NHSMM-MAR-sdNC: A novel data-driven computational framework for state-dependent effective connectivity analysis.

The brain exhibits intrinsic dynamics characterized by spontaneous spatiotemporal reorganization of neural activity or metastability, which is associated closely with functional integration and segregation. Compared to dynamic functional connectivity, state-dependent effective connectivity (i.e., dynamic effective connectivity) is more suitable for exploring the metastability as its ability to infer causalities between brain regions. However, methods for state-dependent effective connectivity are scarce and urgently needed. In this study, a novel data-driven computational framework, named NHSMM-MAR-sdNC integrating nonparametric hidden semi-Markov model combined with multivariate autoregressive model and state-dependent new causality, is proposed to investigate the state-dependent effective connectivity. The framework is not constrained by any biological assumptions. Furthermore, state number can be inferred from the observed data directly and the state duration distributions will be estimated explicitly rather than restricted by geometric form, which overcomes limitations of hidden Markov model. Experimental results of synthetic data show that the framework can identify the state number adaptively and the state-dependent causality networks accurately. The dynamics of state-related causality networks are also revealed by the new method on real-world resting-state fMRI data. Our method provides a new data-driven computational framework for identifying state-dependent effective connectivity, which will facilitate the identification and assessment of metastability and itinerant dynamics of the brain.

Cytoplasmic TP53INP2 acts as an apoptosis partner in TRAIL treatment: the synergistic effect of TRAIL with venetoclax in TP53INP2-positive acute myeloid leukemia.

BACKGROUND: Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor outcomes, especially in older AML patients. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is considered a promising anticancer drug because it selectively induces the extrinsic apoptosis of tumor cells without affecting normal cells. However, clinical trials have shown that the responses of patients to TRAIL are significantly heterogeneous. It is necessary to explore predictable biomarkers for the preselection of AML patients with better responsiveness to TRAIL. Here, we investigated the critical role of tumor protein p53 inducible nuclear protein 2 (TP53INP2) in the AML cell response to TRAIL treatment. METHODS: First, the relationship between TP53INP2 and the sensitivity of AML cells to TRAIL was determined by bioinformatics analysis of Cancer Cell Line Encyclopedia datasets, Cell Counting Kit-8 assays, flow cytometry (FCM) and cell line-derived xenograft (CDX) mouse models. Second, the mechanisms by which TP53INP2 participates in the response to TRAIL were analyzed by Western blot, ubiquitination, coimmunoprecipitation and immunofluorescence assays. Finally, the effect of TRAIL alone or in combination with the BCL-2 inhibitor venetoclax (VEN) on cell survival was explored using colony formation and FCM assays, and the effect on leukemogenesis was further investigated in a patient-derived xenograft (PDX) mouse model. RESULTS: AML cells with high TP53INP2 expression were more sensitive to TRAIL in vitro and in vivo. Gain- and loss-of-function studies demonstrated that TP53INP2 significantly enhanced TRAIL-induced apoptosis, especially in AML cells with nucleophosmin 1 (NPM1) mutations. Mechanistically, cytoplasmic TP53INP2 maintained by mutant NPM1 functions as a scaffold bridging the ubiquitin ligase TRAF6 to caspase-8 (CASP 8), thereby promoting the ubiquitination and activation of the CASP 8 pathway. More importantly, simultaneously stimulating extrinsic and intrinsic apoptosis signaling pathways with TRAIL and VEN showed strong synergistic antileukemic activity in AML cells with high levels of TP53INP2. CONCLUSION: Our findings revealed that TP53INP2 is a predictor of responsiveness to TRAIL treatment and supported a potentially individualized therapeutic strategy for TP53INP2-positive AML patients.

Characterization of the Apoptotic and Antimicrobial Activities of Two Initiator Caspases of Sea Cucumber Apostichopus japonicus.

Caspase (CASP) is a protease family that plays a vital role in apoptosis, development, and immune response. Herein, we reported the identification and characterization of two CASPs, AjCASPX1 and AjCASPX2, from the sea cucumber Apostichopus japonicus, an important aquaculture species. AjCASPX1/2 share similar domain organizations with the vertebrate initiator caspases CASP2/9, including the CARD domain and the p20/p10 subunits with conserved functional motifs. However, compared with human CASP2/9, AjCASPX1/2 possess unique structural features in the linker region between p20 and p10. AjCASPX1, but not AjCASPX2, induced marked apoptosis of human cells by activating CASP3/7. The recombinant proteins of AjCASPX2 and the CARD domain of AjCASPX2 were able to bind to a wide range of bacteria, as well as bacterial cell wall components, and inhibit bacterial growth. AjCASPX1, when expressed in Escherichia coli, was able to kill the host bacteria. Under normal conditions, AjCASPX1 and AjCASPX2 expressions were most abundant in sea cucumber muscle and coelomocytes, respectively. After bacterial infection, both AjCASPX1 and AjCASPX2 expressions were significantly upregulated in sea cucumber tissues and cells. Together, these results indicated that AjCASPX1 and AjCASPX2 were initiator caspases with antimicrobial activity and likely functioned in apoptosis and immune defense against pathogen infection.

