The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species
. However, studies in ...zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
Periodontitis is an infectious inflammation in the gums characterized by loss of periodontal ligaments and alveolar bone. Its persistent inflammation could result in tooth loss and other health ...issues. Ixeris dentata (IXD) and Lactobacillus gasseri media (LGM) demonstrated strong antioxidant activity, which may prevent oxidative and inflammatory periodontitis. Here, IXD and LGM extracts were investigated for antioxidative activity against oral discomfort and evaluated for their synergistic effect against oxidative and inflammatory periodontitis in a mouse model. IXD/LGM suppressed pro-inflammatory cytokines like interleukin (IL)-1β, IL-6, and TNF-α. Additionally, it reduced pro-inflammatory mediators, nitric oxide, iNOS (inducible nitric oxide synthase), and COX-2 (cyclooxygenase-2) and enhanced AKT, Nrf2, and HO-1 activation. Similarly, IXD/LGM treatment elevated osteogenic proteins and mRNAs; alkaline phosphatase, collagen type 1 (COL1), osteopontin (OPN), and runt-related transcription factor 2 (RUNX2). Hematoxylin and Eosin (H&E) staining and micro-CT analysis confirm the positive impact of IXD/LGM on the periodontal structure and its associated inflammation. These findings demonstrate that IXD/LGM inhibits oxidative stress, periodontal inflammation, and its resultant alveolar bone loss in which Akt (also known as protein kinase B)-nuclear factor-erythroid 2-related factor 2 (Nrf2)-hemoxygenase-1 (HO-1) signaling is involved. Thus, IXD/LGM is a potential candidate against oxidative/inflammatory stress-associated periodontitis.
Abstract
As both the industry and academia become more focused on biomass-based smart materials, they are attracting a lot of attention. There has been a significant effort in the field of ...polyurethane (PU) synthesis to replace polyols used in synthesis with bio-derived polyols. Bio-derived polyols have limited application potential for bio-based PU due to their low functionality. Here, we reported castor oil (CO) based multifunctional polyols prepared by grafting thiols such as 1-mercaptoethanol or α–thioglycerol via a facile thiol-ene click reaction method (coded as COM and COT, respectively). Subsequently, bio-based shape memory polyurethanes (SMPU) crosslinked with prepared polyols were synthesized using a 2-step prepolymer method. By confirming the functionality of the synthesized polyols, it was determined that COT has an OH value of 380 mg KOH/g, which is approximately three times that of CO. The successful synthesis of SMPUs was confirmed through chemical structural analysis. It was also proved that the phase separation between the soft and hard segments was limited due to the increase in crosslinking density. As compared to SMPU crosslinked with CO, the mechanical strength of SMPU crosslinked with COT was improved by 80%, while the elongation was decreased by about 26%. As a result of shape memory behavior analysis, it was confirmed that the outstanding SMPU can be synthesized using CO-based multifunctional polyols.
It has been well reported that the emotional experiences of medical students in the gross anatomy laboratory could have significant impacts on their professional identity formation. This qualitative ...study aimed to investigate students' emotions towards cadaver dissection and the educational role of memorial ceremonies.
A total of 37 students from eight teams were recruited in the team-based dissection course during two consecutive academic years (2016 and 2017) at one medical school. In focus group interviews, students were encouraged to express and discuss their emotions regarding cadaver dissection and memorial ceremonies.
The participants described their apprehension and anxiety during their first encounter with cadavers that diminished through gradual exposure. Unfortunately, their positive emotions such as gratitude and responsibility also tended to decline under the pressure of excessive workloads and frequent examinations. Memorial ceremonies, including not only large-scale events but also daily rituals, had educational effects that they prevented the decline of students' responsibility and respect during the dissection course.
Educators should assist medical students in overcoming their initial distress and maintaining respectful attitudes throughout the dissection course. Memorial ceremonies can be effective educational tools for fostering appropriate attitudes and ethical practice in the gross anatomy laboratory.
It was my great honor to be invited as a respondent to the 2020 Russell Family Fellowship Research Conference Lecture by Adam Pryor, who gave a wonderful talk through which he built a new ethical ...foundation from the interaction between the traditional doctrines of the imago Dei, sin, and vocation in Christian theology and astrobiology aiming for integration beyond dialogue. In regard to his claim at the beginning of his argument that astrobiology is moving biology from being a descriptive science to a science based on first principles, I raised the issue whether science should be descriptive or prescriptive. To argue that we should not rely on the first principles too much in doing science, even if they might help, I mentioned that even the physicists, who prefer theories with beauty, have abandoned beautiful theories when they find some unexpected, apparent ugliness in nature. For example, Albert Einstein did not like quantum mechanics because he believed that nature has nothing to do with probability, and Fred Hoyle rejected Big Bang cosmology because his first principle was that the universe is static and eternal. However, empirical evidences have forced physicists to abandon some of their former first principles, which illustrates that it is quite hard to imagine a science based only on unchanging first principles.
