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Citrobacter koseri is an opportnistic pathogen can cause a variety of diseases. Though the mortality rate of C. koseri infections is high but there is a paucity of clinical information on them. Furthermore, the genomic features of this species are poorly studied. Herein, we presented a patient with endogenous endophthalmitis secondary to septicaemia, and collected a C. koseri isolate, CKNJ, from the blood of the patient. Whole genome sequencing revealed that the CKNJ harbors no plasmid and codes for 67 putative virulence factors. Whole genome SNP-based phylogenetic analysis revealed that strain CKNJ was close to the strains with same isolation sites. Compared to the other sequenced C. koseri chromosomes, CKNJ contains several strain-variable regions, including one prophage and two large genomic islands. The sequencing of the first complete genome of a clinical strain from China should reinforce our understanding of the genomic features and pathogenicity of this invasive infection-causing C. koseri with clinical significance.

OBJECTIVE The dynamic adaptive immune responses elicited by the inactivated virus vaccine, CoronaVac, remain elusive. METHODS In a prospective cohort of 100 SARS-CoV-2 naïve healthcare professionals who received two doses of CoronaVac, we analyzed SARS-CoV-2-specific humoral and cellular responses at four different timepoints, including before vaccination (T1), 2 weeks after the first dose (T2), 2 weeks after the booster dose (T3), and 8-10 weeks post the booster dose (T4). SARS-CoV-2-specific antibodies, serum neutralizing activities, peripheral B cells, CD4+ and CD8+ T cells, and their memory subsets were simultaneously measured in this cohort. RESULTS SARS-CoV-2 Spike-specific IgG responses reached the peak (geometric mean titer [GMT] 54827, 30969-97065) after two doses and rapidly declined (GMT 502, 212-1190) at T4, whereas suboptimal IgA responses were detected (GMT 5, 2-9). Spike-specific circulating B cells (0.60%, 0.46-0.73% of total B cells) and memory B cells (1.18%, 0.92-1.44% of total memory B cells) were effectively induced at T3 and sustained over time (0.33%, 0.23-0.43%; 0.87%, 0.05-1.67%, respectively). SARS-CoV-2-specific circulating CD4+ T cells (0.57%, 0.47-0.66%) and CD8+ T cells (1.29%, 1.04-1.54%) were detected at T3. At T4, 0.78% (0.43-1.20%) of memory CD4+ T cells and 0.68% (0.29-1.30%) of memory CD8+ T cells were identified as SARS-CoV-2 specific, while 0.62% (0.51-0.75%) of CD4+ T cells and 0.47% (0.38-0.58%) of CD8+ T cells were SARS-CoV-2 specific terminally differentiated effector memory cells. Furthermore, age and interval between doses affected the magnitude of CoronaVac induced immune responses. SARS-CoV-2 memory CD4+ T cells was strongly associated with both RBD-specific memory B cells (r=0.87, p, Graphical abstract Image 1

Marine bacterial community plays a vital role in the formation of the hypoxia zone in coastal oceans. Yet, their dynamics in the seasonal hypoxia zone of the Bohai Sea (BHS) are barely studied. Here, the 16S rRNA gene-based high-throughput sequencing was used to explore the dynamics of their diversity, structure, and function as well as driving factors during the gradual deoxygenation process in the BHS. Our results evinced that the bacterial community was dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Cyanobacteria, etc. The abundant subcommunity dominated in the number of sequences (49%) while the rare subcommunity dominated in the number of species (99.61%). Although abundant subcommunity accounted for most sequences, rare subcommunity possessed higher diversity, richness and their population dramatically changed (higher turnover) during the hypoxia transition. Further, co-occurrence network analysis proved the vital role of rare subcommunity in the process of community assembly. Additionally, beta diversity partition revealed that both subcommunities possessed a higher turnover component than nestedness and/or richness component, implying species replacement could explain a considerable percentage of community variation. This variation might be governed by both environmental selection and stochastic processes, and further, it influenced the nitrogen cycle (PICRUSt-based prediction) of the hypoxia zone. Overall, this study provides insight into the spatial-temporal heterogeneity of bacterial and their vital role in biogeochemical cycles in the hypoxia zone of the BHS. These findings will extend our horizons about the stabilization mechanism, feedback regulation, and interactive model inside the bacterial community under oxygen-depleted ecosystems.

