In vitro and in vivo models define a molecular signature reference for human embryonic notochordal cells.

Understanding the emergence of human notochordal cells (NC) is essential for the development of regenerative approaches. We present a comprehensive investigation into the specification and generation of bona fide NC using a straightforward pluripotent stem cell (PSC)-based system benchmarked with human fetal notochord. By integrating in vitro and in vivo transcriptomic data at single-cell resolution, we establish an extended molecular signature and overcome the limitations associated with studying human notochordal lineage at early developmental stages. We show that TGF-ß inhibition enhances the yield and homogeneity of notochordal lineage commitment in vitro. Furthermore, this study characterizes regulators of cell-fate decision and matrisome enriched in the notochordal niche. Importantly, we identify specific cell-surface markers opening avenues for differentiation refinement, NC purification, and functional studies. Altogether, this study provides a human notochord transcriptomic reference that will serve as a resource for notochord identification in human systems, diseased-tissues modeling, and facilitating future biomedical research.

Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data.

The rapidly growing collection of public single-cell sequencing data has become a valuable resource for molecular, cellular, and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our benchmarking experiments, Vulture is 66% to 88% faster than local tools (PathogenTrack and Venus) and 41% faster than the state-of-the-art cloud-based tool Cumulus, while achieving comparable microbial read identification. In terms of the cost on cloud computing systems, Vulture also shows a cost reduction of 83% ($12 vs. ${\$}$70). We applied Vulture to 2 coronavirus disease 2019, 3 hepatocellular carcinoma (HCC), and 2 gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell type-specific enrichment of severe acute respiratory syndrome coronavirus 2, hepatitis B virus (HBV), and Helicobacter pylori-positive cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license at https://github.com/holab-hku/Vulture.

Effects of Aluminum Addition on Microstructure and Properties of TiC-TiB2/Fe Coatings In Situ Synthesized by TIG Cladding.

This study focuses on the synthesis of TiC-TiB2/Fe coatings with varying amounts of aluminum (Al) using tungsten inert gas (TIG) cladding and investigates the impact of Al addition on microstructure refinement and performance enhancement of the coatings. The coatings were prepared on a mild steel substrate using TIG cladding. X-ray diffraction (XRD) analysis revealed the presence of TiC, TiB2, AlxTi, and AlxFe phases in the coatings. Scanning electron microscopy (SEM) images showed that the addition of Al improved the microstructure, reducing defects and enhancing the distribution of reinforcing phases within the coatings. The particle size of the reinforcing phases was significantly refined by the addition of Al. The micro-hardness of the coatings was significantly higher than that of the substrate, with the maximum micro-hardness of the coating reaching 955.5 ± 50.7 HV0.1, approximately six times that of the substrates. However, excessive Al addition led to a reduction in hardness due to a decrease in the quantity of hard phases. The wear tests showed that all the coatings had lower wear loss compared to the substrate material, with the wear loss initially decreasing and then increasing with the increasing Al content. Samples with a 28.57 wt.% Al addition exhibited the best wear resistance, with approximately 16.8% of the wear volume loss compared to mild steel under the same testing conditions, attributed to the optimal combination of reinforcement phase quantity and matrix properties.

A high-quality chromosome-level genome assembly of Pelteobagrus vachelli provides insights into its environmental adaptation and population history.

Pelteobagrus vachelli is a freshwater fish with high economic value, but the lack of genome resources has severely restricted its industrial development and population conservation. Here, we constructed the first chromosome-level genome assembly of P. vachelli with a total length of approximately 662.13 Mb and a contig N50 was 14.02 Mb, and scaffolds covering 99.79% of the assembly were anchored to 26 chromosomes. Combining the comparative genome results and transcriptome data under environmental stress (high temperature, hypoxia and Edwardsiella. ictaluri infection), the MAPK signaling pathway, PI3K-Akt signaling pathway and apelin signaling pathway play an important role in environmental adaptation of P. vachelli, and these pathways were interconnected by the ErbB family and involved in cell proliferation, differentiation and apoptosis. Population evolution analysis showed that artificial interventions have affected wild populations of P. vachelli. This study provides a useful genomic information for the genetic breeding of P. vachelli, as well as references for further studies on fish biology and evolution.

Modeling of Dynamic Recrystallization Evolution for Cr8 Alloy Steel and Its Application in FEM.

In the process of Cr8 roller production, the phenomenon of coarse grain size and uneven grain size often appears, which makes the mechanical properties of the material decrease sharply. Accurate dynamic recrystallization model is the basis for predicting the change of grain size during thermal processing, and is an important basis for refining grain and improving material properties. In this study, the isothermal compression experiment was carried out on Cr8 alloy steel at 900-1200 °C and 0.005-0.1 s-1 by Gleeble -1500D thermal simulation compressor, and the stress dates of Cr8 alloy steel were obtained. According to experimental data, the Kopp dynamic recrystallization model of Cr8 alloy steel was established. The dynamic recrystallization volume fraction obtained by Kopp model was compared with that obtained by experiment at the same temperature and strain rate. The correlation value was 0.988, and the root mean square error (RMSE) was 0.053, which proved that the DRX model established was reliable. Through the secondary development of the program, the DRX model of Cr8 alloy steel was written into the software Forge® to verify the microstructure evolution model. The compression process of a cylindrical specimen of Cr8 alloy steel at 0.1 s-1 and 1050 °C was simulated, and the DRX microstructure evolution of the alloy was calculated. The comparison between the final grain size calculation results and the test metallographic photos of samples in different deformation zones shows the relative error of the grain size was less than 10.6%, indicating that the DRX model of Cr8 alloy steel can better predict the dynamic recrystallization of Cr8 alloy steel.

Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle.

Increasing pressures on aquatic ecosystems because of pollutants, nutrient enrichment, and global warming have severely depleted oxygen concentrations. This sudden and significant lack of oxygen has resulted in persistent increases in fish mortality rates. Revealing the molecular mechanism of fish hypoxia adaptation will help researchers to find markers for hypoxia induced by environmental stress. Here, we used a multiomics approach to identify several hypoxia-associated miRNAs, mRNAs, proteins, and metabolites involved in diverse biological pathways in the muscles of Pelteobagrus vachelli. Our findings revealed significant hypoxia-associated changes in muscles over 4 h of hypoxia exposure and discrete tissue-specific patterns. We have previously reported that P. vachelli livers exhibit increased anaerobic glycolysis, heme synthesis, erythropoiesis, and inhibit apoptosis when exposed to hypoxia for 4 h. However, the opposite was observed in muscles. According to our comprehensive analysis, fishes show an acute response to hypoxia, including activation of catabolic pathways to generate more energy, reduction of biosynthesis to decrease energy consumption, and shifting from aerobic to anaerobic metabolic contributions. Also, we found that hypoxia induced muscle dysfunction by impairing mitochondrial function, activating inflammasomes, and apoptosis. The hypoxia-induced mitochondrial dysfunction enhanced oxidative stress, apoptosis, and further triggered interleukin-1ß production via inflammasome activation. In turn, interleukin-1ß further impaired mitochondrial function or apoptosis by suppressing downstream mitochondrial biosynthesis-related proteins, thus resulting in a vicious cycle of inflammasome activation and mitochondrial dysfunction. Our findings contribute meaningful insights into the molecular mechanisms of hypoxia, and the methods and study design can be utilized across different fish species.

Ultrasonic Cavitation Erosion Behavior of AlCoCrxCuFe High Entropy Alloy Coatings Synthesized by Laser Cladding.

Cavitation corrosion resistant coatings are an excellent solution to the cavitation corrosion problem. High entropy alloys provide a new possibility for cavitation resistant coatings due to their excellent comprehensive performance. Laser cladding was employed to synthesize AlCoCrxCuFe (x represents the Cr concentration, x = 0.5, 1.0, 1.5, 2.0) high entropy alloy coatings (HECs) on AISI 304 steel. The phase transformation, microstructure, micro-mechanical properties, and cavitation erosion performance of HECs were studied. Results showed that AlCoCrxCuFe HECs were composed of BCC and FCC duplex phase. The microstructure of HECs showed a typical dendritic structure. The composition segregation of interdendrite structures was observed. Cavitation erosion resistance represented by 20 h volume loss was decreased with the increase in Cr content. AlCoCrxCuFe HECs with the lowest chromium content (AlCoCr0.5CuFe) showed the best cavitation erosion resistance among all samples. The cavitation resistance of AlCoCrxCuFe HECs has good correlation with the mechanical parameter Hn3/Er2 (Hn is nanohardness, Er is elastic modulus) and phase formation parameter δ (δ is atomic radius difference). The surface after 20 h of cavitation erosion testing exposed the dendritic structure of BCC phase, which was caused by the destruction of the interdendrite structure by cavitation impact.

High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500. All sequencing data are deposited in the GEO database under accession number GSE87097.

Complete mitochondrial DNA sequence and phylogenic analysis of Oxyeleotris lineolatus (Perciformes, Eleotridae).

In this study, the mitochondrial genome of Oxyeleotris lineolatus was first determined. The length of entire mtDNA sequence was 16,522 bp with (A + T) content of 53.81%, and it contained 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. The gene order and the orientation are similar to some typical fish species. The data will provide useful molecular information for phylogenetic studies concerning O. lineolatus and its related species.

MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata.

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate gene expression by post-transcriptional repression of mRNAs. Recently, several miRNAs have been confirmed to execute directly or indirectly osmoregulatory functions in fish via translational control. In order to clarify whether miRNAs play relevant roles in the osmoregulation of Anguilla marmorata, three sRNA libraries of A. marmorata during adjusting to three various salinities were sequenced by Illumina sRNA deep sequencing methods. Totally 11,339,168, 11,958,406 and 12,568,964 clear reads were obtained from 3 different libraries, respectively. Meanwhile, 34 conserved miRNAs and 613 novel miRNAs were identified using the sequence data. MiR-10b-5p, miR-181a, miR-26a-5p, miR-30d and miR-99a-5p were dominantly expressed in eels at three salinities. Totally 29 mature miRNAs were significantly up-regulated, while 72 mature miRNAs were significantly down-regulated in brackish water (10‰ salinity) compared with fresh water (0‰ salinity); 24 mature miRNAs were significantly up-regulated, while 54 mature miRNAs were significantly down-regulated in sea water (25‰ salinity) compared with fresh water. Similarly, 24 mature miRNAs were significantly up-regulated, while 45 mature miRNAs were significantly down-regulated in sea water compared with brackish water. The expression patterns of 12 dominantly expressed miRNAs were analyzed at different time points when the eels transferred from fresh water to brackish water or to sea water. These miRNAs showed differential expression patterns in eels at distinct salinities. Interestingly, miR-122, miR-140-3p and miR-10b-5p demonstrated osmoregulatory effects in certain salinities. In addition, the identification and characterization of differentially expressed miRNAs at different salinities can clarify the osmoregulatory roles of miRNAs, which will shed lights for future studies on osmoregulation in fish.