Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution.

The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.

3D Chromatin Structures of Mature Gametes and Structural Reprogramming during Mammalian Embryogenesis.

High-order chromatin structure plays important roles in gene expression regulation. Knowledge of the dynamics of 3D chromatin structures during mammalian embryo development remains limited. We report the 3D chromatin architecture of mouse gametes and early embryos using an optimized Hi-C method with low-cell samples. We find that mature oocytes at the metaphase II stage do not have topologically associated domains (TADs). In sperm, extra-long-range interactions (>4 Mb) and interchromosomal interactions occur frequently. The high-order structures of both the paternal and maternal genomes in zygotes and two-cell embryos are obscure but are gradually re-established through development. The establishment of the TAD structure requires DNA replication but not zygotic genome activation. Furthermore, unmethylated CpGs are enriched in A compartment, and methylation levels are decreased to a greater extent in A compartment than in B compartment in embryos. In summary, the global reprogramming of chromatin architecture occurs during early mammalian development.

Key role for CTCF in establishing chromatin structure in human embryos.

In the interphase of the cell cycle, chromatin is arranged in a hierarchical structure within the nucleus1,2, which has an important role in regulating gene expression3-6. However, the dynamics of 3D chromatin structure during human embryogenesis remains unknown. Here we report that, unlike mouse sperm, human sperm cells do not express the chromatin regulator CTCF and their chromatin does not contain topologically associating domains (TADs). Following human fertilization, TAD structure is gradually established during embryonic development. In addition, A/B compartmentalization is lost in human embryos at the 2-cell stage and is re-established during embryogenesis. Notably, blocking zygotic genome activation (ZGA) can inhibit TAD establishment in human embryos but not in mouse or Drosophila. Of note, CTCF is expressed at very low levels before ZGA, and is then highly expressed at the ZGA stage when TADs are observed. TAD organization is significantly reduced in CTCF knockdown embryos, suggesting that TAD establishment during ZGA in human embryos requires CTCF expression. Our results indicate that CTCF has a key role in the establishment of 3D chromatin structure during human embryogenesis.

A Visual Distance-Based Capillary Immunoassay Using Biomimetic Polymer Nanoparticles for Highly Sensitive and Specific C-Reactive Protein Quantification.

The low-cost daily monitoring of C-reactive protein (CRP) levels is crucial for screening acute inflammation or infections as well as managing chronic inflammatory diseases. In this study, we synthesized novel 2-Methacryloyloxy ethyl phosphorylcholine (MPC)-based biomimetic nanoparticles with a large surface area to develop a visual CRP-quantification assay using affordable glass capillaries. The PMPC nanoparticles, synthesized via reflux precipitation polymerization, demonstrated multivalent binding capabilities, enabling rapid and specific CRP capture. In the presence of CRP, PMPC nanoparticles formed sandwich structures with magnetic nanoparticles functionalized with CRP antibodies, thereby enhancing detection sensitivity and specificity. These sandwich complexes were magnetically accumulated into visible and quantifiable stacks within the glass capillaries, allowing for the rapid, sensitive, and specific quantification of CRP concentrations with a detection limit of 57.5 pg/mL and a range spanning from 0 to 5000 ng/mL. The proposed visual distance-based capillary biosensor shows great potential in routine clinical diagnosis as well as point-of-care testing (POCT) in resource-limited settings.

Natural Course of Ruptured but Untreated Intracranial Aneurysms: A Multicenter 2-Year Follow-Up Study.