The molecular mechanism and evolutionary divergence of caspase 3/7-regulated gasdermin E activation.

Caspase (CASP) is a family of proteases involved in cleavage and activation of gasdermin, the executor of pyroptosis. In humans, CASP3 and CASP7 recognize the same consensus motif DxxD, which is present in gasdermin E (GSDME). However, human GSDME is cleaved by CASP3 but not by CASP7. The underlying mechanism of this observation is unclear. In this study, we identified a pyroptotic pufferfish GSDME that was cleaved by both pufferfish CASP3/7 and human CASP3/7. Domain swapping between pufferfish and human CASP and GSDME showed that the GSDME C-terminus and the CASP7 p10 subunit determined the cleavability of GSDME by CASP7. p10 contains a key residue that governs CASP7 substrate discrimination. This key residue is highly conserved in vertebrate CASP3 and in most vertebrate (except mammalian) CASP7. In mammals, the key residue is conserved in non-primates (e.g., mouse) but not in primates. However, mouse CASP7 cleaved human GSDME but not mouse GSDME. These findings revealed the molecular mechanism of CASP7 substrate discrimination and the divergence of CASP3/7-mediated GSDME activation in vertebrate. These results also suggested that mutation-mediated functional alteration of CASP probably enabled the divergence and specialization of different CASP members in the regulation of complex cellular activities in mammals.

Cell death is essential for an organism to develop and survive as it plays key roles in processes such as embryo development and tissue regeneration. Cell death is also an important form of defence during an infection. A form of programmed cell death known as pyroptosis can be induced in infected cells, which helps to kill the infectious agent as well as alert the immune system to the infection. Pyroptosis is driven by Gasdermin E, a protein made up of two domains. At one end of the protein, the 'N-terminal' domain punctures holes in cell membranes, which can lead to cell death. At the other end, the 'C-terminal' domain inhibits the activity of the N-terminal domain. A family of proteins called caspases activate Gasdermin E by cleaving it, which releases the N-terminal domain from the inhibitory C-terminal domain. In humans, two caspases known as CASP3 and CASP7 recognize a specific sequence of amino acids ­ the building blocks of proteins ­ in Gasdermin E. However, only CASP3 is able to cleave the protein. After discovering that, unlike in humans, pufferfish Gasdermin E can be cleaved by both CASP3 and CASP7, Xu et al. wanted to investigate the underlying mechanisms behind this difference. Swapping the domains of human and pufferfish Gasdermin E and creating different versions of CASP7 revealed that the C-terminal domain of Gasdermin E and a single amino acid in CASP7 determine whether cleavage is possible. Interestingly, the key amino acid sequence required for cleavage by CASP7 is present in most vertebrate CASP3 and CASP7 proteins. However, it is absent in most mammalian CASP7. The findings of Xu et al. suggest that the different activity of human CASP7 and CASP3 is driven by a single amino acid mutation. This change likely played an important role in the process of different CASP proteins evolving to regulate different cellular activities in mammalian cells. This knowledge will be useful for future studies on the evolution and specialization of other closely related proteins.

Research Progress on Surface Damage and Protection Strategies of Armature-Rail Friction Pair Materials for Electromagnetic Rail Launch.

Electromagnetic rail launch technology has attracted increasing attention owing to its advantages in terms of range, firepower, and speed. However, due to electricity-magnetism-heat-force coupling, the surface of the armature-rail friction pair becomes severely damaged, which restricts the development of this technology. A series of studies have been conducted to reduce the damage of the armature-rail friction pair, including an analysis of the damage mechanism and protection strategies. In this study, various types of surface damage were classified into mechanical, electrical, and coupling damages according to their causes. This damage is caused by factors such as mechanical friction, mechanical impact, and electric erosion, either individually or in combination. Then, a detailed investigation of protection strategies for reducing damage is introduced, including material improvement through the use of novel combined deformation and heat treatment processes to achieve high strength and high conductivity, as well as surface treatment technologies such as structural coatings for wear resistance and functional coatings for ablation and melting resistance. Finally, future development prospects of armature-rail friction pair materials are discussed. This study provides a theoretical basis and directions for the development of high-performance materials for the armature-rail friction pair.

