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1.
PLoS Genet ; 16(10): e1008623, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33052904

RESUMO

Plant cells undergo two types of cell cycles-the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2'-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.


Assuntos
Período de Replicação do DNA/genética , Replicação do DNA/efeitos dos fármacos , Raízes de Plantas/genética , Zea mays/genética , Núcleo Celular/efeitos dos fármacos , Núcleo Celular/genética , Centrômero/efeitos dos fármacos , Centrômero/genética , Replicação do DNA/genética , Período de Replicação do DNA/efeitos dos fármacos , DNA de Plantas/efeitos dos fármacos , DNA de Plantas/genética , Desoxiuridina/análogos & derivados , Desoxiuridina/farmacologia , Endocitose/efeitos dos fármacos , Meristema/efeitos dos fármacos , Meristema/genética , Mitose/efeitos dos fármacos , Mitose/genética , Nucleossomos/efeitos dos fármacos , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/crescimento & desenvolvimento , Fase S/genética , Zea mays/crescimento & desenvolvimento
2.
Plant Physiol ; 183(1): 206-220, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32205451

RESUMO

The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis (Arabidopsis thaliana) cells were briefly labeled with 5-ethynyl-2'-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems.


Assuntos
Arabidopsis/metabolismo , Cromatina/metabolismo , DNA de Plantas/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Replicação do DNA/genética , Replicação do DNA/fisiologia , DNA de Plantas/fisiologia , Origem de Replicação/genética , Origem de Replicação/fisiologia
3.
Psychol Res ; 85(3): 1201-1220, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32356009

RESUMO

The ability to silently hear music in the mind has been argued to be fundamental to musicality. Objective measurements of this subjective imagery experience are needed if this link between imagery ability and musicality is to be investigated. However, previous tests of musical imagery either rely on self-report, rely on melodic memory, or do not cater in range of abilities. The Pitch Imagery Arrow Task (PIAT) was designed to address these shortcomings; however, it is impractically long. In this paper, we shorten the PIAT using adaptive testing and automatic item generation. We interrogate the cognitive processes underlying the PIAT through item response modelling. The result is an efficient online test of auditory mental imagery ability (adaptive Pitch Imagery Arrow Task: aPIAT) that takes 8 min to complete, is adaptive to participant's individual ability, and so can be used to test participants with a range of musical backgrounds. Performance on the aPIAT showed positive moderate-to-strong correlations with measures of non-musical and musical working memory, self-reported musical training, and general musical sophistication. Ability on the task was best predicted by the ability to maintain and manipulate tones in mental imagery, as well as to resist perceptual biases that can lead to incorrect responses. As such, the aPIAT is the ideal tool in which to investigate the relationship between pitch imagery ability and musicality.


Assuntos
Percepção Auditiva/fisiologia , Memória de Curto Prazo/fisiologia , Música/psicologia , Adolescente , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Reino Unido , Adulto Jovem
4.
Plant Cell ; 29(9): 2126-2149, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28842533

RESUMO

All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.


Assuntos
Período de Replicação do DNA/genética , Genômica , Meristema/citologia , Meristema/genética , Mitose/genética , Fase S/genética , Zea mays/citologia , Zea mays/genética , Sequência de Bases , Cromossomos de Plantas/genética , Elementos de DNA Transponíveis/genética , Genes de Plantas , Modelos Genéticos , Sequências de Repetição em Tandem/genética , Fatores de Tempo , Transcrição Gênica
5.
Plant Physiol ; 176(3): 2166-2185, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29301956

RESUMO

Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.


Assuntos
Arabidopsis/genética , Cromatina/genética , Cromossomos de Plantas , Período de Replicação do DNA , Cromatina/metabolismo , Elementos de DNA Transponíveis , Citometria de Fluxo , Genoma de Planta , Estudo de Associação Genômica Ampla , Fase S/genética , Análise de Sequência de DNA/métodos
6.
BMC Bioinformatics ; 18(1): 362, 2017 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-28784090

RESUMO

BACKGROUND: Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing. RESULTS: To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds. CONCLUSIONS: Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.


Assuntos
Período de Replicação do DNA , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Software , Genoma , Tamanho do Genoma
7.
Plant Cell ; 26(1): 102-20, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24488963

RESUMO

Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.


