Seismic noise in South China Sea: High-quality time-frequency analysis from 0.01 to 125 Hz.

An efficient and precise time-frequency analysis method for real-time ocean bottom seismometer (RTOBS) data in the South China Sea (SCS) is presented. Overcoming the limitations of conventional methods, the method involves temporal segmentation, unique frequency octaves, and Fourier transforms to generate power spectral density (PSD) and probability density function profiles. The method demonstrates superior precision, computational efficiency, and full-bandwidth (0 to Nyquist) capability compared to traditional techniques, as validated through theoretical and empirical evaluations. Applied to SCS RTOBS data, it unveils temporal PSD variations, shedding light on underwater noise sources like earthquakes, offshore blasting, ship-induced disturbances, and tidal effects. Establishing background noise levels in the SCS supports noise source categorization and ocean environment monitoring. Furthermore, comparing onshore and offshore seismic stations advances interdisciplinary research, fostering a comprehensive understanding of acoustics and seismology in the region.

Reversible Redox-Dependent Conformational Switch of the C-Terminal α-Helical Lid of Human Hsp70 Observed by In-Cell NMR.

Glutathionylation of human stress-inducible Hsp70 (hHsp70) under oxidative stress conditions has been suggested to act as an on/off switch of hHsp70 chaperone activity and thus transfer redox signals to hHsp70 clients through a change in conformation. The mechanism of this switch involves unfolding of the C-terminal α-helical lid, SBDα, upon glutathionylation, which then binds to and blocks the hHsp70 substrate-binding site. This process is reversible and redox-regulated and has been demonstrated for purified protein in solution. Here, we found that this redox-regulated reversible process also occurs in the cellular environment. Using Escherichia coli as a model system, in-cell NMR data clearly indicate that hHsp70 SBDα undergoes a conformational transition from ordered to disordered after diamide stimulation. The disordered SBDα could spontaneously recover back to the helix bundle conformation over time. This oxidative-stress induced process also occurred in cell lysate, with a similar unfolding rate as in cells, but the refolding rate was significantly slower in cell lysate. Increased temperature accelerates this process. Under heat stress alone, unfolding of the SBDα could not be detected in cells. Our in-cell NMR results provide direct support for the molecular switch model of hHsp70 redox regulation and also demonstrate the power of in-cell NMR for real-time study of protein structures during biological processes in living cells.

Construction of a new automatic grading system for jaw bone mineral density level based on deep learning using cone beam computed tomography.

To develop and verify an automatic classification method using artificial intelligence deep learning to determine the bone mineral density level of the implant site in oral implant surgery from radiographic data obtained from cone beam computed tomography (CBCT) images. Seventy patients with mandibular dentition defects were scanned using CBCT. These Digital Imaging and Communications in Medicine data were cut into 605 training sets, and then the data were processed with data standardization, and the Hounsfiled Unit (HU) value level was determined as follows: Type 1, 1000-2000; type 2, 700-1000; type 3, 400-700; type 4, 100-400; and type 5, - 200-100. Four trained dental implant physicians manually identified and classified the area of the jaw bone density level in the image using the software LabelMe. Then, with the assistance of the HU value generated by LabelMe, a physician with 20 years of clinical experience confirmed the labeling level. Finally, the HU mean values of various categories marked by dental implant physicians were compared to the mean values detected by the artificial intelligence model to assess the accuracy of artificial intelligence classification. After the model was trained on 605 training sets, the statistical results of the HU mean values of various categories in the dataset detected by the model were almost the same as the HU grading interval on the data annotation. This new classification provides a more detailed solution to guide surgeons to adjust the drilling rate and tool selection during preoperative decision-making and intraoperative hole preparation for oral implant surgery.

Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1.

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.

[Asymmetrical flow field flow fractionation combined with ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry used to screen allergen protein epitopes].

Asymmetrical flow field flow fractionation (AF4) combined with ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was used to screen allergen protein epitopes. The selected allergen protein (tropomyosin, TM) was enzymatically digested into peptide segments and analyzed via UPLC-QTOF-MS to establish a protein-specific peptide database. The peptide segments were incubated with immunoglobulin E (IgE) for 30 min. During the incubation procedure, the specific peptide segments (with the antigen epitope) combine with IgE while the other peptide segments remain in solution. After incubation, the solution was injected into the AF4 device. The combined peptide segments flowed out of the outlet along with IgE, and the other peptide segments flowed into the waste liquid. The components of outlet were then collected, analyzed by UPLC-QTOF-MS, and the results matched with the spectra of the protein peptides. Eventually the specific peptide segments were identified to detect the antigen epitopes. This study extends the application of AF4 with a preliminary exploration of the detection of an allergen protein epitope, providing a novel research strategy for the screening of allergen epitopes.

Resonance assignments for the tandem PWWP-ARID domains of human RBBP1.