BACKGROUND: The current understanding of untreated ruptured intracranial aneurysms has been limited by study design and inaccurate patient data. Multicenter clinical registry studies on untreated ruptured intracranial aneurysms in Chinese patients are scarce. We aimed to calculate the mortality of patients with untreated ruptured intracranial aneurysms in a current, clearly defined hospital cohort in China, with emphasis on mortality predictors over a 2-year period. METHODS: Patients with saccular untreated ruptured intracranial aneurysms were identified from the Chinese Multicenter Cerebral Aneurysm Database, a multicenter, prospective, observational database registered in China, which involved 32 tertiary medical centers covering 4 northern Chinese provincial regions. Patients with intracranial aneurysms, regardless of ruptured status, shape, age, or comorbidities, were consecutively included in 12 of 32 medical centers between 2017 and 2020. Survival probabilities were computed using the Kaplan-Meier method. Univariate and multivariate Cox regression analyses were conducted to determine the risk factors for the cumulative 2-year mortality. We analyzed the reasons for treatment decisions stratified by demographic characteristics and clinical features. RESULTS: For 941 enrolled patients, 58.6% of patients died within 1 month of symptom onset; and 68.1% within 2 years. 98 patients underwent surgical repair during follow-up. Multivariate Cox regression analysis identified Hunt and Hess grades 3 to 5 (hazard ratio, 1.54 [95% CI, 1.01-2.35]; P=0.047), loss of consciousness at symptom onset (hazard ratio, 1.56 [95% CI, 1.18-2.07]; P=0.002), and largest aneurysm size of ≥5 mm (hazard ratio, 1.29 [95% CI, 1.05-1.59]; P=0.014) as mortality predictors during the 2-year follow-up. Among patients who were successfully followed up, 42.6% (280) of them refused surgical treatment. CONCLUSIONS: Patients with poor Hunt and Hess grades, loss of consciousness at symptom onset, or largest aneurysms ≥5 mm in size showed a high mortality rate. A high number of treatment refusals was present in this study. These findings have implications for medical insurance policy, doctor-patient communication, and popular science education.

Single-cell analysis of ploidy and the transcriptome reveals functional and spatial divergency in murine megakaryopoiesis.

Megakaryocytes (MKs), the platelet progenitor cells, play important roles in hematopoietic stem cell (HSC) maintenance and immunity. However, it is not known whether these diverse programs are executed by a single population or by distinct subsets of cells. Here, we manually isolated primary CD41+ MKs from the bone marrow (BM) of mice and human donors based on ploidy (2N-32N) and performed single-cell RNA sequencing analysis. We found that cellular heterogeneity existed within 3 distinct subpopulations that possess gene signatures related to platelet generation, HSC niche interaction, and inflammatory responses. In situ immunostaining of mouse BM demonstrated that platelet generation and the HSC niche-related MKs were in close physical proximity to blood vessels and HSCs, respectively. Proplatelets, which could give rise to platelets under blood shear forces, were predominantly formed on a platelet generation subset. Remarkably, the inflammatory responses subpopulation, consisting generally of low-ploidy LSP1+ and CD53+ MKs (≤8N), represented ∼5% of total MKs in the BM. These MKs could specifically respond to pathogenic infections in mice. Rapid expansion of this population was accompanied by strong upregulation of a preexisting PU.1- and IRF-8-associated monocytic-like transcriptional program involved in pathogen recognition and clearance as well as antigen presentation. Consistently, isolated primary CD53+ cells were capable of engulfing and digesting bacteria and stimulating T cells in vitro. Together, our findings uncover new molecular, spatial, and functional heterogeneity within MKs in vivo and demonstrate the existence of a specialized MK subpopulation that may act as a new type of immune cell.

SD-36 promotes growth inhibition and induces apoptosis via suppression of Mcl-1 in glioma.