In rice, high-temperature stress (HT) during flowering results in decreased grain yield via a reduction in spikelet fertility; however, the effect of plant water status on spikelet fertility under HT remains unknown. To investigate the relationship between spikelet water status and spikelet fertility under HT, two experiments were performed under temperature-controlled conditions using four genotypes with varying tolerance to HT. Rice plants were exposed to HT for seven consecutive days during the flowering stage under three soil water treatments (soil water potential 0, −20, and −40 kPa), as well as under hydroponic conditions in a separate experiment. HT significantly decreased spikelet fertility, pollen fertility, and anther dehiscence under each of the three water treatments. HT significantly increased the spikelet transpiration rate, and this change was accompanied by a significant decrease in the internal temperature of the spikelets. HT decreased pollen grain diameter in heat-sensitive genotypes. HT had varying effects on the water potential of panicles and anthers but increased anther soluble-sugar concentration. Different aquaporin genes showed different expression profiles under HT, and the expression levels of PIPs for plasma membrane intrinsic proteins and TIPs for tonoplast intrinsic proteins increased in anthers but decreased in glumes. Correlation analyses showed that anther dehiscence and pollen (spikelet) fertility were tightly associated with anther water status, and the expression levels of almost all anther aquaporin genes were significantly correlated with anther dehiscence under HT. In summary, an increased spikelet transpiration rate and decreased internal spikelet temperature were associated with alleviation of the effects of HT in rice genotypes with varying degrees of heat tolerance, and the response of spikelet water status to HT, involving increased total expression of aquaporins and soluble sugar content, thereby improved pollen fertility, anther dehiscence, and spikelet fertility, especially in heat-resistant genotypes. The heat-resistant genotypes N22 and SY63 may adopt different approaches to reduce heat damage.

Background and objective Few head-to-head evaluations of immune responses to different vaccines have been reported. Methods Surrogate virus neutralization test (sVNT) antibody levels of adults receiving either two doses of BNT162b2 (n = 366) or CoronaVac (n = 360) vaccines in Hong Kong were determined. An age-matched subgroup (BNT162b2 [n = 49] vs. CoronaVac [n = 49]) was tested for plaque reduction neutralization (PRNT) and spike-binding antibody and T-cell reactivity in peripheral blood mononuclear cells. Results One month after the second dose of vaccine, BNT162b2 elicited significantly higher PRNT50 , PRNT90 , sVNT, spike receptor binding, spike N-terminal domain binding, spike S2 domain binding, spike FcR binding and antibody avidity levels than CoronaVac. The geometric mean PRNT50 titres in those vaccinated with BNT162b2 and CoronaVac vaccines were 251.6 and 69.45, while PRNT90 titres were 98.91 and 16.57, respectively. All of those vaccinated with BNT162b2 and 45 (91.8%) of 49 vaccinated with CoronaVac achieved the 50% protection threshold for PRNT90. Allowing for an expected seven-fold waning of antibody titres over 6 months for those receiving CoronaVac, only 16.3% would meet the 50% protection threshold versus 79.6% of BNT162b2 vaccinees. Age was negatively correlated with PRNT90 antibody titres. Both vaccines induced SARS-CoV-2-specific CD4+ and CD8+ T-cell responses at 1 month post-vaccination but CoronaVac elicited significantly higher structural protein-specific CD4+ and CD8+ T-cell responses. Conclusion Vaccination with BNT162b2 induces stronger humoral responses than CoronaVac. CoronaVac induces higher CD4+ and CD8+ T-cell responses to the structural protein than BNT162b2.

This study aims to evaluate the effect of non‐alcoholic fatty liver disease (NAFLD) on the susceptibility and consequences of coronavirus disease 2019 (COVID‐19). We retrospectively collected data from 218 adult COVID‐19 patients who showed no evidence of excessive alcohol consumption and underwent abdominal ultrasound examinations. Of these patients, 39.4% patients had been diagnosed with NAFLD, which indicates a much higher prevalence of NAFLD than that reported in the general population. Significantly elevated white blood cell count (p = 0.008), alanine aminotransferase (p = 0.000), aspartate aminotransferase (p = 0.006) and C reactive protein (p = 0.012) were found in the patients with NAFLD. These patients also had significantly higher proportions of hypertension (p = 0.006) and diabetes (p = 0.049) than the non‐NAFLD cases. No significant differences existed in the severity, mortality, viral shedding time and length of hospital stay between patients with or without NAFLD in the sample population. However, subgroup analyses found that in patients with normal body mass index (BMI), NAFLD sufferers were more likely to experience a severe event (30.0% vs 11.5%, p = 0.021). Kaplan‐Meier curve (log‐rank p = 0.017) and Cox regression (HR = 3.26, 95% CI: 1.17–9.04, p = 0.023) analyses confirmed that before and after adjusting for gender, age and comorbidities, NAFLD patients with normal BMI had a higher incidence of suffering severe events. People with NAFLD may have a higher proportion of COVID‐19. NAFLD may be correlated with the severity of COVID‐19 patients in the normal BMI group.

