Prediction and Analysis of Protein Hydroxyproline and Hydroxylysine

BACKGROUND: Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we developed a novel sequence-based method for identifying the two main types of hydroxylation sites--hydroxyproline and hydroxylysine. First, feature selection was made on three kinds of features consisting of amino acid indices (AAindex) which includes various physicochemical properties and biochemical properties of amino acids, Position-Specific Scoring Matrices (PSSM) which represent evolution information of amino acids and structural disorder of amino acids in the sliding window with length of 13 amino acids, then the prediction model were built using incremental feature selection method. As a result, the prediction accuracies are 76.0% and 82.1%, evaluated by jackknife cross-validation on the hydroxyproline dataset and hydroxylysine dataset, respectively. Feature analysis suggested that physicochemical properties and biochemical properties and evolution information of amino acids contribute much to the identification of the protein hydroxylation sites, while structural disorder had little relation to protein hydroxylation. It was also found that the amino acid adjacent to the hydroxylation site tends to exert more influence than other sites on hydroxylation determination. CONCLUSIONS/SIGNIFICANCE: These findings may provide useful insights for exploiting the mechanisms of hydroxylation

Dopamine D2-receptor neurons in nucleus accumbens regulate sevoflurane anesthesia in mice

IntroductionThe mechanism of general anesthesia remains elusive. In recent years, numerous investigations have indicated that its mode of action is closely associated with the sleep-wake pathway. As a result, this study aimed to explore the involvement of dopamine D2 receptor (D2R) expressing neurons located in the nucleus accumbens (NAc), a critical nucleus governing sleep-wake regulation, in sevoflurane anesthesia.MethodsThis exploration was carried out using calcium fiber photometry and optogenetics technology, while utilizing cortical electroencephalogram (EEG), loss of righting reflex (LORR), and recovery of righting reflex (RORR) as experimental indicators.ResultsThe findings from calcium fiber photometry revealed a decrease in the activity of NAcD2R neurons during the induction phase of sevoflurane anesthesia, with subsequent recovery observed during the anesthesia’s emergence phase. Moreover, the activation of NAcD2R neurons through optogenetics technology led to a reduction in the anesthesia induction process and an extension of the arousal process in mice. Conversely, the inhibition of these neurons resulted in the opposite effect. Furthermore, the activation of NAcD2R neurons projecting into the ventral pallidum (VP) via optogenetics demonstrated a shortened induction time for mice under sevoflurane anesthesia.DiscussionIn conclusion, our research outcomes suggest that NAcD2R neurons play a promotive role in the sevoflurane general anesthesia process in mice, and their activation can reduce the induction time of anesthesia via the ventral pallidum (VP)

Nitrification and denitrification processes in a zero-water exchange aquaculture system: characteristics of the microbial community and potential rates

​The zero-water exchange aquaculture has been identified as a promising method of farming to decrease the environment pressure of aquaculture and to increase profits. However, the ecological functions (e.g., nitrogen removal) and microbial biodiversity of the zero-water exchange pond aquaculture system are relatively understudied. In the present study, the zero-water exchange pond aquaculture system were constructed to investigated the microbial communities, sediment potential nitrification and denitrification production rates. And five functional genes (AOA amoA, AOB amoA, nirS, nosZ, and hzsB) were used to quantify the abundance of nitrifying and denitrifying microorganisms. The results showed that the sediment of the system had excellent potential nitrification-denitrification performance, with potential nitrification and denitrification rate were 149.77-1024.44 ng N g−1 h−1 and 48.32-145.01 ng N g−1 h−1, respectively. The absolute copy numbers of nitrogen functional genes and total bacterial 16S rRNA were 1.59×105-1.39×109 and 1.55×1010-2.55×1010copies g−1, respectively, with the dominant phyla, i.e., Proteobacteria, Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes. The relative abundances of the genera related to nitrification and denitrification, varied from 0.01% to 0.79% and from 0.01% to 15.54%, respectively. The potential nitrification rate was positively related to the sediment TOC concentration; and the potential denitrification rate had a positive correlation with sediment nitrate concentration. The genera Bacillus positively correlated with sediment NO3‐-N concentration, whereas Flavobacterium and Shewanella positively correlated with sediment NH4+-N concentration, which could be the functional bacteria for nitrogen removal. These findings may shed light on quantitative molecular mechanisms for nitrogen removal in zero-water exchange ponds, providing a sustainable solution to nitrogen pollution problem in the freshwater aquaculture ecosystems

Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation

Abstract Background Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricornutum at late exponential phase. Results Neutral lipid contents per cell subsequently increased 2.4-fold, both the number and total volume of oil bodies increased markedly, and cell density rose slightly. Transcriptional profile analyzed by RNA-Seq showed that expression levels of 1213 genes (including key carbon fixation, TCA cycle, glycerolipid metabolism and nitrogen assimilation genes) increased, with a false discovery rate cut-off of 0.001, under N deprivation. However, most light harvesting complex genes were down-regulated, extensive degradation of chloroplast membranes was observed under an electron microscope, and photosynthetic efficiency declined. Further identification of lipid classes showed that levels of MGDG and DGDG, the main lipid components of chloroplast membranes, dramatically decreased and triacylglycerol (TAG) levels significantly rose, indicating that intracellular membrane remodeling substantially contributed to the neutral lipid accumulation. Conclusions Our findings shed light on the molecular mechanisms of neutral lipid accumulation and the key genes involved in lipid metabolism in diatoms. They also provide indications of possible strategies for improving microalgal biodiesel production.http://deepblue.lib.umich.edu/bitstream/2027.42/112455/1/13068_2012_Article_291.pd

High-efficiency broadband second harmonic generation in single hexagonal GaAs nanowire

AbstractIn this paper, we investigate second harmonic generation in a single hexagonal GaAs nanowire. An excellent frequency converter based on this nanowire excited using a femtosecond laser is demonstrated to operate over a range from 730 nm to 1960 nm, which is wider than previously reported ranges for nanowires in the literature. The converter always operates with a high conversion efficiency of ~10−5 W−1 which is ~103 times higher than that obtained from the surface of bulk GaAs. This nanoscale nolinear optical converter that simultaneously owns high efficiency and broad bandwidth may open a new way for application in imaging, bio-sensing and on-chip all-optical signal processing operations.</jats:p

Photometric calibration of the Stellar Abundance and Galactic Evolution Survey (SAGES): Nanshan One-meter Wide-field Telescope g, r, and i band imaging data

In this paper, a total of approximately 2.6 million dwarfs were constructed as standard stars, with an accuracy of about 0.01-0.02 mag for each band, by combining spectroscopic data from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope Data Release 7, photometric data from the corrected Gaia Early Data Release 3, and photometric metallicities. Using the spectroscopy based stellar color regression method (SCR method) and the photometric-based SCR method (SCR' method), we performed the relative calibration of the Nanshan One-meter Wide-field Telescope imaging data. Based on the corrected Pan-STARRS DR1 photometry, the absolute calibration was also performed. In the photometric calibration process, we analyzed the dependence of the calibration zero points on different images (observation time), different gates of the CCD detector, and different CCD positions. We found that the stellar flat and the relative gain between different gates depend on time. The amplitude of gain variation in three channels is approximately 0.5%-0.7% relative to the other channel, with a maximum value of 4%. In addition, significant spatial variations of the stellar flat fitting residual are found and corrected. Using repeated sources in the adjacent images, we checked and discovered internal consistency of about 1-2 mmag in all the filters. Using the PS1 magnitudes synthesized by Gaia DR3 BP/RP spectra by the synthetic photometry method, we found that the photometric calibration uniformity is about 1-2 mmag for all the bands, at a spatial resolution of 1.3 degree. A detailed comparison between the spectroscopy-based SCR and photometric-based SCR method magnitude offsets was performed, and we achieved an internal consistency precision of about 2 mmag or better with resolutions of 1.3 degree for all the filters. Which is mainly from the position-dependent errors of the E(B-V) used in SCR' method.Comment: 15 pages in Chinese language, 8 figures, Chinese Science Bulletin accepted and published online (https://www.sciengine.com/CSB/doi/10.1360/TB-2023-0052), see main results in Figures 6, 7 and