Glioma is one of the most commonly observed tumours, representing approximately 75% of brain tumours in the adult population. Generally, glioma therapy includes surgical resection followed by radiotherapy and chemotherapy. The transcription factor STAT3 (signal transducer and activator of transcription 3) is a promising target for the treatment of cancer and several other diseases. At nanomolar concentrations, SD-36 induces rapid cellular degradation of STAT3 but cannot degrade other STAT proteins. The current study demonstrates the therapeutic efficacies of the STAT3 degraders SD-36 against glioma, as well as understanding the elucidating mechanisms and identifying molecular markers that determine cell sensitivity to STAT3 degraders. Glioma cell lines possessed similar response patterns to SD-36 but different responses to the STAT3 inhibitor Stattic. SD-36 potently induced apoptosis in glioma cells along with a reduction in Mcl-1 levels, which are critical for mediating the induction of apoptosis and enhancing TMZ-induced apoptosis. Accordingly, SD-36 sensitizes the antitumour effect of TMZ in patient-derived xenograft. In addition, the downregulation of Mcl-1 expression-mediated antitumour effect of SD-36 was analysed in cell-derived xenograft. These observations need to be validated clinically to confirm the efficacy of STAT3 degraders in glioma.

Ultralight, High Capacitance, Mechanically Strong Graphene-Cellulose Aerogels.

With increasing energy demand driving the need for eco-friendly and efficient energy storage technology, supercapacitors are becoming increasingly prevalent in wearable devices because of their portability and stability. The performance of these supercapacitors is highly dependent on the choice of electrode material. The high capacitance and mechanical properties needed for these materials can be achieved by combining graphene's stable electrical properties with renewable cellulose's excellent mechanical properties into porous aerogels. In this study, graphene-cellulose hydrogels were prepared by a one-step hydrothermal method, with porous, ultra-light, and mechanically strong graphene-cellulose aerogels then prepared by freeze-drying. These composite aerogels possess excellent mechanical strength and high specific capacitance, capable of bearing about 1095 times the pressure of their own weight. Electrochemical tests show the specific capacitance of these composite aerogels can reach 202 F/g at a scanning rate of 5 mA/cm2. In view of their high surface area and fast charge transport provided by their 3D porous structure, graphene-cellulose aerogels have great potential as sustainable supercapacitor electrodes.

Impact Assessment of GNSS Spoofing Attacks on INS/GNSS Integrated Navigation System.

In the face of emerging Global Navigation Satellite System (GNSS) spoofing attacks, there is a need to give a comprehensive analysis on how the inertial navigation system (INS)/GNSS integrated navigation system responds to different kinds of spoofing attacks. A better understanding of the integrated navigation system’s behavior with spoofed GNSS measurements gives us valuable clues to develop effective spoofing defenses. This paper focuses on an impact assessment of GNSS spoofing attacks on the integrated navigation system Kalman filter’s error covariance, innovation sequence and inertial sensor bias estimation. A simple and straightforward measurement-level trajectory spoofing simulation framework is presented, serving as the basis for an impact assessment of both unsynchronized and synchronized spoofing attacks. Recommendations are given for spoofing detection and mitigation based on our findings in the impact assessment process.

Comparison of σ-Hole and π-Hole Tetrel Bonds Formed by Pyrazine and 1,4-Dicyanobenzene: The Interplay between Anion-π and Tetrel Bonds.

The σ-hole tetrel bond in pyrazine/1,4-dicyanobenzene⋅⋅⋅TH3 F (T=C and Si) and the π-hole tetrel bond in pyrazine/1,4-dicyanobenzene⋅⋅⋅F2 TO have been compared. The π-hole tetrel bond is stronger than the corresponding σ-hole tetrel bond, with a larger interaction energy, shorter binding contact, greater electron density, and bigger charge transfer. Pyrazine forms a more stable tetrel-bonded complex than 1,4-dicyanobenzene even though the nitrogen atom in the former has a smaller negative electrostatic potential than the latter. An interesting cooperative effect was found when anion-π and tetrel-bond interactions coexisted in the same multicomponent complex of X- ⋅⋅⋅pyrazine/1,4-dicyanobenzene⋅⋅⋅TH3 F/F2 TO (X=F, Cl, and Br). Both interactions displayed a positive cooperative effect, as shown by the larger interaction energies, shorter binding separations, and greater electron densities. The enhancement in the tetrel bond is dependent on the strength of the anion-π interaction and it becomes larger in the order Br-

FANCD2 and REV1 cooperate in the protection of nascent DNA strands in response to replication stress.