Emx1IRES-Cre, D6-Cre and hGFAP-Cre are commonly used to conditionally manipulate gene expression or lineage tracing because of their specificity in the dorsal telencephalon during early neurogenesis as previously described. However, the spatiotemporal differences in Cre recombinase activity would lead to divergent phenotypes. Here, we compared the patterns of Cre activity in the early embryos among the three lines by mating with reporter mice. The activities of Emx1IRES-Cre, D6-Cre and hGFAP-Cre were observed in the dorsal telencephalon, starting from approximately embryonic day 9.5, 11.5 and 12.5, respectively. Although all the three lines have activity in radial glial cells, Emx1IRES-Cre fully covers the dorsal and medial telencephalon, including the archicortex and cortical hem. D6-Cre is highly restricted to the dorsal telencephalon with anterior-low to posterior-high gradients, partially covers the hippocampus, and absent in the cortical hem. Moreover, both Emx1IRES-Cre and hGFAP-Cre exhibit Cre activity outside the dorsal neocortex. Meanwhile, we used the three Cre lines to mediate Dicer knockout and observed inconsistent phenotypes, including discrepancies in radial glial cell number, survival and neurogenesis in the neocortex and hippocampus. Together we proved differences in Cre activity can perturb the resultant phenotypes, which aid researchers in appropriate experimental design.

Red ginseng (RG) is mainly divided into Chinese red ginseng (CRG), American red ginseng (ARG), and Korean red ginseng (KRG). The three red ginsengs exhibit good bioactivities because of rich rare ginsenosides than ginseng. Additionally, there are obvious distinctions from the chemical composition and content of CRG, ARG, and KRG, thereby leading to differences in various application, together with a wide range of red ginseng products on the market with uneven quality. Therefore, people can’t distinguish high-quality red ginseng well at the time of purchase. Just currently, there have been no systematic reports on processing technologies, chemical compositions, and bioactivities among the three red ginsengs. Accordingly, a comprehensive description of CRG, ARG, and KRG is necessarily performed to show their similarities and differences. In particular, the processing technologies of the three red ginsengs are summarized and compared in detail, which provides appropriate reference for the technical improvement of processing red ginseng in the future. More importantly, it is helpful for people to understand the similarities and differences from the three red ginsengs better to buy genuine red ginseng products they want.

The genus Phyllothelys Wood-Mason (Mantodea: Hymenopodidae: Phyllothelyinae) includes 18 species in the world, among which 12 species were recorded in China. However, most Phyllothelys species have...

Amyloid-β peptide (Aβ) aggregation is the hallmark of Alzheimer’s disease (AD). The imbalance between the production and clearance of Aβ results in the accumulation and aggregation of Aβ in the brain. Thus far, few drugs are available for AD treatment, but exercise has been recognized for its cognition-enhancing properties in AD patients. The underlying mechanisms remain unclear. Our recent study showed that long-term running exercise could activate the lysosomal function in the brains of mice. In this study, we investigated whether exercise could reduce Aβ accumulation by activating lysosomal function in APP/PSEN1 transgenic mice. Started at the age of 5 months, the mice were trained with a running wheel at the speed of 18 r/min, 40 min/d, 6 d/week for 5 months, and were killed at the end of the 10th month, then brain tissue was collected for biochemical analyses. The cognitive ability was assessed in the 9th month. We showed that long-term exercise significantly mitigated cognitive dysfunction in AD mice, accompanied by the enhanced lysosomal function and the clearance of Aβ in the brain. Exercise significantly promoted the nuclear translocation of transcription factor EB (TFEB), and increased the interaction between nuclear TFEB with AMPK-mediated acetyl-CoA synthetase 2, thus enhancing transcription of the genes associated with the biogenesis of lysosomes. Exercise also raised the levels of mature cathepsin D and cathepsin L, suggesting that more Aβ peptides could be degraded in the activated lysosomes. This study demonstrates that exercise may improve the cognitive dysfunction of AD by enhancing lysosomal function.

