Sequence-dependent histone variant positioning signatures

Background: Nucleosome, the fundamental unit of chromatin, is formed by wrapping nearly 147bp of DNA around an octamer of histone proteins. This histone core has many variants that are different from each other by their biochemical compositions as well as biological functions. Although the deposition of histone variants onto chromatin has been implicated in many important biological processes, such as transcription and replication, themechanisms of how they are deposited on target sites are still obscure. Results: By analyzing genomic sequences of nucleosomes bearing different histone variants from human, including H2A.Z, H3.3 and both (H3.3/H2A.Z, so-called double variant histones), we found that genomic sequencecontributes in part to determining target sites for different histone variants. Moreover, dinucleotides CA/TG are remarkably important in distinguishing target sites of H2A.Z-only nucleosomes with those of H3.3-containing (both H3.3-only and double variant) nucleosomes. Conclusions: There exists a DNA-related mechanism regulating the deposition of different histone variants onto chromatin and biological outcomes thereof. This provides additional insights into epigenetic regulatory mechanisms of many important cellular processes

The potential of combining UAV and remote sensing in supporting precision mapping of irrigation systems for paddy land in urban agricultural areas: study case in the Hoa Vang district, Danang city, Central Vietnam

This research was carried out to test the potential of combining unmanned aerial vehicle (UAV) and remote sensing (RS) to support precision mapping of irrigation systems for paddy land. The study area is an urban/agricultural area of Central Vietnam. The Sentinel-2A imagery acquired on 30 June 2018 was interpreted according an object-based classification method aiming to map paddy land and irrigation systems for the Hoa Vang district; the total accuracy was 91.33% with a Kappa coefficient of 0.87. However, with the spatial resolution from the Sentinel-2A images (20 meters x 20 meters) it was difficult to classify paddy land and water from other objects within small and scattered parcel areas. This research was designed on five experimental flying zones, collecting 2,085 images by the UAV. With the very high spatial resolution data of the UAV, it was possible to clearly identify the boundaries of paddy land parcels, water sources such as rivers and lakes, and other objects such as canals and concrete irrigation systems. This classification derived from the orthogonal images from the five experimental zones using an object-based classification method, correcting the interpretation results of the Sentinel 2A images. Outcomes indicate that, the combination of UAV and RS can be applied to support precision mapping of irrigation systems for paddy land in urban agricultural areas.Nghiên cứu này được thực hiện nhằm thử nghiệm khả năng kết hợp giữa UAV với viễn thám trong hỗ trợ độ chính xác của bản đồ hệ thống nước tưới cho đất trồng lúa ở vùng nông nghiệp đô thị tại Miền trung Việt Nam. Ảnh viễn thám Sentinel- 2A thu nhận vào 30/6/2018 đã được giải đoán bằng phương pháp định hướng đối hướng để thành lập bản đồ hệ thống nguồn nước tưới cho huyện Hòa Vang vào năm 2018, với kết quả độ chính xác tổng số là 91,33% và hệ số kappa là 0,87. Mặc dù với kết quả giải đoán có độ chính xác cao nhưng với độ phân giải không gian của ảnh Sentinel-2A là 20m x 20m rất khó để phân loại được các vùng đất lúa có diện tích nhỏ và phân bố phân tán. Nghiên cứu này đã thiết kế 5 khu vực bay thử nghiệm với 2.085 ảnh để thu thập dữ liệu từ UAV. Có thể thấy rằng dữ liệu ảnh từ UAV với độ phân giải siêu cao có thể nhận diện và phân biệt được một cách rõ ràng không chỉ ranh giới của các thửa đất lúa, hệ thống nguồn nước như sông hồ, mà còn cả những đối tượng kênh mương thủy lợi nhỏ. Kết quả giải đoán các ảnh bay chụp bằng UAV sử dụng dụng phương pháp định hướng đối tượng, nghiên cứu này đã hiệu chỉnh được kết quả giải đoán ảnh Sentinel 2A. Kết quả cho thấy việc kết hợp dữ liệu viễn thám với UAV là hoàn toàn có khả năng sử dụng để hỗ trợ độ chính xác thành lập bản đồ hệ thống nguồn nước cho đất trồng lúa ở vùng nông nghiệp đô thị

Safety and efficacy of fluoxetine on functional outcome after acute stroke (AFFINITY): a randomised, double-blind, placebo-controlled trial