REV1 is a eukaryotic member of the Y-family of DNA polymerases involved in translesion DNA synthesis and genome mutagenesis. Recently, REV1 is also found to function in homologous recombination. However, it remains unclear how REV1 is recruited to the sites where homologous recombination is processed. Here, we report that loss of mammalian REV1 results in a specific defect in replication-associated gene conversion. We found that REV1 is targeted to laser-induced DNA damage stripes in a manner dependent on its ubiquitin-binding motifs, on RAD18, and on monoubiquitinated FANCD2 (FANCD2-mUb) that associates with REV1. Expression of a FANCD2-Ub chimeric protein in RAD18-depleted cells enhances REV1 assembly at laser-damaged sites, suggesting that FANCD2-mUb functions downstream of RAD18 to recruit REV1 to DNA breaks. Consistent with this suggestion we found that REV1 and FANCD2 are epistatic with respect to sensitivity to the double-strand break-inducer camptothecin. REV1 enrichment at DNA damage stripes also partially depends on BRCA1 and BRCA2, components of the FANCD2/BRCA supercomplex. Intriguingly, analogous to FANCD2-mUb and BRCA1/BRCA2, REV1 plays an unexpected role in protecting nascent replication tracts from degradation by stabilizing RAD51 filaments. Collectively these data suggest that REV1 plays multiple roles at stalled replication forks in response to replication stress.

Design and Implementation of Foot-Mounted Inertial Sensor Based Wearable Electronic Device for Game Play Application.

Wearable electronic devices have experienced increasing development with the advances in the semiconductor industry and have received more attention during the last decades. This paper presents the development and implementation of a novel inertial sensor-based foot-mounted wearable electronic device for a brand new application: game playing. The main objective of the introduced system is to monitor and identify the human foot stepping direction in real time, and coordinate these motions to control the player operation in games. This proposed system extends the utilized field of currently available wearable devices and introduces a convenient and portable medium to perform exercise in a more compelling way in the near future. This paper provides an overview of the previously-developed system platforms, introduces the main idea behind this novel application, and describes the implemented human foot moving direction identification algorithm. Practical experiment results demonstrate that the proposed system is capable of recognizing five foot motions, jump, step left, step right, step forward, and step backward, and has achieved an over 97% accuracy performance for different users. The functionality of the system for real-time application has also been verified through the practical experiments.

Tetrel-hydride interaction between XH3F (X = C, Si, Ge, Sn) and HM (M = Li, Na, BeH, MgH).

A tetrel-hydride interaction was predicted and characterized in the complexes of XH3F···HM (X = C, Si, Ge, Sn; M = Li, Na, BeH, MgH) at the MP2/aug-cc-pVTZ level, where XH3F and HM are treated as the Lewis acid and base, respectively. This new interaction was analyzed in terms of geometrical parameters, interaction energies, and spectroscopic characteristics of the complexes. The strength of the interaction is essentially related to the nature of X and M groups, with both the larger atomic number of X and the increased reactivity of M giving rise to a stronger tetrel-hydride interaction. The tetrel-hydride interaction exhibits similar substituent effects to that of dihydrogen bonds, where the electron-donating CH3 and Li groups in the metal hydride strengthen the binding interactions. NBO analyses demonstrate that both BD(H-M) → BD*(X-F) and BD(H-M) → BD*(X-H) orbital interactions play the stabilizing role in the formation of the complex XH3F···HM (X = C, Si, Ge, and Sn; M = Li, Na, BeH, and MgH). The major contribution to the total interaction energy is electrostatic energy for all of the complexes, even though the dispersion/polarization parts are nonnegligible for the weak/strong tetrel-hydride interaction, respectively.

Mismatch repair protein MSH2 regulates translesion DNA synthesis following exposure of cells to UV radiation.