Background: C-C motif ligand 5 (CCL5) is reported to play a key role in acute and chronic liver diseases. However, the association between CCL5 and chronic hepatitis B (CHB) remains to be explored. We aimed to investigate the CCL5 expression in the liver tissues of CHB patients and compared the CCL5 expression among CHB patients with different stages of liver inflammation and fibrosis. Methods: Liver tissue specimens from 51 CHB patients who underwent liver biopsy and twelve healthy liver donors were included in the present study. CCL5 expression in the liver tissues was analyzed using immunohistochemistry. The hepatic inflammation grades and fibrotic stages of CHB patients were assessed by the Scheuer classification system. Results: Livers of CHB patients exhibited significantly accumulated CCL5+ cells when compared to those of healthy controls (42.80 ± 4.37 vs. 7.25 ± 0.99/HPF, P < .001). CHB patients with higher hepatic inflammation grades had more CCL5+ cells in their livers than those with lower grades (P < .05). However, the numbers of CCL5+ cells were not correlated with the fibrotic stages in CHB patients (r = .073, P = .61). The number of CCL5+ cells in the liver tissues of CHB patients was positively correlated with alanine transaminase levels (r = .278, P = .041) and aspartate aminotransferase levels (r = .328, P = .009). Conclusions: CHB patients have a significant accumulation of CCL5+ cells in the liver, and CCL5 may play a pathological role in hepatic inflammation of CHB.

An experiment was conducted to elucidate the negative impacts of drought on growth and hormones of Leymus chinensis. Results showed that plant height, dry weight and zeatin riboside contents declined under drought condition over the control. Whereas indole acetic acid, gibberellic acid and abscisic acid contents were augmented under stress environment over the normal conditions. Exogenous application of NPK and/or 5-aminolevulinic acid (ALA) depicted more pronouncing response to alleviate adversities of drought. Conclusively, foliar application of 'Urea (1%) + KH2PO4 (1%) + ALA (50 mg/l)' produced better results under drought stress on the evaluated parameters.

Global concerns arose as the emerged and rapidly spreading SARS-CoV-2 variants might escape host immunity induced by vaccination. In this study, a heterologous prime-boost immunization strategy for COVID-19 was designed to prime with a DNA vaccine encoding wild type (WT) spike protein receptor-binding domain (RBD) followed by S1 protein-based vaccine in rabbits. Four vaccine-elicited rabbit monoclonal antibodies (RmAbs), including 1H1, 9H1, 7G5, and 5E1, were isolated for biophysical property, neutralization potency and sequence analysis. All RmAbs recognized RBD or S1 protein with KD in the low nM or sub nM range. 1H1 and 9H1, but neither 7G5 nor 5E1, can bind to all RBD protein variants derived from B.1.351. All four RmAbs were able to neutralize wild type (WT) SARS-CoV-2 strain in pseudovirus assay, and 1H1 and 9H1 could neutralize the SARS-CoV-2 WT authentic virus with IC50 values of 0.136 and 0.026 μg/mL, respectively. Notably, 1H1 was able to neutralize all 6 emerging SARS-CoV-2 variants tested including D614G, B.1.1.7, B.1.429, P.1, B.1.526, and B.1.351 variants, and 5E1 could neutralize against the above 5 variants except P.1. Epitope binning analysis revealed that 9H1, 5E1 and 1H1 recognized distinct epitopes, while 9H1 and 7G5 may have overlapping but not identical epitope. In conclusion, DNA priming protein boost vaccination was an effective strategy to induce RmAbs with potent neutralization capability against not only SARS-CoV-2 WT strain but also emergent variants, which may provide a new avenue for effective therapeutics and point-of-care diagnostic measures.