Assuntos
Proteínas de Arabidopsis/fisiologia , Arabidopsis/genética , Regiões de Interação com a Matriz , Nucleossomos/metabolismo , Poli dA-dT/metabolismo , Fatores de Transcrição/fisiologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cromatina/metabolismo , Regulação da Expressão Gênica de Plantas , Motivos de Nucleotídeos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
8.
Chaos ; 27(11): 113105, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29195322

RESUMO

Stochastic averaging problems with Gaussian forcing have been the subject of numerous studies, but far less attention has been paid to problems with infinite-variance stochastic forcing, such as an α-stable noise process. It has been shown that simple linear systems driven by correlated additive and multiplicative (CAM) Gaussian noise, which emerge in the context of reduced atmosphere and ocean dynamics, have infinite variance in certain parameter regimes. In this study, we consider the stochastic averaging of systems where a linear CAM noise process in the infinite variance parameter regime drives a comparatively slow process. We use (semi)-analytical approximations combined with numerical illustrations to compare the averaged process to one that is forced by a white α-stable process, demonstrating consistent properties in the case of large time-scale separation. We identify the conditions required for the fast linear CAM process to have such an influence in driving a slower process and then derive an (effectively) equivalent fast, infinite-variance process for which an existing stochastic averaging approximation is readily applied. The results are illustrated using numerical simulations of a set of example systems.

9.
Neuroimage ; 135: 142-51, 2016 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-27132045

RESUMO

While most normal hearing individuals can readily use prosodic information in spoken language to interpret the moods and feelings of conversational partners, people with congenital amusia report that they often rely more on facial expressions and gestures, a strategy that may compensate for deficits in auditory processing. In this investigation, we used EEG to examine the extent to which individuals with congenital amusia draw upon visual information when making auditory or audio-visual judgments. Event-related potentials (ERP) were elicited by a change in pitch (up or down) between two sequential tones paired with a change in spatial position (up or down) between two visually presented dots. The change in dot position was either congruent or incongruent with the change in pitch. Participants were asked to judge (1) the direction of pitch change while ignoring the visual information (AV implicit task), and (2) whether the auditory and visual changes were congruent (AV explicit task). In the AV implicit task, amusic participants performed significantly worse in the incongruent condition than control participants. ERPs showed an enhanced N2-P3 response to incongruent AV pairings for control participants, but not for amusic participants. However when participants were explicitly directed to detect AV congruency, both groups exhibited enhanced N2-P3 responses to incongruent AV pairings. These findings indicate that amusics are capable of extracting information from both modalities in an AV task, but are biased to rely on visual information when it is available, presumably because they have learned that auditory information is unreliable. We conclude that amusic individuals implicitly draw upon visual information when judging auditory information, even though they have the capacity to explicitly recognize conflicts between these two sensory channels.


Assuntos
Transtornos da Percepção Auditiva/fisiopatologia , Mapeamento Encefálico/métodos , Potenciais Evocados Auditivos , Potenciais Evocados Visuais , Percepção da Altura Sonora , Percepção Visual , Tomada de Decisões , Feminino , Humanos , Masculino , Tempo de Reação , Análise e Desempenho de Tarefas , Adulto Jovem
10.
Plant Mol Biol ; 89(4-5): 339-51, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26394866

RESUMO

Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.


Assuntos
Replicação do DNA/genética , Endorreduplicação/genética , Zea mays/crescimento & desenvolvimento , Zea mays/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Período de Replicação do DNA/genética , DNA de Plantas/biossíntese , DNA de Plantas/genética , Genes de Plantas , Imageamento Tridimensional , Meristema/genética , Meristema/crescimento & desenvolvimento , Meristema/metabolismo , Modelos Biológicos , Fase S/genética , Zea mays/metabolismo
11.
J Exp Bot ; 65(10): 2747-56, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24449386

RESUMO

The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation.


Assuntos
Replicação do DNA , DNA de Plantas/biossíntese , Raízes de Plantas/crescimento & desenvolvimento , Zea mays/crescimento & desenvolvimento , Sequência de Bases , Núcleo Celular/genética , Hibridização in Situ Fluorescente , Sondas de Oligonucleotídeos , Zea mays/genética
12.
Exp Brain Res ; 232(4): 1193-206, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24452777

RESUMO

The ability to predict the actions of other agents is vital for joint action tasks. Recent theory suggests that action prediction relies on an emulator system that permits observers to use a model of their own movement kinematics to predict the actions of other agents. If this is the case, then people should be more accurate at generating predictions about actions that are similar to their own. We tested this hypothesis in two experiments in which participants were required to predict the occurrence and timing of particular critical points in an observed action. In Experiment 1, we employed a self/other prediction paradigm in which prediction accuracy for recordings of self-generated movements was compared with prediction accuracy for recordings of other-generated movements. As expected, prediction was more accurate for recordings of self-generated actions because in this case the movement kinematics of the observer and observed stimuli are maximally similar. In Experiment 1, people were able to produce actions at their own tempo and, therefore, the results might be explained in terms of self-similarity in action production tempo rather than in terms of movement kinematics. To control for this possibility in Experiment 2, we compared prediction accuracy for stimuli that were matched in tempo but differed only in terms of kinematics. The results showed that participants were more accurate when predicting actions with a human kinematic profile than tempo-matched stimuli that moved with non-human kinematics. Finally, in Experiment 3, we confirmed that the results of Experiment 2 cannot be explained by human-like stimuli containing a slowing down phase before the critical points. Taken together, these findings provide further support for the role of motor emulation in action prediction, and they suggest that the action prediction mechanism produces output that is available rapidly and available to drive action control suggesting that it can plausibly support joint action coordination.