Dynamic monitoring of serum tumor markers as prognostic factors in patients with advanced non-small-cell lung cancer treated with first-line immunotherapy: a multicenter retrospective study.

Background: To date, no specific studies have reported the use of dynamic serum tumor markers (STMs) as prognostic factors in patients with advanced non-small-cell lung cancer (NSCLC) who receive first-line immunotherapy. Therefore, it is unclear whether STMs can be used as a prognostic factor for first-line immunotherapy in advanced NSCLC. Objectives: To elucidate the role of STMs in monitoring immunotherapy response in advanced NSCLC. Patients were treated with first-line programmed cell death-1/programmed cell death ligand-1 inhibitors at four Chinese centers. Design: This was a multicenter retrospective study. Methods: Blood samples were collected at baseline and after 6-8 weeks of treatment. Computed tomography scans were used to evaluate treatment efficacy according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. Post-treatment drops in STMs [Serum carcinoembryonic antigen (CEA), neuron-specific enolase (NSE), cytokeratin fragment 19 (CYFRA21-1), carbohydrate antigen 19-9 (CA19-9), and carbohydrate antigen 125 (CA125)] were decreased ⩾20% (Group C) over baseline was used as cutoff level for defining a marker response. If STMs were increased by ⩾20% after treatment, the therapeutic effect was limited (Group A). Patients with STM changes between a 20% increase or decrease were enrolled in Group B. In univariate and multivariate stepwise Cox regression analyses, STMs and RECIST responses were analyzed for their impact on progression-free survival (PFS) and overall survival (OS). Results: The analysis included 716 patients. By multivariate analysis, CEA, NSE, CYFRA21-1, CA19-9, and CA125 (Group A versus Group B and Group A versus Group C) were associated with significant differences in PFS. Similar results were observed in the OS analysis. Similar results were observed in the adenocarcinoma subgroup analyses. In squamous cell carcinoma subgroup analyses, there was no statistical difference in PFS (p = 0.147) or OS (p = 0.068) between Group A and Group B for CA125. Conclusion: The increase and decrease in serum levels of STMs might be reliable prognostic factors for immunotherapy efficacy in NSCLC patients.

Comparison of first-line immunotherapy efficacy between advanced lung squamous cell carcinoma and pulmonary lymphoepithelioma-like carcinoma: A propensity score matching multicenter study.

Background: Compared with other lung squamous cell carcinomas (LUSC), pulmonary lymphoepithelioma-like carcinoma (pLELC) is closely associated with Epstein-Barr virus (EBV) infections with a unique molecular profile and immune microenvironment. This study was thus established to compare the treatment response and effectiveness of immunotherapy between pLELC and LUSC. Material and Methods: We enrolled 31 patients with pLELC and 116 with LUSC receiving first-line immunotherapy at three centers in China and compared the treatment response and effectiveness of immunotherapy. Propensity score matching (PSM) was used to balance the differences in baseline data between the two groups. Results: Before PSM, progression-free survival and overall survival were longer in the pLELC group than in the LUSC group (progression-free survival: hazard ratio (HR), 1.67, 95% CI: 1.05-2.63, P = 0.028; overall survival: HR, 1.90, 95% CI: 1.06-3.40, P = 0.028). This remained unchanged after PSM (progression-free survival: HR, 1.79, 95% CI: 1.02-3.15, P = 0.044; overall survival: HR, 2.20; 95% CI: 1.10-4.37, P = 0.022). Conclusion: pLELC showed a clinically meaningful survival benefit compared with traditional LUSC following immunotherapy. Subsequent studies should consider the role of the EBV in the tumor immune microenvironment of pLELC.

Baseline serum tumor markers predict the survival of patients with advanced non-small cell lung cancer receiving first-line immunotherapy: a multicenter retrospective study.

