The excessive use of plastics has been accompanied by severe ecologically damaging effects. The recent discovery of a PETase from Ideonella sakaiensis that decomposes poly(ethylene terephthalate) (PET) under mild conditions provides an attractive avenue for the biodegradation of plastics. However, the inherent instability of the enzyme limits its practical 20 15 and the Biological Resources Program (KFJ-BRP-009) of the Chinese Academy of Sciences.
Background: Although the acupuncture treatment of major depressive disorder(MDD) has been recognized by the latest clinical practice guidelines of the American Academy of Internal Medicine, complex therapeutic mechanisms need further to clarify. The aim of the study is investigate whether the aberrant resting state brain network in MDD patients could be regulated by acupuncture at GV20 using functional magnetic resonance imaging(fMRI) combined with degree centrality(DC) method. Results: Compared to healthy subjects, MDD patients exhibited significantly aberrant DC in widely brain regions, including cortical(PFC, precuneus, temporal, insula) and sub-cortical (thalamus, putamen and caudate) structures. Furthermore, results showed that acupuncture at GV20 induced down-regulation the DC of abnormal brain regions in MDD patients. Conclusions: Our findings provide imaging evidence to support that GV20-related acupuncture stimulation may modulate the abnormal brain function state in MDD patients by using fMRI technique combined with DC analysis. This study may partly interpret the neural mechanisms of acupuncture at GV20 which is used to treat patients with MDD in clinical. Trial registration: ChiCTR, ChiCTR-IOR-15006357. Registered 05 May 2015, http://www.chictr.org.cn/showproj.aspx?proj=10922.
Large-scale chromatin compaction is nonuniform across the human genome and correlates with gene expression and genome organization. Current methodologies for assessing large-scale chromatin compaction are indirect and largely based on assays that probe lower levels of chromatin organization, primarily at the level of the nucleosome and/or the local compaction of nearby nucleosomes. These assays assume a one-to-one correlation between local nucleosomal compaction and large-scale compaction of chromosomes that may not exist. Here we describe a method to identify interphase chromosome regions with relatively high levels of large-scale chromatin decondensation using TSA-seq, which produces a signal proportional to microscopic-scale distances relative to a defined nuclear compartment. TSA-seq scores that change rapidly as a function of genomic distance, detected by their higher slope values, identify decondensed large-scale chromatin domains (DLCDs), as then validated by 3D DNA-FISH. DLCDs map near a subset of chromatin domain boundaries, defined by Hi-C, which separate active and repressed chromatin domains and correspond to compartment, subcompartment, and some TAD boundaries. Most DLCDs can also be detected by high slopes of their Hi-C compartment score. In addition to local enrichment in cohesin (RAD21, SMC3) and CTCF, DLCDs show the highest local enrichment to super-enhancers, but are also locally enriched in transcription factors, histone-modifying complexes, chromatin mark readers, and chromatin remodeling complexes. The localization of these DLCDs to a subset of Hi-C chromatin domain boundaries that separate active versus inactive chromatin regions, as measured by two orthogonal genomic methods, suggests a distinct role for DLCDs in genome organization.
AbstractionIn this article, we have designed a sensitive and recycled DNB (DNA nanoball) nanoarrays sequencing complex structures based on BGISEQ-500RS sequencer for the monitoring performance of Exo III activity. In the shortage of Exo III, the effective number ratio of DNB would be captured by an optical system due to one fluorescent. In contrast, in the presence of Exo III, some DNB would disappear or discard from the fields of the optical system by fluorescence extinction and uncleaned fluorescent, respectively. As a result, the effective number of DNB of this strategy was relative to the concentration of Exo III. For Exo III, our strategy showed a highly sensitive linear response in the low detection range of 0.01 U/mL to 0.5 U/mL, with detection limits below 0.01 U/mL. With the comparison between DNB nanoarrays and other fluorescent sensors, this study possessed superior sensitivity, selectivity, and reusability, accompanying with the low cost and simple setup.
38 Three-dimensional genome organization plays an important role in many biological 39 processes. Yet, how the genome is packaged at the molecular level during mammalian 40 spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential 41 stages during mouse spermatogenesis. We found that topological associating 42 domains (TADs) and chromatin loops underwent highly dynamic reorganization. They 43 displayed clear existence in primitive type A spermatogonia, disappearance at 44 pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the 45 absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at 46 TAD boundary regions (identified in primitive type A spermatogonia). Additionally, 47 many enhancers and promoters exhibited features of open chromatin and transcription 48 remained active at pachytene stage. A/B compartmentalization and segmentation ratio 49 were conserved in different stages of spermatogenesis in autosomes, although there 50 were A/B compartment switching events correlated with gene activity changes. 51 Intriguingly, A/B compartment structure on the X chromosome disappeared during 52 pacSC, rST and eST stages. Together, our work uncovered a dynamic three-53 dimensional chromatin organization during mouse spermatogenesis and suggested 54 that transcriptional regulation could be independent of TADs and chromatin loops at 55 specific developmental stages. 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Introduction72 Studies using open-ended Chromosome Conformation Capture (3C) methodology, Hi-73 C, have revealed fundamental insights into higher-order chromatin structure and 74 three-dimensional (3D) genome organization in eukaryotes [1,2]. The higher-order 75 chromatin is spatially packaged into a hierarchy of chromatin A/B compartments, 76 topological associating domains (TADs), and chromatin loops [3,4]. Principal 77 component analysis [1] (PCA) of Hi-C data uncovered that the genome is segmented 78 into two types of compartments, where compartment A is associated with active 79 chromatin regions while compartment B is associated with repressive chromatin 80 regions. The switch between A/B compartments is related to transcriptional regulation 81 and cell fate decision [5]. Although A/B compartments are pervasive and highly 82 dynamic between different cells, the underlying mechanism of A/B compartment 83 formation remains elusive. Unlike A/B compartments, which vary among cell types, 84 TADs are largely invariant between different cell types and species except in the 85 mitotic stage [3,6,7]. CTCF and cohesin, two key weavers of chromatin structure, were 86 demonstrated to be highly enriched on TAD boundaries [3]. Recent studies reported 87 that rapid degradation of CTCF or cohesin could eliminate TADs [8-10], suggesting 88 that CTCF and cohesin are important for TADs formation and maintenance, while 89 super-resolution chromatin tracing showed that TAD-like structures remained in a 90 subset of single cells after cohesin depletion [11]. In additi...
MicroRNA is a vital biomarker because of its abnormal expression in the emergence and development of diseases, especially in cancers. Herein, a label-free fluorescent sensing platform is proposed for detecting microRNA-21, coupled with the cascade toehold-mediated strand displacement reaction and magnetic beads. Target microRNA-21 acts as an initiator to trigger the cascade toehold-mediated strand displacement reaction and it outputs double-stranded DNA. After magnetic separation, the double-stranded DNA is intercalated by SYBR Green I, resulting in an amplified fluorescent signal. Under the optimal conditions, a wide linear range (0.5-60 nmol/L) and low limits of detection (0.19 nmol/L) are exhibited. What's more, the biosensor shows great specificity and reliability between microRNA-21 and other microRNAs involved in cancer . Owing to the properties of fabulous sensitivity, high selectivity, and simplicity of operator, the proposed method paves a promising way for microRNA-21 detection in cancer diagnosis and biological research.
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