Nature's biocatalytic processes are driven by photosynthesis, whereby photosystems I and II are connected in series for light-stimulated generation of fuel products or electricity. Externally supplying electricity directly to the photosynthetic electron transfer chain (PETC) has numerous potential benefits, although strategies for achieving this goal have remained elusive. Here we report an integrated photo-electrochemical architecture which shuttles electrons directly to PETC in living cyanobacteria. The cathode of this architecture electrochemically interfaces with cyanobacterial cells that have a lack of photosystem II activity and cannot perform photosynthesis independently. Illumination of the cathode channels electrons from an external circuit to intracellular PETC through photosystem I, ultimately fueling cyanobacterial conversion of CO2 into acetate. We observed acetate formation when supplying both illumination and exogenous electrons under intermittent conditions (e.g., in a 30 s supply plus 30 min interval condition of both light and exogenous electrons). The energy conversion efficiency for acetate production under programmed intermittent LED illumination (400–700 nm) and exogenous electron supply reached ca. 9%, when taking into account the number of photons and electrons received by the biotic system, and ca. 3% for total photons and electrons supplied to the cyanobacteria. This approach is applicable for generating various CO2 reduction products by using engineered cyanobacteria, one of which has enabled electrophototrophic production of ethylene, a broadly used hydrocarbon in the chemical industry. The resulting bio-electrochemical hybrid has the potential to produce fuel chemicals with numerous potential advantages over standalone natural and artificial photosynthetic approaches.

Dysregulated lipid metabolism represents an important metabolic alteration in cancer. Fatty acids, cholesterol, and phospholipid are the three most prevalent lipids that act as energy producers, signaling molecules, and source material for the biogenesis of cell membranes. The enhanced synthesis, storage, and uptake of lipids contribute to cancer progression. The rewiring of lipid metabolism in cancer has been linked to the activation of oncogenic signaling pathways and cross talk with the tumor microenvironment. The resulting activity favors the survival and proliferation of tumor cells in the harsh conditions within the tumor. Lipid metabolism also plays a vital role in tumor immunogenicity via effects on the function of the noncancer cells within the tumor microenvironment, especially immune‐associated cells. Targeting altered lipid metabolism pathways has shown potential as a promising anticancer therapy. Here, we review recent evidence implicating the contribution of lipid metabolic reprogramming in cancer to cancer progression, and discuss the molecular mechanisms underlying lipid metabolism rewiring in cancer, and potential therapeutic strategies directed toward lipid metabolism in cancer. This review sheds new light to fully understanding of the role of lipid metabolic reprogramming in the context of cancer and provides valuable clues on therapeutic strategies targeting lipid metabolism in cancer., Lipid metabolic reprogramming‐mediated crosstalk between cancer cells and tumor microenvironment contributes to cancer progression. Stromal cells, such as adipocyte, CAF, epithelia cells contribute to lipid metabolic reprogramming in cancer cells. Cancer cells undergo lipid metabolism rewiring to generate building materials for membrane, lipid second messenger and energy supply. Cancer cells can also secret lipid metabolites to affect immune cell functions, creating a tumor‐favoring immune microenvironment.

Significance As a genetic malignancy, retinoblastoma (Rb) is caused by RB1 mutations; however, its developmental origin and drug agents for human Rb remain largely unexplored. Here we describe an innovative Rb organoid model derived from human embryonic stem cells with a biallelic mutagenesis of the RB1 gene. We identify tumorigenic growth in the Rb organoids, as well as properties consistent with human primary Rb. We confirm that the Rb cell of origin stemmed from ARR3+ maturing cone precursor cells and SYK inhibitors displaying a significant therapeutic response. Our elegant in-dish Rb organoid model can be used to efficiently and effectively dissect the origin of Rb and mechanisms of Rb tumorigenesis, as well as screen novel therapies., Retinoblastoma (Rb) is the most prevalent intraocular malignancy in children, with a worldwide survival rate

Owing to the formation of aggregation and gelation during storage, certain proteins and peptides exhibit limited applications in aqueous protein food products. The purpose of this study was to investigate the influence of homogenization and xanthan gum addition on the dispersion stability of Mytilus edulis hydrolysate (PHM). High-pressure homogenization (HPH) at 360 and 40 bar in the first and second values, respectively, and adding xanthan gum at a concentration of 1 mg/mL showed significantly improvement on the stability of the PHM solution. PHM-xanthan gum solutions (PHMX) showed the highest polypeptide precipitation rate and turbidity retention rate compared with those of PHM. Moreover, the centrifugal precipitation rate of PHMX without HPH was higher than that of homogeneous PHMX. After HPH treatment at 400 bar, the percentage of smaller particles in PHM and PHMX was increased, the aqueous system became more uniform, and the fluorescence intensity reached its maximum. HPH pre-treatment improved the polypeptide dispersion stability and turbidity retention rate of PHM and PHMX and reduced the fluorescence intensity. The interactions of xanthan gum and polypeptide render the network microstructure more uniform under the conditions of homogenization, thus improving the dispersion stability of PHMX solutions. Therefore, under the premise of adding xanthan gum, HPH can better enhance the dispersion stability of the polypeptide in PHM.