Translesion DNA synthesis (TLS) can use specialized DNA polymerases to insert and/or extend nucleotides across lesions, thereby limiting stalled replication fork collapse and the potential for cell death. Recent studies have shown that monoubiquitinated proliferating cell nuclear antigen (PCNA) plays an important role in recruitment of Y-family TLS polymerases to stalled replication forks after DNA damage treatment. To explore the possible roles of other factors that regulate the ultraviolet (UV)-induced assembly of specialized DNA polymerases at arrested replication forks, we performed immunoprecipitation experiments combined with mass spectrometry and established that DNA polymerase kappa (Polκ) can partner with MSH2, an important mismatch repair protein associated with hereditary non-polyposis colorectal cancer. We found that depletion of MSH2 impairs PCNA monoubiquitination and the formation of foci containing Polκ and other TLS polymerases after UV irradiation of cells. Interestingly, expression of MSH2 in Rad18-deficient cells increased UV-induced Polκ and REV1 focus formation without detectable changes in PCNA monoubiquitination, indicating that MSH2 can regulate post-UV focus formation by specialized DNA polymerases in both PCNA monoubiquitination-dependent and -independent fashions. Moreover, we observed that MSH2 can facilitate TLS across cyclobutane pyrimidine dimers photoproducts in living cells, presenting a novel role of MSH2 in post-UV cellular responses.

Design of highly sensitive phosphorescence sensor for determination of procaterol hydrochloride based on inhibition of KClO3 oxidation fluorescein isothiocyanate.

Procaterol hydrochloride (Prh) can inhibit KClO3 oxidation of fluorescein isothiocyanate (FITC) to form a non-phosphorescent compound, which causes room temperature phosphorescence (RTP) of FITC in the system to enhance sharply the linear relationship between ∆Ip and the Prh content. Thus, a rapid response and highly sensitive phosphorescence sensor for the determination of Prh has been developed based on the inhibiting effect of Prh on KClO3 oxidation of FITC. This simple, high sensitivity (detection limit (LD) calculated by 3Sb /k was 0.019 fg/spot, sample volume 0.40 µl, corresponding concentration 4.8 × 10(-14) g ml(-1) ) and selective sensor with a wide linear range (0.080-11.20 g/spot) has been applied to detect Prh in blood samples, and the results were consistent with those obtained by high-performance liquid chromatography (HPLC). Simultaneously, the mechanism of the phosphorescence sensor for the detection of Prh was also investigated using infrared spectroscopy.

Highly sensitive fluorescent probe for clenbuterol hydrochloride detection based on its catalytic oxidation of eosine Y by NaIO4.

A highly sensitive fluorescent probe for clenbuterol hydrochloride (CLB) detection has been first designed based on its catalytic effect on NaIO4 oxidating eosine Y (R). And this environment-friendly, simple, rapid, selective and sensitive fluorescent probe has been utilized to detect CLB in the practical samples with the results consisting with those obtained by GC/MS. The structures of R and CLB were characterized by infrared spectra. The mechanism of the proposed assay for the detection of CLB was also discussed.

A highly sensitive solid substrate room temperature phosphorimetry for carbaryl detection based on its activating effect on NaIO4 oxidizing fluorescein.

Fluorescein (HFin) could emit strong and stable room temperature phosphorescence (RTP) signal on polyamide membrane (PAM) using Pb(2+) as the ion perturber. Carbaryl could activate effect on NaIO4 oxidating HFin, which caused the RTP signal of the system to quench sharply. The phosphorescence intensity (ΔI p) of activating system higher 3.3 times (119.4/36.0) than that of non-activating system, and is directly proportional to the content of carbaryl. Thus, an activating solid substrate room temperature phosphorimetry (SSRTP) for carbaryl detection has been established. This sensitive (the limit of quantification (LOQ) was 2.0 × 10(-13) g mL(-1)), selective, simple and rapid method has been applied to determine trace carbaryl in water samples with the results consisting with those obtained by fluorimetry, showing its high accuracy. The apparent activation energy (E) and rate constant (k) of this activating reaction were 20.77 kJ mol(-1) and 1.85 × 10(-4) s(-1), respectively. Meanwhile, the mechanism of activating SSRTP for carbaryl detection was also discussed using infrared spectra (IR).