Assuntos
Percepção de Movimento/fisiologia , Movimento/fisiologia , Estimulação Luminosa/métodos , Desempenho Psicomotor/fisiologia , Adolescente , Adulto , Fenômenos Biomecânicos/fisiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Fatores de Tempo , Adulto Jovem
13.
PLoS Genet ; 6(6): e1000982, 2010 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-20548960

RESUMO

DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.


Assuntos
Arabidopsis/genética , Cromatina/genética , Cromossomos de Plantas , Replicação do DNA , Fase S , Arabidopsis/citologia , Epigênese Genética , Citometria de Fluxo , Análise de Sequência com Séries de Oligonucleotídeos , Replicon
14.
Exp Brain Res ; 216(1): 51-60, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22038717

RESUMO

Common Coding theory predicts that perceived action should resonate in produced action to which it bears some resemblance. Here we show that the qualities of motion commonly attributed to melodies are instantiated in motor plans that control timed movements. Participants attempted to tap a steady beat. Each tap triggered a sounded tone, and successive tones were systematically varied in pitch to form short melodies. Tapping behavior was monitored with motion capture. Although instructed to ignore them, triggered tones systematically affected timing and finger movement. When slower melodic motion was implied by a contour change or a smaller pitch displacement, the interval-tap interval (ITI) was longer. When faster melodic motion was implied by a preserved pitch contour or a larger pitch displacement, ITI was shorter. Kinematic recordings suggested that ITI Error arose from an initial failure to disambiguate perception (i.e., velocity implied by melodic motion) from action (i.e., finger velocity [FV]). Early in the tap trajectory, slower FV was associated with longer ITI and faster FV was associated with shorter ITI. These associations were reversed near mid-trajectory, suggesting a transition from execution of motor planning to online control (Glover et al. in Exp Brain Res 154:103-108, 2004).


Assuntos
Percepção de Movimento , Música , Percepção da Altura Sonora/fisiologia , Desempenho Psicomotor/fisiologia , Estimulação Acústica , Adolescente , Feminino , Dedos/inervação , Humanos , Masculino , Fatores Desencadeantes , Tempo de Reação , Estatística como Assunto , Fatores de Tempo , Adulto Jovem
15.
Methods Mol Biol ; 2382: 29-72, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34705232

RESUMO

DNA replication during S phase in eukaryotes is a highly regulated process that ensures the accurate transmission of genetic material to daughter cells during cell division. Replication follows a well-defined temporal program, which has been studied extensively in humans, Drosophila, and yeast, where it is clear that the replication process is both temporally and spatially ordered. The replication timing (RT) program is increasingly considered to be a functional readout of genomic features and chromatin organization. Although there is increasing evidence that plants display important differences in their DNA replication process compared to animals, RT programs in plants have not been extensively studied. To address this deficiency, we developed an improved protocol for the genome-wide RT analysis by sequencing newly replicated DNA ("Repli-seq") and applied it to the characterization of RT in maize root tips. Our protocol uses 5-ethynyl-2'-deoxyuridine (EdU) to label replicating DNA in vivo in intact roots. Our protocol also eliminates the need for synchronization and frequently associated chemical perturbations as well as the need for cell cultures, which can accumulate genetic and epigenetic differences over time. EdU can be fluorescently labeled under mild conditions and does not degrade subnuclear structure, allowing for the differentiation of labeled and unlabeled nuclei by flow sorting, effectively eliminating contamination issues that can result from sorting on DNA content alone. We also developed an analysis pipeline for analyzing and classifying regions of replication and present it in a point-and-click application called Repliscan that eliminates the need for command line programming.


Assuntos
Período de Replicação do DNA , Meristema , Animais , DNA , Replicação do DNA , Humanos , Fase S
16.
PLoS Biol ; 6(12): 2880-95, 2008 Dec 09.
Artigo em Inglês | MEDLINE | ID: mdl-19071958

RESUMO

Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.