BACKGROUND: This study aimed to investigate the association between baseline serum tumor markers (STMs) (carcinoembryonic antigen [CEA], neuron-specific enolase [NSE], cytokeratin-19 fragment [CYFRA21-1], carbohydrate antigen 19-9 [CA19-9], and carbohydrate antigen 125 [CA125]) and the efficacy of first-line immunotherapy in patients with advanced non-small cell lung cancer. METHODS: This multicenter retrospective study evaluated patients who received first-line immunotherapy between July 2017 and July 2022. The endpoints were progression-free survival (PFS) and overall survival (OS), as defined by the Response Evaluation Criteria in Solid Tumors version 1.1. We divided the patients into three groups based on STM levels: Group A ≥ threefold upper limit of normal, threefold upper limit of normal > Group B > upper limit of normal, and Group C ≤ upper limit of normal. RESULTS: In total, 716 patients were included in this study. In Cox proportional hazards analyses, the STM levels in Group C were independently associated with superior PFS and OS in patients with lung adenocarcinoma (LUAD). Except for CA19-9 level, the STM levels in Group C were independently associated with superior PFS and OS in patients with lung squamous carcinoma (LUSC). Except for CEA and CA19-9 levels, the levels in Group A were independently associated with inferior PFS and OS in patients with LUAD and LUSC. CONCLUSIONS: Serum CEA, NSE, CYFRA21-1, and CA125 levels can predict PFS and OS in patients with LUAD and LUSC, and serum CA19-9 levels can predict PFS and OS in patients with LUAD. The higher the serum NSE, CYFRA21-1, and CA125 levels, the worse the PFS and OS in patients with LUAD and LUSC. In addition, the higher the serum CA19-9 level, the worse the OS in patients with LUAD.

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions.

BACKGROUND: Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. RESULTS: We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F1 hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species. CONCLUSIONS: We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.

Pyroptotic gasdermin exists in Mollusca and is vital to eliminating bacterial infection.

Gasdermin (GSDM) is a family of proteins that execute pyroptosis in vertebrate. In invertebrate, pyroptotic GSDM was documented only in coral. Recent studies identified abundant GSDM structural homologs in Mollusca, but their functions are unclear. Herein, we report a functional GSDM from Pacific abalone Haliotis discus (HdGSDME). HdGSDME is specifically activated by abalone caspase 3 (HdCASP3) cleavage at two distinct sites, generating two active isoforms with pyroptotic and cytotoxic activities. HdGSDME possesses evolutionarily conserved residues that proved to be essential to the N-terminal pore-formation and C-terminal auto-inhibition capacities. Bacterial challenge activates the HdCASP3-HdGSDME pathway and induces pyroptosis and extracellular traps in abalone. Blockage of the HdCASP3-HdGSDME axis promotes bacterial invasion and host mortality. Collectively, this study reveals the existence of functionally conserved and yet distinct-featured GSDM in Mollusca and provides insights into the function and evolution of invertebrate GSDM.

Quantile-Adaptive Sufficient Variable Screening by Controlling False Discovery.

Sufficient variable screening rapidly reduces dimensionality with high probability in ultra-high dimensional modeling. To rapidly screen out the null predictors, a quantile-adaptive sufficient variable screening framework is developed by controlling the false discovery. Without any specification of an actual model, we first introduce a compound testing procedure based on the conditionally imputing marginal rank correlation at different quantile levels of response to select active predictors in high dimensionality. The testing statistic can capture sufficient dependence through two paths: one is to control false discovery adaptively and the other is to control the false discovery rate by giving a prespecified threshold. It is computationally efficient and easy to implement. We establish the theoretical properties under mild conditions. Numerical studies including simulation studies and real data analysis contain supporting evidence that the proposal performs reasonably well in practical settings.

Survival on land: A dark-grown seedling searching for path.

To initiate its development into a plant, a small dark-grown seedling (prior to its emergence from the ground) must penetrate through the growth media. The path that the seedling takes during this journey has yet to be explained. As such, we conducted non-destructive tests using CT scans to observe the growth of dark-grown seedlings in soil over time; we also developed a model to simulate the dynamics of an emerging seedling, and to examine effects of various growth medium conditions, including Lunar soil. It was previously postulated that, with gravitropism in a terrestrial growth medium, a dark-grown seedling would grow directly upright. However, our CT scan results showed that dark-grown soybean seedlings departed from the vertical path in soil, as far as a lateral distance of approximately 10 mm. The phenomenon of the non-straight path was also demonstrated by the model results. Through simulations, we found that an emerging seedling naturally weaves through the particles of growth medium, in search for the path of least resistance. As a result, the seedling ends up travelling a longer distance. Compared with a seedling that was artificially forced to take a straight path in a growth media, the seedling taking the natural path encountered significantly lower resistances (20% lower) from the growth medium, while travelled 12% longer distance during the emergence process. A seedling encountered a much higher impedance in Lunar soil. Our results suggest that taking the path of least resistance, in addition to shaping and orientating itself for mechanical advantage, are strategies evolved by plant species that have contributed to its vast success. An understanding of plant behavior and survival strategies on Earth lay the foundation for future research in agriculture in novel environments, including on celestial bodies.