Measurement and Analysis of the Vibration Responses of Piano Soundboards with Different Structures.

The effect of structure on the vibration response was explored for four piano soundboards with different but commonly adopted structures. The vibration response was obtained using the free-vibration method, and the values of the dynamic modulus of elasticity and dynamic shear modulus obtained using the free-vibration frequency method (EF and GF) were compared with the dynamic modulus of elasticity obtained using the Euler beam method (EE) and dynamic shear modulus obtained using the free-plate torsional vibration method (GT), respectively. It was found that the soundboards with different structures had different vibration modes and that excitation at different locations highlighted different vibration modes. For all the soundboards analyzed, the EE and GT were higher than EF and GF by 2.2% and 24.3%, respectively. However, the trends of the results of these methods were the same. The four piano soundboards with different structures possessed varying dynamic moduli of elasticity and dynamic shear moduli. These rules are consistent with the grain directions of the soundboards and the anisotropy of the wood (the direction of the units of the soundboards). The results show that the vibration mode of the piano soundboard is complex. The dynamic elastic modulus of the soundboard can be calculated using the Euler beam method. The results provide a reference for studies on the vibration response, material selection, production technology, and testing of piano soundboards.

Epigenomic landscapes during prefrontal cortex development and aging in rhesus.

The prefrontal cortex (PFC) is essential for higher-level cognitive functions. How epigenetic dynamics participates in PFC development and aging is largely unknown. Here, we profiled epigenomic landscapes of rhesus monkey PFCs from prenatal to aging stages. The dynamics of chromatin states, including higher-order chromatin structure, chromatin interaction and histone modifications are coordinated to regulate stage-specific gene transcription, participating in distinct processes of neurodevelopment. Dramatic changes of epigenetic signals occur around the birth stage. Notably, genes involved in neuronal cell differentiation and layer specification are pre-configured by bivalent promoters. We identified a cis-regulatory module and the transcription factors (TFs) associated with basal radial glia development, which was associated with large brain size in primates. These TFs include GLI3, CREB5 and SOX9. Interestingly, the genes associated with the basal radial glia (bRG)-associated cis-element module, such as SRY and SOX9, are enriched in sex differentiation. Schizophrenia-associated single nucleotide polymorphisms are more enriched in super enhancers (SEs) than typical enhancers, suggesting that SEs play an important role in neural network wiring. A cis-regulatory element of DBN1 is identified, which is critical for neuronal cell proliferation and synaptic neuron differentiation. Notably, the loss of distal chromatin interaction and H3K27me3 signal are hallmarks of PFC aging, which are associated with abnormal expression of aging-related genes and transposon activation, respectively. Collectively, our findings shed light on epigenetic mechanisms underlying primate brain development and aging.

Allelic reprogramming of chromatin states in human early embryos.

The reprogramming of parental epigenomes in human early embryos remains elusive. To what extent the characteristics of parental epigenomes are conserved between humans and mice is currently unknown. Here, we mapped parental haploid epigenomes using human parthenogenetic and androgenetic embryos. Human embryos have a larger portion of genome with parentally specific epigenetic states than mouse embryos. The allelic patterns of epigenetic states for orthologous regions are not conserved between humans and mice. Nevertheless, it is conserved that maternal DNA methylation and paternal H3K27me3 are associated with the repression of two alleles in humans and mice. In addition, for DNA-methylation-dependent imprinting, we report 19 novel imprinted genes and their associated germline differentially methylated regions. Unlike in mice, H3K27me3-dependent imprinting is not observed in human early embryos. Collectively, allele-specific epigenomic reprogramming is different in humans and mice.