scholarly journals Identification of Chromatin Accessibility During The Early Stage of Pig SCNT Embryo Reprogramming by ATAC-Seq

2020 ◽  
Author(s):  
Xue Zhang ◽  
Juan Li ◽  
Ruixin Tao ◽  
Aiwen Jiang ◽  
Changyin Zhou ◽  
...  
Keyword(s):  
Histone Modification ◽  
Large Scale ◽  
Transcriptional Activity ◽  
Early Stage ◽  
Enrichment Analysis ◽  
Chromatin Accessibility ◽  
Nuclear Transplantation ◽  
Dynamic Changes ◽  
Accessible Chromatin ◽  
Insight Into

Abstract Background: Somatic cell nuclear transplantation (SCNT) can transform highly differentiated donor nuclei into pluripotent nuclei through the large-scale reprogramming of chromatin. The reprogramming of chromatin has been documented to take place in the first few hours after SCNT embryo activation. Thus, studies that characterize dynamic changes in chromatin during the first few hours after embryo activation could provide insight into the mechanism and significance of genome-wide reprogramming. However, few studies have examined the epigenetic remodeling of reconstructed embryos during the early stage of reprogramming.Results: We conducted ATAC-seq on 50 porcine SCNT-HMC embryos and 50 parthenogenetic activation (PA) embryos 10 h after activation. Along with pig embryonic fibroblast (PEF) ATAC-seq data, we found low levels of chromatin accessibility and gene transcription in SCNT and PA embryos. Moreover, PEF genes and the X chromosome became inaccessible during embryo reprogramming. GO enrichment analysis revealed that the molecular functions related to accessible chromatin in embryos primarily included transcriptional regulatory activity and SMAD binding. The differentially accessible chromatin sites between SCNT and PEF were primarily related to transcriptional activity and histone modification.Conclusions: Despite the tight chromatin structure during the early stage of embryo reprogramming, some accessible chromatin sites, which were primarily distributed in the intergenic region, were still detected. Dynamic changes in chromatin accessibility during reprogramming were primarily related to transcriptional activity and histone modification. Generally, this study provided new insight into the dynamics and importance of chromatin accessibility during the early stages of embryo reprogramming.

On the use of jerk and snap in condition monitoring of machinery – review and case studies

2021 ◽  
Vol 63 (8) ◽  
pp. 457-464
Author(s):  
S Lahdelma
Keyword(s):  
Condition Monitoring ◽  
Large Scale ◽  
Early Stage ◽  
Time Derivative ◽  
Additional Insight ◽  
Rolling Bearings ◽  
Monitoring Applications ◽  
Derivatives Of ◽  
Insight Into ◽  
Peak Value

The time derivatives of acceleration offer a great advantage in detecting impact-causing faults at an early stage in condition monitoring applications. Defective rolling bearings and gears are common faults that cause impacts. This article is based on extensive real-world measurements, through which large-scale machines have been studied. Numerous laboratory experiments provide additional insight into the matter. A practical solution for detecting faults with as few features as possible is to measure the root mean square (RMS) velocity according to the standards in the frequency range from 10 Hz to 1000 Hz and the peak value of the second time derivative of acceleration, ie snap. Measuring snap produces good results even when the upper cut-off frequency is as low as 2 kHz or slightly higher. This is valuable information when planning the mounting of accelerometers.

scholarly journals Chromatin variation associated with liver metabolism is mediated by transposable elements

2016 ◽  
Author(s):  
Juan Du ◽  
Amy Leung ◽  
Candi Trac ◽  
Brian W. Parks ◽  
Aldons J. Lusis ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transposable Elements ◽  
Complex Traits ◽  
Phenotypic Diversity ◽  
Enrichment Analysis ◽  
Chromatin Accessibility ◽  
Genomic Region ◽  
Long Interspersed Nuclear Elements ◽  
Accessible Chromatin ◽  
High Sucrose

AbstractBackgroundFunctional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of transcriptional regulation and variation in chromatin accessibility across individuals has been liked to complex traits and disease susceptibility. While mechanisms responsible for chromatin variation across individuals have been investigated, the overwhelming majority of chromatin variation remains unexplained. Furthermore, the processes through which the variation of chromatin accessibility contributes to phenotypic diversity remain poorly understood.ResultsWe profiled chromatin accessibility in liver from seven strains of mice with phenotypic diversity in response to a high-fat/high-sucrose (HF/HS) diet and identified reproducible chromatin variation across the genome. We found that sites of variable chromatin accessibility were more likely to coincide with particular classes of transposable elements (TEs) than sites with common chromatin features. Evolutionarily younger long interspersed nuclear elements (LINEs) are particularly enriched for variable chromatin sites. These younger LINEs are enriched for binding sites of immune-associated transcription factors, whereas older LINEs are enriched for liver-specific transcription factors. Genomic region enrichment analysis indicates that variable chromatin sites at TEs contribute to liver metabolic pathways. Finally, we show that polymorphism of TEs and differential DNA methylation at TEs can both contribute to chromatin variation.ConclusionsOur results demonstrate specific classes of TEs contribute to chromatin accessibility variation across strains of mice that display phenotypic diversity in response to a HF/HS diet. These results indicate that regulatory variation at TEs is an important contributor to phenotypic variation among populations.

