Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus.

Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.

Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala.

Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.

The effect of vitreomacular interface in neovascular age-related macular degeneration treated with intravitreal injection of anti-VEGF.

BACKGROUND: The purpose of this study is to study the effect of repeated intravitreal injection of anti-vascular endothelial growth factor (anti-VEGF) drugs on vitreomacular interface. METHODS: Neovascular age-related macular degeneration patients who received intravitreal injections of anti-VEGF drugs were included. Eyes with severe vitreous opacity, uveitis, complicated cataract surgery and previous vitrectomy were excluded. Vitreomacular interface, best corrected visual acuity (BCVA) and central retinal thickness (CRT) assessment were performed once a month for at least 3 months. The nature and time of the change event are recorded. Groups were divided according to whether vitreomacular interface change events occurred. To analyse the risk factors of vitreomacular interface changes and their influence on treatment effect. RESULTS: A total of 87 eyes were evaluated. Vitreomacular interface change event occurred in 9 eyes. Pre-existing vitreomacular interface abnormality (VMIA) was a risk factor for the VMI change (P = 0.033, OR = 16.518, 95% CI: 1.258 to 216.939). 60% of interface events occurred in the first 3 months of treatment. The final BCVA of eyes with vitreomacular interface unchanged was significantly higher than that at baseline (P = 0.001), and the final CRT was also significantly lower than that at baseline (P < 0.001). The final CRT of eyes vitreomacular interface changed was significantly lower than that at baseline (P = 0.015), however, there was no statistical significance in BCVA (P = 0.468). CONCLUSION: Intravitreal injection of anti-VEGF drugs has a certain probability to cause changes in the vitreomacular interface, and the risk is higher in eyes with pre-existing vitreomacular interface abnormality. The effect of intravitreal injections on the vitreomacular interface was concentrated in the first three injections, and subsequent increases in the number of injections did not significantly increase the risk of vitreomacular interface abnormality. Ophthalmologists should increase attention to the vitreomacular interface in the early stages of anti-VEGF therapy and counsel patients accordingly.

Recent Advances in Basalt Fiber Reinforced Asphalt Mixture for Pavement Applications.

This paper conducts a thorough review of the literature on the feasibility and current state-of-the-art incorporation of basalt fiber (BF) into asphalt pavement materials, focusing on fiber characteristics, dosage, incorporation methods, mixture properties, and surface modification techniques. The optimum basalt fiber dosage should be determined based on engineering performance parameters such as asphalt type, fatigue cracking, thermal cracking, rutting, and moisture resistance of asphalt mixtures. Basalt fibers are added to asphalt mixes by dry method or mixed method to achieve better dispersion. Adding BF to asphalt mixtures increased performance characteristics like cracking resistance, rutting resistance, and fatigue resistance. Overall, incorporating BF into asphalt mixtures would lower costs while increasing pavement service life. More research is needed to fully understand the effects of different sizes of BF on pavement performance and the possible environmental and economic repercussions of fiber surface alteration.

On-site and quantitative SERS detection of trace 1, 2, 3-benzotriazole in transformer oil with colloidal lignin particles-based green pretreatment reagents.

Since 1, 2, 3-Benzotriazole (BTA) is one of the most commonly used metal passivators in transformer oil, on-site and quantitative detection of BTA plays a significant role in fast evaluation of the performance of the insulating oil. Herein, we proposed a cycle-growth synthetic protocol for yielding two-dimensional (2D) plane-based surface-enhanced Raman scattering (SERS) substrates with tunable optical property and controllable interparticle distance, and an extraction material, so called colloidal lignin particles (CLPs), for the fast separation of BTA from oil matrix. After BTA from transformer oil were adsorbed by hydrophilic CLPs, highly reproducible SERS signal of BTA can be obtained by dropping on the substrate. The characteristic Raman shift at 1386 cm-1 of BTA has been selected to establish a good linearity between its relative intensity and concentration in the range of 1-300 mg/L, and the detection limit for BTA was down to 0.12 mg/L. Moreover, the time consumption for the whole detection process of real sample including sample pretreatment and SERS measurements was less than 30 min. It is highly expected that the combination of CLPs with SERS can accomplish the on-site detection of trace BTA in transformer oil.