Background Trials of fluoxetine for recovery after stroke report conflicting results. The Assessment oF FluoxetINe In sTroke recoverY (AFFINITY) trial aimed to show if daily oral fluoxetine for 6 months after stroke improves functional outcome in an ethnically diverse population. Methods AFFINITY was a randomised, parallel-group, double-blind, placebo-controlled trial done in 43 hospital stroke units in Australia (n=29), New Zealand (four), and Vietnam (ten). Eligible patients were adults (aged ≥18 years) with a clinical diagnosis of acute stroke in the previous 2–15 days, brain imaging consistent with ischaemic or haemorrhagic stroke, and a persisting neurological deficit that produced a modified Rankin Scale (mRS) score of 1 or more. Patients were randomly assigned 1:1 via a web-based system using a minimisation algorithm to once daily, oral fluoxetine 20 mg capsules or matching placebo for 6 months. Patients, carers, investigators, and outcome assessors were masked to the treatment allocation. The primary outcome was functional status, measured by the mRS, at 6 months. The primary analysis was an ordinal logistic regression of the mRS at 6 months, adjusted for minimisation variables. Primary and safety analyses were done according to the patient's treatment allocation. The trial is registered with the Australian New Zealand Clinical Trials Registry, ACTRN12611000774921. Findings Between Jan 11, 2013, and June 30, 2019, 1280 patients were recruited in Australia (n=532), New Zealand (n=42), and Vietnam (n=706), of whom 642 were randomly assigned to fluoxetine and 638 were randomly assigned to placebo. Mean duration of trial treatment was 167 days (SD 48·1). At 6 months, mRS data were available in 624 (97%) patients in the fluoxetine group and 632 (99%) in the placebo group. The distribution of mRS categories was similar in the fluoxetine and placebo groups (adjusted common odds ratio 0·94, 95% CI 0·76–1·15; p=0·53). Compared with patients in the placebo group, patients in the fluoxetine group had more falls (20 [3%] vs seven [1%]; p=0·018), bone fractures (19 [3%] vs six [1%]; p=0·014), and epileptic seizures (ten [2%] vs two [<1%]; p=0·038) at 6 months. Interpretation Oral fluoxetine 20 mg daily for 6 months after acute stroke did not improve functional outcome and increased the risk of falls, bone fractures, and epileptic seizures. These results do not support the use of fluoxetine to improve functional outcome after stroke

Computational reconstruction of transcriptional relationships from ChIP-Chip data

Eukaryotic gene transcription is a complex process, which requires the orchestrated recruitment of a large number of proteins, such as sequence-specific DNA binding factors, chromatin remodelers and modifiers, and general transcription machinery, to regulatory regions. Previous works have shown that these regulatory proteins favor specific organizational theme along promoters. Details about how they cooperatively regulate transcriptional process, however, remain unclear. We developed an unbiased method to reconstruct a Bayesian network-based model representing functional relationships among various transcriptional components. Independently, the positive(+)/negative(-) influence between these components was measured from protein binding and nucleosome occupancy data and embedded into the model. Application on S.cerevisiae ChIP-Chip data showed that the proposed method can recover confirmed relationships, such as Isw1-Pol II, TFIIH-Pol II, TFIIBTBP, Pol II-H3K36Me3, H3K4Me3-H3K14Ac, etc. Moreover, it can distinguish co-locating components from functionally related ones. Novel relationships, e.g., ones between Mediator and chromatin remodeling complexes (CRCs), and the combinatorial regulation of Pol II recruitment and activity by CRCs and general transcription factors (GTFs), were also suggested. Conclusion: Protein binding events during transcription positively influence each other. Among contributing components, GTFs and CRCs play pivotal roles in transcriptional regulation. These findings provide insights into the regulatory mechanism. Also, the proposed method can be extended to reconstruct more accurate model as new data become available.The 10th Asia Pacific Bioinformatics Conference, Melbourne, Australia, 17-19 January 201

Quantitatively assessing the effects of regulatory factors on nucleosome dynamics by multiple kernel learning

Nucleosome, a nucleoprotein structure formed by coiling 147bp of DNA around an octamer of histone proteins, is the fundamental repeating unit of eukaryotic chromatin. By regulating the access of biological machineries to underlying cis-regulatory elements, its mobility has been implicated in many important cellular processes. Although it has been known that various factors, such as DNA sequences, histone modifications, etc., cooperatively affect nucleosome mobility, the contribution of each factor in the common impact remains unclear. We propose, in this work, a novel computational approach based on Multiple Kernel Learning (MKL) for quantitatively assessing the effects of two important factors, i.e., genomic sequence and post-translational histone modifications (PTMs), on nucleosome dynamics. Our result on S.cerevisiae shows that, epigenetic feature, such as histone modifications, plays more important role than genomic sequence in regulating nucleosome dynamics. Based on that, we carried further analysis on each PTM to reveal their combinatory effects on nucleosome dynamics and found out that some pairs of PTMs such as H3K9Ac?H4H14Ac, H4K5Ac?H4K12Ac and H4K5Ac?H3K14Ac might co-operate in altering nucleosome stability in gene regulation

Preliminary insights into the diversity of the rice root microbiome in a field highly infested by Meloidogyne graminicola

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