scholarly journals The accessible promoter–mediated supplementary effect of ACE2 provides new insight into the tissue tropism of SARS-CoV-2

2020 ◽  
Author(s):  
Qi Jiang ◽  
Guifang Du ◽  
Junting Wang ◽  
XiaoHan Tang ◽  
Xuejun wang ◽  
...  
Keyword(s):  
Cell Lines ◽  
High Throughput Sequencing ◽  
Chromatin Accessibility ◽  
Tissue Tropism ◽  
Open Chromatin ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Novel Coronavirus ◽  
Accessible Chromatin ◽  
Insight Into

Abstract Background：Angiotensin-converting enzyme 2 (ACE2) has been confirmed to be a receptor for the newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, cell surface ACE2 expression is reported to be inconsistent with clinical tissue tropism of SARS-CoV-2, which complicates understanding of the pathogenesis of 2019 novel coronavirus disease (COVID-19). The consumption of ACE2 by internalization and shedding processes may explain this discordance. Results：To understand the discordance between ACE2 expression and the tissue tropism of SARS-CoV-2, we examined the chromatin accessibility of ACE2 promoter in hundreds of tissues and cell lines using public DNase-seq and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. We find that ACE2 promoter is only accessible in three tissues including lung, large intestine and placenta. Also, we examined tumors tissues and ACE2 promoter is observed accessible in five tumors with reported SARS-CoV-2 susceptibility. We confirmed the susceptibility by performing SARS-CoV-2 pseudovirus infection in several cell lines. Conclusions：We propose that open chromatin at the promoter mediates the ACE2 supplementary effect and ensures the entry of SARS-CoV-2. This hypothesis provides a new view and potential clues for further investigation of COVID-19 pathogenesis.

scholarly journals A combinatorial indexing strategy for epigenomic profiling of plant single cells

2021 ◽  
Author(s):  
Xiaoyu Tu ◽  
Alexandre P Marand ◽  
Robert J. Schmitz ◽  
Silin Zhong
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Arabidopsis Root ◽  
Indexing Method ◽  
Specialized Equipment ◽  
Cell Type Specific ◽  
Accessible Chromatin ◽  
Insight Into

Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we profiled the Arabidopsis root single-cell epigenome using a combinatorial index and dual PCR barcode strategy without the need of any specialized equipment. We generated chromatin accessibility profiles for 13,576 Arabidopsis thaliana root nuclei with an average of 12,784 unique Tn5 integrations per cell and 85% of the Tn5 insertions localizing to discrete accessible chromatin regions. Comparison with data generated from a commercial microfluidic platform revealed that our method is capable of unbiased identification of cell type-specific chromatin accessibility with improved throughput, quality, and efficiency. We anticipate that by removing cost, instrument, and other technical obstacles, this combinatorial indexing method will be a valuable tool for routine investigation of single-cell epigenomes and usher new insight into plant growth, development and their interactions with the environment.

scholarly journals Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5′ and 3′ flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion

2019 ◽  
Vol 48 (2) ◽  
pp. 589-604 ◽  
Author(s):  
Mária Csumita ◽  
Attila Csermely ◽  
Attila Horvath ◽  
Gergely Nagy ◽  
Fanny Monori ◽  
...  
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Inflammatory Responses ◽  
Enrichment Analysis ◽  
Chromatin Accessibility ◽  
Machine Learning Method ◽  
Learning Method ◽  
Overlapping Sets ◽  
Accessible Chromatin