A laser metallurgy route for the batch preparation of mm-scale 3D silver/graphite heteronanoclusters in air.

We report a batch preparation of mm-scale 3D Ag hetero-nanoclusters which exhibit an excellent surface plasmon resonance ability via facile laser metallurgy. Under laser irradiation, the porous AgI-based coordination network crystals were instantly converted into 3D graphite-encapsulated Ag hetero-nanoclusters with uniform sizes and gaps in several seconds. The obtained hetero-nanoclusters exhibited superior 3D confocal laser energy utilization compared with the other 0D, 1D and 2D SERS substrates, solving the bottleneck caused by laser focusing deviation in the SERS active depth. The mass-produced SERS devices were ultra-sensitive for the detection of life and industrial organic pollutants in terms of low detection and enriched capacity.

Improved thickness measurement method for choroidal hyperpermeability in central serous chorioretinopathy.

AIM: To observe choroidal thickness changes in the choroidal hyperpermeability area (CHA) in patients with central serous chorioretinopathy (CSC) after photodynamic therapy (PDT) using indocyanine green angiography (ICGA) combined with optical coherence tomography (OCT). METHODS: This was a cohort study of 17 eyes (17 patients) with CSC. In all patients, the range of CHA was determined by ICGA. The patients were divided into two groups based on CHA covered the fovea (group A) or not (group B). All patients received half-dose verteporfin PDT over CHA in ICGA. Choroidal thickness was measured by OCT before, 1, and 3mo after treatment. The choroidal thickness values of the fovea and CHAs were obtained for each measurement. Secondary outcomes were changes in the best-corrected visual acuity (BCVA) and amount of subretinal fluid (SRF). RESULTS: The differences in center choroidal thickness at baseline and at 1 and 3mo post-PDT were statistically significant in group A and all patients (both P<0.001). There was no significant difference in group B (P=0.059). The differences of thickness of CHA and BCVA at baseline and 1 and 3mo post-PDT were statistically significant in group A, group B, and all patients (all P<0.01). All patients showed complete SRF absorption at 3mo post-PDT. CONCLUSION: Center choroidal thickness does not accurately reflect changes in CHA of patients whose CHA does not covered the fovea center. Using CHA as the observation target can make up for this limitation, expand the scope of application, and reduce bias.

On-Site and Quantitative Detection of Trace Methamphetamine in Urine/Serum Samples with a Surface-Enhanced Raman Scattering-Active Microcavity and Rapid Pretreatment Device.

Here, it reports a high-throughput detection method for reliably quantitative analysis of illegal drugs in complex biological samples by means of a surface-enhanced Raman scattering (SERS) active microcavity and rapid pretreatment device. Based on the well-made hemispherical microcavities that regularly distributed on a glass array, the quality-controllable microcavity device is fabricated by the compact self-assembly of core-shell nanopeanuts (CSNPs) onto the inside surface. Both the CSNPs with a quantifiable internal standard signal of crystal violet acetate anchored inside their gap and the well-made microcavity referred to the physical amplification of the microscale groove surface will do well in trace analysis, which will allow us to realize the accurately quantitative SERS analysis of targeted analytes spread on the bottom area of the microcavity array. As an example, 0.8 nM malachite green and 160 ppb methamphetamine (MATM) have been successively detected in a wide range as standard, while even 0.01 ppm MATM mixed in the urine/serum samples has been efficiently tested by the microcavity device equipped with a rapid pretreatment device (manual monolithic column syringe needle). All of the above suggest that the SERS-active microcavity equipped with a rapid pretreatment device has potential in the on-site quick test of trace amounts of illegal drugs in bodily fluid samples or other field analysis of food sanitation, environmental safety, and public health.

Ultrafast Structural Evolution and Chromophore Inhomogeneity inside a Green-Fluorescent-Protein-Based Ca(2+) Biosensor.