Retinoblastoma-binding protein 1 (RBBP1), also known as AT-rich interaction domain 4A (ARID4A), is a tumour suppressor involved in the regulation of the epigenetic programming in leukemia and Prader-Willi/Angelman syndromes. The ARID domain of RBBP1 binds to DNA non-specifically and has gene suppression activity. However, no structural data has been obtained for the human RBBP1 ARID domain so far. Here we report the near-complete 1H, 13C, 15N backbone and side-chain NMR assignment of a 27 kDa tandem PWWP-ARID domain construct that spans residues 171-414 with the removal of a short disordered region between the two domains. The predicted secondary structure based on the assigned chemical shifts is consistent with the structures of the isolated PWWP domain of human RBBP1 previously solved and the homologous ARID domains of other proteins.

[Impact of carrier flow composition on membrane adsorption and aggregation of ovalbumin in asymmetrical flow field-flow fractionation].

Asymmetrical flow field-flow fractionation (AF4) is a kind of moderate separation technology for the analysis of macromolecules, including proteins with a wide range of sizes. In the separation channel, the membrane adsorption and aggregation of proteins affected by the carrier fluid (CF) composition lead to changes in analyte recovery and size distribution, thereby restricting the application of AF4 to biomolecules. Different pH levels (6.2, 7.4, 8.2), several types of cations (Na+, K+, Mg2+) and various ion strengths (0-0.1 mol/L)were studied to demonstrate the influence of carrier fluid composition on the membrane adsorption and aggregation of proteins. The results revealed the following:a) higher ion strength of CF resulted in a greater degree of membrane adsorption and aggregation; b) the zeta potential, determined by the pI of the protein and the pH of the CF, influenced the adsorption and aggregation; c) divalent cations (Mg2+) caused serious adsorption and aggregation. The experimental results can help us achieve better recovery and mitigate aggregate formation by using the optimal CF components in future AF4 studies. Moreover, the findings indicate that AF4 would find extensive application in protein biochemistry assays.

[Present situation and development trends of asymmetrical flow field-flow fractionation].

Field-flow fractionation (FFF) is a kind of mature separation technologies in the field of bioanalysis, feasible of separating analytes with the differences of certain physical and chemical properties by the combination effects of two orthogonal force fields (flow field and external force field). Asymmetrical flow field-flow fractionation (AF4) is a vital subvariant of FFF, which applying a vertical flow field as the second dimension force field. The separation in AF4 opening channel is carried out by any composition carrier fluid, universally and effectively used in separation of bioparticles and biopolymers due to the non-invasivity feature. Herein, bio-analytes are held in bio-friendly environment and easily sterilized without using degrading carrier fluid which is conducive to maintain natural conformation. In this review, FFF and AF4 principles are briefly described, and some classical and emerging applications and developments in the bioanalytical fields are concisely introduced and tabled. Also, special focus is given to the hyphenation of AF4 with highly specific, sensitive detection technologies.

Effects of comprehensive function of factors on retention behavior of microparticles in gravitational field-flow fractionation.

Gravitational field-flow fractionation (GrFFF) is a useful technique for separation and characterization for micrometer-sized particles. Elution behavior of micrometer-sized particles in GrFFF was researched in this study. Particles in GrFFF channel are subject to hydrodynamic lift forces (HLF), fluid inertial forces and gravity, which drive them to different velocities by carrier flow, resulting in a size-based separation. Effects of ionic strength, flow rate and viscosity as well as methanol were investigated using polystyrene latex beads as model particles. This study is devoted to experimental verification of the effect of every factor and their comprehensive function. All experiments were performed to show isolated influence of every variable factor. The orthogonal design test was used to evaluate various factors comprehensively. Results suggested that retention ratio of particles increases with increasing flow rate or the viscosity of carrier liquid by adjusting external forces acting on particles. In addition, retention ratio increases as ionic strength decreases because of decreased electrostatic repulsion between particles and channel accumulation wall. As far as methanol, there is no general trend due to the change of both density and viscosity. On the basis of orthogonal design test it was found that viscosity of carrier liquid plays a significant role in determining resolution of micrometer-sized particles in GrFFF.

[Effects of carrier liquid and flow rate on the separation in gravitational field-flow fractionation].

Gravitational field-flow fractionation is the simplest field-flow fractionation technique in terms of principle and operation. The earth' s gravity is its external field. Different sized particles are injected into a thin channel and carried by carrier fluid. The different velocities of the carrier liquid in different places results in a size-based separation. A gravitational field-flow fractionation (GrFFF) instrument was designed and constructed. Two kinds of polystyrene (PS) particles with different sizes (20 µm and 6 µm) were chosen as model particles. In this work, the separation of the sample was achieved by changing the concentration of NaN3, the percentage of mixed surfactant in the carrier liquid and the flow rate of carrier liquid. Six levels were set for each factor. The effects of these three factors on the retention ratio (R) and plate height (H) of the PS particles were investigated. It was found that R increased and H decreased with increasing particle size. On the other hand, the R and H increased with increasing flow rate. The R and H also increased with increasing NaN3 concentration. The reason was that the electrostatic repulsive force between the particles and the glass channel wall increased. The force allowed the samples approach closer to the channel wall. The results showed that the resolution and retention time can be improved by adjusting the experimental conditions. These results can provide important values to the further applications of GrFFF technique.