Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous ...signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (
s). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant ...modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
MicroRNAs are non-coding small RNA molecules that are involved in the post-transcriptional regulation of the genes that control various developmental processes in plants, including zygotic ...embryogenesis (ZE). miRNAs are also believed to regulate somatic embryogenesis (SE), a counterpart of the ZE that is induced
in plant somatic cells. However, the roles of specific miRNAs in the regulation of the genes involved in SE, in particular those encoding transcription factors (TFs) with an essential function during SE including
), remain mostly unknown. The aim of the study was to reveal the function of miR165/166 and miR160 in the
-controlled pathway of SE that is induced in
cultured Arabidopsis explants.In ZE, miR165/166 controls the
/
(
) genes, which are the positive regulators of
, while miR160 targets the
(
) that control the auxin signaling pathway, which plays key role in LEC2-mediated SE. We found that a deregulated expression/function of miR165/166 and miR160 resulted in a significant accumulation of auxin in the cultured explants and the spontaneous formation of somatic embryos. Our results show that miR165/166 might contribute to SE induction via targeting
, a positive regulator of LEC2 that controls embryogenic induction via activation of auxin biosynthesis pathway (Wójcikowska et al., 2013). Similar to miR165/166, miR160 was indicated to control SE induction through auxin-related pathways and the negative impact of miR160 on
was shown in an embryogenic culture. Altogether, the results suggest that the miR165/166- and miR160-node contribute to the LEC2-mediated auxin-related pathway of embryogenic transition that is induced in the somatic cells of Arabidopsis. A model summarizing the suggested regulatory interactions between the miR165/166-PHB and miR160-ARF10/ARF16/ARF17 nodes that control SE induction in Arabidopsis was proposed.
Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence ...that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole (Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA (including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In this study, we explore the simulation setup in computational neuroscience. We use GENESIS, a general purpose simulation engine for sub-cellular components and biochemical reactions, realistic ...neuron models, large neural networks, and system-level models. GENESIS supports developing and running computer simulations but leaves a gap for setting up today's larger and more complex models. The field of realistic models of brain networks has overgrown the simplicity of earliest models. The challenges include managing the complexity of software dependencies and various models, setting up model parameter values, storing the input parameters alongside the results, and providing execution statistics. Moreover, in the high performance computing (HPC) context, public cloud resources are becoming an alternative to the expensive on-premises clusters. We present Neural Simulation Pipeline (NSP), which facilitates the large-scale computer simulations and their deployment to multiple computing infrastructures using the infrastructure as the code (IaC) containerization approach. The authors demonstrate the effectiveness of NSP in a pattern recognition task programmed with GENESIS, through a custom-built visual system, called RetNet(8 × 5,1) that uses biologically plausible Hodgkin-Huxley spiking neurons. We evaluate the pipeline by performing 54 simulations executed on-premise, at the Hasso Plattner Institute's (HPI) Future Service-Oriented Computing (SOC) Lab, and through the Amazon Web Services (AWS), the biggest public cloud service provider in the world. We report on the non-containerized and containerized execution with Docker, as well as present the cost per simulation in AWS. The results show that our neural simulation pipeline can reduce entry barriers to neural simulations, making them more practical and cost-effective.
The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern ...Europe, analyzing contemporary genetic structure to identify the role of a potential 'northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Understanding how humans evaluate credibility is an important scientific question in the era of fake news. Source credibility is among the most important aspects of credibility evaluations. One of ...the most direct ways to understand source credibility is to use measurements of brain activity of humans who make credibility evaluations. This article reports the results of an experiment during which we have measured brain activity during credibility evaluation using EEG. In the experiment, participants had to learn source credibility of fictitious students based on a preparatory stage, during which they evaluated message credibility with perfect knowledge. The experiment allowed for identification of brain areas that were active when a participant made positive or negative source credibility evaluations. Based on experimental data, we modeled and predicted human source credibility evaluations using EEG brain activity measurements with F1 score exceeding 0.7 (using 10-fold cross-validation). We are also able to model and predict message credibility evaluations with perfect knowledge, and to compare both models obtained from a single experiment.
The shape and size of the skull are determined by various factors. These factors act not only on single individuals in their ontogenesis, but can affect entire populations in the long term, thus ...determining developmental trends. The aim of this study was to determine whether the craniometric features of the European bison skull and their proportions are constant or change over time. In total, 1097 European bison skulls from the Mammal Research Institute of the Polish Academy of Sciences and Warsaw University of Life Sciences were examined. It has been shown that almost all examined skull dimensions tend to decrease. The opposite phenomenon was observed for the height of the skull in males. The results of the work prove that European bison adapt to changing environmental conditions related to climate warming, food availability, and population density.
The self-face has a prioritized status in the processing of incoming visual inputs. As the self-face changes over the lifespan, this stimulus seems to be well-suited for investigation of the self ...across time. Here, steady-state visual evoked potentials (SSVEP, oscillatory responses to periodic stimulation with a frequency that mirrors the frequency of stimulation) were used to investigate this topic. Different types of faces (present self, past self, close-other's, unknown, scrambled) flickered four times per second in two types of stimulation ('identical', with the same image of a given type of face; 'different', with different images of the same type of face). Each of the 10 stimulation sessions lasted 90 seconds and was repeated three times. EEG data were recorded and analyzed in 20 participants. In general, faces evoked higher SSVEP than scrambled faces. The impact of identical and different stimulation was similar for faces and scrambled faces: SSVEP to different stimuli (faces, scrambled faces) was enhanced in comparison to identical ones. Present self-faces evoked higher SSVEP responses than past self-faces in the different stimulation condition only. Thus, our results showed that the physical aspects of the present and past selves are differentiated on the neural level in the absence of an overt behavior.
A very good knowledge of material properties is required in the analysis of severe plastic deformation problems in which the classical material processing methods are accelerated by the application ...of the additional cyclic load. A general fuzzy logic-based approach is proposed for the analysis of experimental and numerical data in this paper. As an application of the fuzzy analysis, the calibration of Chaboche–Lemaitre model hardening parameters of PA6 aluminum is considered here. The experimental data obtained in a symmetrical strain-controlled cyclic tension–compression test were used to estimate the material’s hardening parameters. The numerically generated curves were compared to the experimental ones. For better fitting of numerical and experimental results, the optimization approach using the least-square method was applied. Unfortunately, commonly accepted calibration methods can provide various sets of hardening parameters. In order to choose the most reliable set, the fuzzy analysis was used. Primarily selected values of hardening parameters were assumed to be fuzzy input parameters. The error of the hysteresis loop approximation for each set was used to compute its membership function. The discrete value of this error was obtained in the defuzzification step. The correct selections of hardening parameters were verified in ratcheting and mean stress relaxation tests. The application of the fuzzy analysis has improved the convergence between experimental and numerical stress–strain curves. The fuzzy logic allows analyzing the variation of elastic–plastic material response when some imprecisions or uncertainties of input parameters are taken into consideration.
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