Understanding excited-state structural dynamics of fluorescent-protein-based biosensors for Ca(2+) imaging is crucial for developing new in vivo Ca(2+) indicators and advancing bioimaging. We implemented wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) with a 530 nm Raman pump to uncover the working mechanism of an intensiometric fluorescent-protein biosensor, G-GECO1.1, highlighting the deprotonation process of its embedded chromophore. Besides confirming the dynamic difference of excited-state proton transfer (ESPT) in the Ca(2+)-free/bound protein, we revealed a chromophore two-ring twisting process with time constants of 36/60 ps that competes with ESPT. In contrast with FSRS data collected using the 800 nm Raman pump, the bluer Raman pump enables us to access a subset of reactant population with partially deprotonated character that exhibits an additional ESPT component on the ∼5 ps time scale. These findings provide deep mechanistic insights into the inhomogeneity and subpopulation-specific conformational dynamics of biosensor chromophores, which will guide the rational design of improved biosensors for metal ion imaging.

Distinct broadband third-harmonic generation on a thin amorphous medium-air interface.

We achieve a series of distinct broadband third-harmonic generation (THG) signals at the amorphous glass-air interface attributed to third-order and cascaded third-order nonlinear processes. A novel THG laser sideband arises from cascaded interaction between fundamental pulses and the cascaded four-wave mixing signals. The spatially separated THG sidebands with distinct spectral profiles manifest femtosecond quantum beats. Using a versatile setup with two crossing near-IR pulses temporally delayed to each other, we design an incident pulse polarization control method on the THG sideband lasers and also acquire the low-frequency surface Raman spectrum of the amorphous medium.

Early time excited-state structural evolution of pyranine in methanol revealed by femtosecond stimulated Raman spectroscopy.

To understand chemical reactivity of molecules in condensed phase in real time, a structural dynamics technique capable of monitoring molecular conformational motions on their intrinsic time scales, typically on femtoseconds to picoseconds, is needed. We have studied a strong photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS, pK(a)* ≈ 0) in pure methanol and observed that excited-state proton transfer (ESPT) is absent, in sharp contrast with our previous work on HPTS in aqueous solutions wherein ESPT prevails following photoexcitation. Two transient vibrational marker bands at ~1477 (1454) and 1532 (1528) cm(-1) appear in CH3OH (CD3OD), respectively, rising within the instrument response time of ~140 fs and decaying with 390-470 (490-1400) fs and ~200 ps time constants in CH3OH (CD3OD). We attribute the mode onset to small-scale coherent proton motion along the pre-existing H-bonding chain between HPTS and methanol, and the two decay stages to the low-frequency skeletal motion-modulated Franck-Condon relaxation within ~1 ps and subsequent rotational diffusion of H-bonding partners in solution before fluorescence. The early time kinetic isotope effect (KIE) of ~3 upon methanol deuteration argues active proton motions particularly within the first few picoseconds when coherent skeletal motions are underdamped. Pronounced quantum beats are observed for high-frequency modes consisting of strong phenolic COH rocking (1532 cm(-1)) or H-out-of-plane wagging motions (952 cm(-1)) due to anharmonic coupling to coherent low-frequency modes impulsively excited at ca. 96, 120, and 168 cm(-1). The vivid illustration of atomic motions of HPTS in varying H-bonding geometry with neighboring methanol molecules unravels the multidimensional energy relaxation pathways immediately following photoexcitation, and provides compelling evidence that, in lieu of ESPT, the photoacidity of HPTS promptly activates characteristic low-frequency skeletal motions to search phase space mainly concerning the phenolic end and to efficiently dissipate vibrational energy via skeletal deformation and proton shuttling motions within the intermediate, relatively confined excited-state HPTS-methanol complex on a solvent-dependent dynamic potential energy surface.

Ultrafast conformational dynamics of pyranine during excited state proton transfer in aqueous solution revealed by femtosecond stimulated Raman spectroscopy.