Assuntos
Arabidopsis/genética , Células Cultivadas , Cromossomos de Plantas/fisiologia , Epigênese Genética/genética , Arabidopsis/citologia , Arabidopsis/crescimento & desenvolvimento , Sequência de Bases , Imunoprecipitação da Cromatina , Metilação de DNA , Elementos de DNA Transponíveis/genética , Expressão Gênica , Genes de Plantas/genética , Genoma de Planta , Histonas/metabolismo , Folhas de Planta/química , RNA de Plantas/química , RNA Interferente Pequeno/metabolismo
17.
Cogn Emot ; 25(4): 573-84, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21547761

RESUMO

Several studies have used a visual search task to demonstrate that schematic negative-face targets are found faster and/or more efficiently than positive ones, with these findings taken as evidence that negative emotional expression is capable of guiding attentional allocation in visual search. A common hypothesis is that these effects should be disrupted by face inversion; however, this has not been consistently demonstrated, and raises the possibility of a perceptual confound. One candidate confound is the feature of "closure" (see Wolfe & Horowitz, 2004) caused by the down-turned mouth adjacent to edge of the face. This was investigated in the present series of experiments. In Experiment 1, the speed advantage for upright negative faces was replicated. In Experiment 2, the effect was not disrupted with inversion, and an efficiency advantage emerged, suggesting that perceptual features could be causing the advantage. In Experiment 3, speed and efficiency effects were seen when this perceptual characteristic remained but face features were scrambled. Taken together, these findings suggest that visual search using schematic faces containing a curved-line mouth feature cannot provide a valid test of guided search by negative facial emotion unless this confound is controlled.


Assuntos
Atenção , Discriminação Psicológica , Emoções , Expressão Facial , Reconhecimento Visual de Modelos , Adulto , Feminino , Humanos , Pessoa de Meia-Idade , Testes Neuropsicológicos , Tempo de Reação
18.
Curr Biol ; 31(3): 591-600.e4, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33275892

RESUMO

5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.


Assuntos
Arabidopsis , Metilação de DNA , Arabidopsis/genética , Arabidopsis/metabolismo , Ciclo Celular , Citosina , DNA de Plantas , Regulação da Expressão Gênica de Plantas , Células Germinativas/metabolismo , Histonas/genética , Histonas/metabolismo , Plantas/metabolismo , RNA Interferente Pequeno/genética
19.
Biotechnol Bioeng ; 104(5): 947-56, 2009 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-19585523

RESUMO

In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive alpha-amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic alpha-amylase from Thermotoga maritima. While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant-produced alpha-amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant-made enzyme retained 85% of its initial activity after 3 h incubation at 100 degrees C, whereas the E. coli-produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca(2+) or plant cell extracts from tobacco and sweetpotato to the E. coli-produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium-rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available.


Assuntos
Cálcio/farmacologia , Coenzimas/farmacologia , Nicotiana/enzimologia , Plantas Geneticamente Modificadas/enzimologia , Thermotoga maritima/enzimologia , alfa-Amilases/química , alfa-Amilases/metabolismo , Estabilidade Enzimática , Escherichia coli/enzimologia , Escherichia coli/genética , Temperatura Alta , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Thermotoga maritima/genética , Nicotiana/genética , alfa-Amilases/genética
20.
Sci Rep ; 9(1): 16823, 2019 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-31727968

RESUMO

Recent magnetoencephalography (MEG) studies have established that sensorimotor brain rhythms are strongly modulated during mental imagery of musical beat and rhythm, suggesting that motor regions of the brain are important for temporal aspects of musical imagery. The present study examined whether these rhythms also play a role in non-temporal aspects of musical imagery including musical pitch. Brain function was measured with MEG from 19 healthy adults while they performed a validated musical pitch imagery task and two non-imagery control tasks with identical temporal characteristics. A 4-dipole source model probed activity in bilateral auditory and sensorimotor cortices. Significantly greater ß-band modulation was found during imagery compared to control tasks of auditory perception and mental arithmetic. Imagery-induced ß-modulation showed no significant differences between auditory and sensorimotor regions, which may reflect a tightly coordinated mode of communication between these areas. Directed connectivity analysis in the θ-band revealed that the left sensorimotor region drove left auditory region during imagery onset. These results add to the growing evidence that motor regions of the brain are involved in the top-down generation of musical imagery, and that imagery-like processes may be involved in musical perception.


Assuntos
Percepção Auditiva/fisiologia , Imagens, Psicoterapia/métodos , Magnetoencefalografia/métodos , Córtex Sensório-Motor/fisiologia , Adulto , Córtex Auditivo/fisiologia , Feminino , Voluntários Saudáveis , Humanos , Imaginação , Masculino , Música
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