Facile Hydrogels of AIEgens Applied as Reusable Sensors for In Situ and Early Warning of Metallic Corrosion.

Early detection of metallic corrosion is one considerable method to reduce imperceptible disasters nowadays. Fluorescent coatings with high sensitivity and long lifetimes for use in the early detection of metallic corrosion are in high demand, but they are presently difficult to prepare. Inspired by the chameleon's skin, which is capable of switching its color in different atmospheres sensitively and reversibly, we proposed herein a facile and universal all-in-one strategy of combining the fluorescent sensitivity and dynamic hydrogen bonds in a hydrogel to develop a reusable corrosion detection tape to cover metal surfaces. The fluorescent hydrogel tape was constructed using free radical copolymerization of monomers [hydroxyethyl methylacrylate (HEMA) and tetraphenylethene derivatives (TPEPy)]. Due to the aggregation-induced emission (AIE) behavior of TPEPy, the poly(HEMA-co-TPEPy) hydrogel is capable of monitoring the traces of corrosion via the release of ferric ions with a concentration as low as 10-5 M. Moreover, due to the dynamic hydrogen bonds of hydroxyethyl groups in hydrogel networks, the fluorescent hydrogel tape exhibited good adhesion and well reusability for over 10 applications to effectively warn against early corrosion of stainless steel. This non-destructive and reversible method of early corrosion detection can provide valuable signals when maintenance is needed before the metal suffers serious damage.

The evolutionary diversification and antimicrobial potential of MPEG1 in Metazoa.

Macrophage-expressed gene 1 (MPEG1) is an ancient immune effector known to exist in Cnidaria, Mollusca, Actinopterygii, and Mammalia. In this study, we examined the evolution and antibacterial potential of MPEG1 across Metazoa. By unbiased data-mining, MPEG1 orthologs were found in 11 of 34 screened phyla. In invertebrates, MPEG1 is present in the major phyla and exhibits intensive duplication. In vertebrates, class-based clades were formed by the major, generic MPEG1 (gMPEG1) in each class. However, there is a minority of unique MPEG1 (uMPEG1) from 71 species of 4 classes that clustered into a separate clade detached from all major class-based clades. gMPEG1 and uMPEG1 exhibit strong genomic collinearity and are surrounded by high-density transposons. gMPEG1 and uMPEG1 transcript expressions were most abundant in immune organs, but differed markedly in tissue specificity. Systematic analysis identified an antimicrobial peptide (AMP)-like segment in the C-terminal (CT) tail of MPEG1. Peptides based on the AMP-like regions of 35 representative MPEG1 were synthesized. Bactericidal activities were displayed by all peptides. Together these results suggest transposon-propelled evolutionary diversification of MPEG1 in Metazoa that has likely led to functional specialisation. This study also reveals a possible antimicrobial mechanism mediated directly and solely by the CT tail of MPEG1.

A Non-Canonical Teleost NK-Lysin: Antimicrobial Activity via Multiple Mechanisms.

NK-lysin (NKL) is a family of antimicrobial proteins with an important role in innate and adaptive immunity. In this study, a non-canonical NK-lysin (NKLnc) was identified in the Japanese flounder (Paralichthys olivaceus), which shares low sequence identities (15.8-20.6%) with previously reported fish NKLs and was phylogenetically separated from the canonical NKLs in teleost. NKLnc expression was upregulated in flounder tissues during bacterial infection, and interference with NKLnc expression impaired the ability of flounder cells to eliminate invading bacteria. When expressed in Escherichia coli, NKLnc was detrimental to the host cells. P35, a peptide derived from the saposin B domain (SapB) of NKLnc, bound major bacterial surface molecules and killed both Gram-negative and Gram-positive bacteria by inflicting damage to bacterial cell structure and genomic DNA. The bactericidal activity, but not the bacteria-binding capacity, of P35 required the structural integrity of the alpha 2/3 helices in SapB. Furthermore, P35 induced the migration of flounder peripheral blood leukocytes, inhibited bacterial dissemination in fish tissues, and facilitated fish survival after bacterial challenge. Together our study reveals that NKLnc plays an important part in flounder immune defense, and that NKLnc peptide exerts an antimicrobial effect via multiple mechanisms by targeting both bacteria and fish cells.