Abstract IRF3, IRF5 and IRF9 are transcription factors, which play distinct roles in the regulation of antiviral and inflammatory responses. The determinants that mediate IRF-specific enhancer selection are not fully understood. To uncover regions occupied predominantly by IRF3, IRF5 or IRF9, we performed ChIP-seq experiments in activated murine dendritic cells. The identified regions were analysed with respect to the enrichment of DNA motifs, the interferon-stimulated response element (ISRE) and ISRE half-site variants, and chromatin accessibility. Using a machine learning method, we investigated the predictability of IRF-dominance. We found that IRF5-dominant regions differed fundamentally from the IRF3- and IRF9-dominant regions: ISREs were rare, while the NFKB motif and special ISRE half-sites, such as 5′-GAGA-3′ and 5′-GACA-3′, were enriched. IRF3- and IRF9-dominant regions were characterized by the enriched ISRE motif and lower frequency of accessible chromatin. Enrichment analysis and the machine learning method uncovered the features that favour IRF3 or IRF9 dominancy (e.g. a tripartite form of ISRE and motifs for NF-κB for IRF3, and the GAS motif and certain ISRE variants for IRF9). This study contributes to our understanding of how IRF members, which bind overlapping sets of DNA sequences, can initiate signal-dependent responses without activating superfluous or harmful programmes.

Konkurrenz zwischen Stieleiche und Buche auf Lothar-Sturmflächen | Competition between pedunculate oak and European beech on Lothar windthrow areas

2009 ◽  
Vol 160 (5) ◽  
pp. 114-123 ◽  
Author(s):  
Daniel Otto ◽  
Sven Wagner ◽  
Peter Brang
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Tree Height ◽  
European Beech ◽  
Threshold Value ◽  
Test Methods ◽  
Permanent Plots ◽  
Pedunculate Oak ◽  
Competitive Pressure ◽  
Competition Index

The competitive pressure of naturally regenerated European beech (Fagus sylvatica) saplings on planted pedunculate oak (Quercus robur) was investigated on two 1.8 ha permanent plots near Habsburg and Murten (Switzerland). The plots were established with the aim to test methods of artificial oak regeneration after large-scale windthrow. On both plots, 80 oaks exposed to varying levels of competitive pressure from at most 10 neighbouring beech trees were selected. The height of each oak as well as stem and branch diameters were measured. The competitive pressure was assessed using Schütz's competition index, which is based on relative tree height, crown overlap and distance from competing neighbours. Oak trees growing without or with only slight competition from beech were equally tall, while oaks exposed to moderate to strong competition were smaller. A threshold value for the competition index was found above which oak height decreased strongly. The stem and branch diameters of the oaks started to decrease even if the competition from beech was slight, and decreased much further with more competition. The oak stems started to become more slender even with only slight competition from beech. On the moderately acid beech sites studied here, beech grow taller faster than oak. Thus where beech is competing with oak and the aim is to maintain the oak, competitive pressure on the oak must be reduced at an early stage. The degree of the intervention should, however, take the individual competitive interaction into account, with more intervention if the competition is strong.

Care for delirium superimposed on dementia at an early stage

2020 ◽  
Keyword(s):  
Behavioral Problems ◽  
Healthcare Professionals ◽  
Early Stage ◽  
Good Care ◽  
Structured Interviews ◽  
Ethical Considerations ◽  
Appropriate Care ◽  
Adequate Care ◽  
Insight Into ◽  
Delirium Superimposed On Dementia

Delirium is a common serious complication in dementia that is associated with poor prognosis and a high burden on caregivers and healthcare professionals. Appropriate care is therefore important at an early stage for patients with delirium superimposed on dementia To gain insight into the care of six patients with delirium superimposed on dementia, 19 semi-structured interviews were conducted focused on the experiences of caregivers and professionals. The interviews revealed four themes that appeared to play a role: 1. experiences with and views on behavioral problems of these patients, 2. recognition and diagnosis of delirium in dementia, 3. views on good care and 4. organizational aspects. Knowledge gaps about delirium in dementia, as well as ethical considerations, play an important role in organizing timely and adequate care for patients with delirium superimposed on dementia.

scholarly journals Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon A. Huws ◽  
Joan E. Edwards ◽  
Wanchang Lin ◽  
Francesco Rubino ◽  
Mark Alston ◽  
...  
Keyword(s):  
Energy Harvesting ◽  
Perennial Ryegrass ◽  
Transcriptional Activity ◽  
Ecological Niches ◽  
Ecological Interactions ◽  
Carbohydrate Degradation ◽  
Host Nutrition ◽  
Role Based ◽  
Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

scholarly journals The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kuo Yang ◽  
Jian-Ping An ◽  
Chong-Yang Li ◽  
Xue-Na Shen ◽  
Ya-Jing Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transcription Factor ◽  
Liquid Chromatography ◽  
Zinc Finger ◽  
Leaf Senescence ◽  
Transcriptional Activity ◽  
Molecular Mechanisms ◽  
Liquid Chromatography Mass Spectrometry ◽  
Zinc Finger Transcription Factor ◽  
Insight Into

AbstractJasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

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