A novel optical biosensor for detecting target DNA, utilizing gold nanorods (GNRs) as molecular probes is demonstrated. This sensor is based on simultaneous biorecognition-mediated hybridization of ...target DNA in a sandwich type manner with two different capture probe DNA sequences modified separately with identical sets of GNRs, which leads to aggregation of GNRs. The hybridization induced aggregation as revealed by TEM analysis, promotes the modulation of surface plasmon resonance of GNRs, which forms the basis of complementary target DNA detection from the
Chlamydia trachomatis pathogen. Thermally induced reversible dissociation of hybridized DNA is demonstrated by melting analysis. The present sensing strategy is successfully demonstrated by detecting PCR amplified
C. trachomatis pathogen gene isolated from human urine sample in a concentration range of 0.25–20
nM. Furthermore, this sensor displays excellent specificity by discriminating the target DNA versus other non-specific pathogenic genes.
A controller PHY for high-capacity DRAM is presented. To reduce precursor and postcursor intersymbol interference due to its dispersive channel characteristics and a heavy load of many DRAM chips and ...to attenuate reflection on a highly reflective command/address (C/A) channel, a damping-resistor-aided three-tap pulse-based feed-forward equalizer (PB-FFE) is introduced. An appropriate damping resistance can attenuate reflection, and the PB-FFE compensates for increased insertion loss due to the damping resistor. In addition, the current flows only before and after a signal transition in the PB-FFE, improving energy efficiency and maintaining the turn-ON resistance during the no-transition region. A controller PHY based on this equalizer was fabricated in a 55-nm CMOS process. The PB-FFE increases the timing margin of the C/A signal from 0.23 to 0.29 UI at 1067 Mb/s. At 2133 Mb/s, the read timing and voltage margins of the DQ signal are 0.53 UI and 211 mV after read training, and its write margin is 0.72 UI and 230 mV, respectively, after write training.
Additive‐type flame retardants used in polyurethane foams (PUFs) have low compatibility with the matrix and have a large particle size which reduces the mechanical strength. To overcome this, ...cellulose‐based additive‐type flame retardants were prepared. Microcrystalline cellulose (MCC) was grinded to a suitable size to be applying as a reinforcement for urethane foam. The ground MCC was coated with the mussel‐derived adhesive protein, dopamine, and formed the iron phosphonate coordination network on the surface. It was confirmed that the modification proceeded well by structural analysis by Fourier‐transform infrared spectrometer and morphology analysis by scanning electron microscope. In the synthesis of PUF, expandable graphite (EG) was added to obtain high flame retardancy. The PUF mixed with 3 wt% of ground MCC‐based flame retardant and 12 wt% of EG (GCF3) was found to have an excellent limiting oxygen index (LOI) of 25.3%, while the LOI of pure PUF was 19.3%. In particular, the compressive strength of GCF3 was remarkably enhanced (21 wt%) compared with the PUF containing 15 wt% of EG. This study produced a new additive‐type flame retardant to improve mechanical strength. This provides a simple and comprehensive solution for PUF applications requiring high flame retardancy and mechanical strength.
This study investigated a reflective transparent structure to improve the optical efficiency of 850 nm infrared light-emitting diodes (IR-LEDs), by effectively enhancing the number of extracted ...photons emitted from the active region. The reflective transparent structure was fabricated by combining transparent epitaxial and reflective bonding structures. The transparent epitaxial structure was grown by the liquid-phase epitaxy method, which efficiently extracted photons emitted from the active area in IR-LEDs, both in the vertical and horizontal directions. Furthermore, a reflective bonding structure was fabricated using an omnidirectional reflector and a eutectic metal, which efficiently reflected the photons emitted downwards from the active area in an upward direction. To evaluate reflective transparent IR-LED efficiency, a conventional absorbing substrate infrared light-emitting diode (AS IR-LED) and a transparent substrate infrared light-emitting diode (TS IR-LED) were fabricated, and their characteristics were analyzed. Based on the power-current (L-I) evaluation results, the output power (212 mW) of the 850 nm IR-LED with the reflective transparent structure increased by 76% and 26%, relative to those of the AS IR-LED (121 mW) and TS IR-LED (169 mW), respectively. Furthermore, the reflective transparent structure possesses both transparent and reflective properties, as confirmed by photometric and radial theta measurements. Therefore, light photons emitted from the active area of the 850 nm IR-LED were efficiently extracted upward and sideways, because of the reflective transparent structure.
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