Impairment of IgG Fc functions promotes tumor progression and suppresses NK cell antitumor actions.

Natural killer (NK) cells mediate antibody dependent cytotoxic killing of cancer cells via cross-linking FcγR on NK cells with IgG-Fc. Studies have shown that the single-hinge cleaved IgGs (scIgGs) have dysfunctional Fc and failed engagement with FcγRs on immune cells. However, little is known about how scIgGs impact on antitumor immunity in the tumor microenvironment. In this study, we revealed a significant association of tumor scIgGs with tumor progression and poor outcomes of breast cancer patients (n = 547). Using multiple mouse tumor models, we demonstrated that tumor scIgGs reduced NK cell cytotoxic activities and resulted in aggressive tumor progression. We further showed that an anti-hinge specific monoclonal antibody (AHA) rescued the dysfunctional Fc in scIgGs by providing a functional Fc and restored NK cell cytotoxic activity. These findings point to a novel immunotherapeutic strategy to enhance Fc engagement with FcγRs for activation of anticancer immunity.

New insights into the evolutionary dynamic and lineage divergence of gasdermin E in metazoa.

Gasdermin (GSDM) is a family of pore-forming proteins that induce pyroptosis. To date, the origin and evolution of GSDM in Metazoa remain elusive. Here, we found that GSDM emerged early in Placozoa but is absent in a large number of invertebrates. In the lower vertebrate, fish, three types of GSDME, i.e., GSDMEa, GSDMEb, and a previously unreported type (designated GSDMEc), were idenitied. Evolutionarily, the three GSDMEs are distinctly separated: GSDMEa is closely related to tetrapod GSDME; GSDMEb exists exclusively in fish; GSDMEc forms the lineage root of tetrapod GSDMA/B/C/D. GSDMEc shares conserved genomic features with and is probably the prototype of GSDMA, which we found existing in all tetrapod classes. GSDMEc displays fast evolutionary dynamics, likely as a result of genomic transposition. A cross-metazoan analysis of GSDME revealed that GSDMEa shares a conserved caspase recognition motif with the GSDME of tetrapods and cnidarians, whereas GSDMEb has a unique caspase recognition motif similar to that of mammalian GSDMD, and GSDMEc exhibits no apparent caspase recognition motif. Through functional test, four highly conserved residues in vertebrate GSDME proved to be essential to auto-inhibition. Together our results provide new insights into the origin, evolution, and function of metazoan GSDMs.

Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologies.

The largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game or domesticated fish. Here a high-quality chromosome-level reference genome of M. salmoides was produced by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. Ultimately, the genome was assembled into 844.88 Mb with a contig N50 of 15.68 Mb and scaffold N50 length of 35.77 Mb. About 99.9% assembly genome sequences (844.00 Mb) could be anchored to 23 chromosomes, and 98.03% assembly genome sequences could be ordered and directed. The genome contained 38.19% repeat sequences and 2693 noncoding RNAs. A total of 26,370 protein-coding genes from 3415 gene families were predicted, of which 97.69% were functionally annotated. The high-quality genome assembly will be a fundamental resource to study and understand how M. salmoides adapt to novel and changing environments around the world, and also be expected to contribute to the genetic breeding and other research.

Characterization of the pathogenicity of a Bacillus cereus isolate from the Mariana Trench.

Bacillus cereus is an important opportunistic pathogen widely distributed in the environment. In this study, we reported the isolation and characterization of a B. cereus isolate, MB1, from the Challenger Deep of the Mariana Trench. MB1 is aerobic, motile, and able to form endospores. It possesses 5966 genes distributed on a circular chromosome and two plasmids. The MB1 genome contains 14 sets of 23S, 5S, and 16S ribosomal RNA operons, 106 tRNA genes, 4 sRNA genes, 12 genomic islands, 13 prophages, and 302 putative virulence genes, including enterotoxins and cytolysins. Infection studies showed that MB1 was able to cause acute and lethal infection in fish and mice, and was highly toxic to mammalian cells. MB1 induced, in a dose-dependent manner, pyroptotic cell death, characterized by activation of caspase-1, cleavage of gasdermin D, and release of IL-1ß and IL-18. MB1 spores exhibited swimming and haemolytic capacity, but were severely attenuated in pathogenicity, which, however, was regained to the full extent when the spores germinated under suitable conditions. Taken together, these results provide new insights into the biological and pathogenic mechanism of deep sea B. cereus.