STDP can explain connectivity aftereffects of dual-site tACS. However, not all combinations of tACS frequency and application sites are expected to effectively modulate connectivity via STDP. We therefore suggest using appropriate computational models and/or EEG analysis for planning and interpretation of dual-site tACS studies relying on aftereffects.HighlightsNetwork model with STDP explains EEG connectivity change after dual-site tACSEffects are predicted to depend on tACS frequency and conduction delaysEEG data confirm dependence on conduction delays between regionsModel can be used to estimate and maximize experimental effects
Spatiotemporal shifts in the role of floral traits in shaping tropical plant-pollinator interactions
Authors: Klomberg Yannick , Tropek Robert , Mertens Jan E.J. , Kobe Ishmeal N. , Hodeček Jiří , Raška Jan , Fominka Nestoral T. , Souto-Vilarós Daniel , Janeček Štěpán 
Published: October 2020

AbstractThe pollination syndrome hypothesis predicts that plants pollinated by the same pollinator group bear convergent combinations of specific floral traits. Nevertheless, some studies have shown relatively low predictive power for these floral trait combinations. This discrepancy may be caused by changes in the importance of specific floral traits for shaping interactions under different environmental conditions and for different pollinator groups. To test this, we studied pollination systems and floral traits along an elevational gradient on Mount Cameroon during wet and dry seasons. Using Random Forest models, allowing the ranking of traits by significance, we demonstrated that some floral traits are more important than others in shaping interactions and that these traits predict pollinators relatively well. However, the distribution and importance of traits varies under different environmental conditions. Our results imply the need to improve our trait-based understanding of plant-pollinator interactions to better inform the debate surrounding pollination syndrome hypothesis.