Proton transfer reaction plays an essential role in a myriad of chemical and biological processes, and to reveal the choreography of the proton motion intra- and intermolecularly, a spectroscopic technique capable of capturing molecular structural snapshots on the intrinsic time scale of proton transfer motions is needed. The photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) serves as a paradigm case to dissect excited state proton transfer (ESPT) events in aqueous solution, triggered precisely by photoexcitation. We have used femtosecond stimulated Raman spectroscopy (FSRS) to yield novel insights into the ultrafast conformational dynamics of photoexcited HPTS in complex with water and acetate molecules. Marker bands attributed to the deprotonated form of HPTS (1139 cm(-1), ∼220 fs rise) appear earlier and faster than the monomer acetic acid peak (864 cm(-1), ∼530 fs rise), indicating that water molecules actively participate in the ESPT chain. Several key low-frequency modes at 106, 150, 195, and 321 cm(-1) have been identified to facilitate ESPT at different stages from 300 fs, 1 ps, to 6 ps and beyond, having distinctive dynamics contributing through hydrogen bonds with 0, 1, and more intervening water molecules. The time-resolved FSRS spectroscopy renders a direct approach to observe the reactive coupling between the vibrational degrees of freedom of photoexcited HPTS in action, therefore revealing the anharmonicity matrix both within HPTS and between HPTS and the neighboring acceptor molecules. The observed excited state conformational dynamics are along the ESPT multidimensional reaction coordinate and are responsible for the photoacidity of HPTS in aqueous solution.

Zero kinetic energy photoelectron spectroscopy of jet cooled benzo[a]pyrene from resonantly enhanced multiphoton ionization.

We report zero kinetic energy (ZEKE) photoelectron spectroscopy of benzo[a]pyrene (BaP) via resonantly enhanced multiphoton ionization (REMPI). Our analysis concentrates on the vibrational modes of the first excited state (S(1)) and those of the ground cationic state (D(0)). Similar to pyrene, another peri-condensed polycyclic aromatic hydrocarbon we have investigated, the first two electronically excited states of BaP exhibit extensive configuration interactions. However, the two electronic states are of the same symmetry, hence vibronic coupling does not introduce any out-of-plane modes in the REMPI spectrum, and Franck-Condon analysis is qualitatively satisfactory. The ZEKE spectra from the in-plane modes observed in the REMPI spectrum demonstrate strong propensity in preserving the vibrational excitation of the intermediate state. Although several additional bands in combination with the vibrational mode of the intermediate state are identifiable, they are much lower in intensity. This observation implies that the molecular structure of BaP has a tremendous capability to accommodate changes in charge density. All observed bands of the cation are IR active, establishing the role of ZEKE spectroscopy in mapping out far infrared bands for astrophysical applications.

Zero kinetic energy photoelectron spectroscopy of pyrene.

We report zero kinetic energy photoelectron (ZEKE) spectroscopy of pyrene via resonantly enhanced multiphoton ionization. Our analysis centers on the symmetry of the first electronically excited state (S(1)), its vibrational modes, and the vibration of the ground cationic state (D(0)). From comparisons between the observed vibrational frequencies and those from ab initio calculations at the configuration interaction singles level using the 6-311G (d,p) basis set, and based on other previous experimental and theoretical reports, we confirm the (1)B(2u) symmetry for the S(1) state. This assignment represents a reversal in the energy order of the two closely spaced electronically excited states from our theoretical calculation, and extensive configuration interactions are attributed to this result. Among the observed vibrational levels of the S(1) state, three are results of vibronic coupling due to the nearby second electronically excited state. The ZEKE spectroscopy obtained via the vibronic levels of the S(1) state reveals similar modes for the cation as those of the intermediate state. Although we believe that the ground ionic state can be considered a single electron configuration, the agreement between theoretical and experimental frequencies for the cation is limited. This result is somewhat surprising based on our previous work on cata-condensed polycyclic aromatic hydrocarbons and small substituted aromatic compounds. Although a relatively small molecule, pyrene demonstrates its nonrigidity via several out-of-plane bending modes corresponding to corrugation of the molecular plane. The adiabatic ionization potential of neutral pyrene is determined to be 59 888 ± 7 cm(-1).