Previous study has shown that Hibiscus sulfite oxidase (SO) interacts with Hibiscus chlorotic ringspot virus (HCRSV) coat protein (CP) and triggers sulfur enhanced defense (SED). In this study, we show the interaction of Arabidopsis SO (AtSO) and Turnip crinkle virus (TCV) CP in Arabidopsis thaliana plants. We identified the binding sites of TCV CP (W274) and AtSO (D223) using bioinformatics and confirmed it experimentally. Mutation of binding site W274 to A274 in TCV CP resulted in failure of TCV infection. TCV accumulation in SO over-expression (SO_OE) plants was lower than that in wild-type (WT) and SO knock-out (SO_KO) plants at 7 dpi but reached a level similar to that of WT and SO_KO plants at 10 dpi. AtSO competed with Argonaute 1 (AGO1) for TCV CP binding in vitro. AtSO may serve as an anti-viral factor through sequestering TCV CP for binding with AGO1 and confers virus resistance.

Allomantispa Liu et al., 2015 is the only extant genus of the mantidfly subfamily Drepanicinae from Eurasia, being endemic to the Oriental region. It currently consists of only two species from southeastern Tibet and northern Myanmar, respectively. Here we describe a new species of this rarely observed mantidfly genus, namely Allomantispa coniprocessa sp. nov. from Yunnan, China. Interestingly, the new species displays distinctive sexual dimorphic characters on the pronotum. The molecular identification reveals obvious genetic divergence between the allopatric individuals of the new species. Their morphological variations are illustrated and compared. In addition, some characters with taxonomic or phylogenetic significance present on the pronotum, the abdomen and the genitalia in Allomantispa are also discussed. Our finding updates the morphological and distributional information on Allomantispa and implies a more diverse fauna of this genus in the Oriental region than previously assumed.

The gamma-glutamyl transpeptidase (GGT) to platelet ratio (GPR) was proposed as a novel index for predicting liver inflammation in chronic hepatitis B (CHB) patients. We aimed to investigate GPR for predicting significant liver inflammation in CHB patients with normal (≤1×upper limit of normal, ULN) or mildly elevated (≤2×ULN) alanine transaminase (ALT).431 treatment-naïve CHB patients with normal or mildly elevated ALT who underwent liver biopsy were enrolled. Comparision of GPR and other parameters for significant liver inflammation (G≥3).For patients with ALT≤2×ULN, the receiver-operating characteristic curves (AUROCs) of GPR in predicting significant liver inflammation were 0.837 (95%CI 0.796 to 0.878), 0.860 (95%CI 0.809 to 0.910) and 0.809 (95%CI 0.739 to 0.878) in the entire patients, HBeAg positive and HBeAg negative CHB patients, respectively. The diagnostic performance of GPR was higher than ALT (P0.001, P0.001, respectively), aspartate transaminase (AST) (P=0.001, P=0.003, respectively) and GGT (P=0.002, P=0.002, respectively) in the entire and HBeAg positive patients, but was comparable with AST (P=0.096) and GGT (P=0.273) in the HBeAg negative CHB patients. For patients with ALT≤1×ULN, the diagnostic accuracy of GPR was significantly higher than ALT, AST and GGT in the entire (P0.001, P=0.008 and P=0.043, respectively) and HBeAg positive CHB patients (P0.001, P=0.009 and P=0.024, respectively), while was comparable to AST (P=0.209) and GGT(P=0.555) in the HBeAg negative CHB patients.GPR has a better diagnostic value than conventional parameters to predict significant liver inflammation in CHB patients with normal or mildly elevated ALT levels, especially for HBeAg positive CHB.

MotivationThe mutations of cancers can encode the seeds of their own destruction, in the form of T-cell recognizable immunogenic peptides, also known as neoantigens. It is computationally challenging, however, to accurately prioritize the potential neoantigen candidates according to their ability of activating the T-cell immunoresponse, especially when the somatic mutations are abundant. Although a few neoantigen prioritization methods have been proposed to address this issue, advanced machine learning model that is specifically designed to tackle this problem is still lacking. Moreover, none of the existing methods considers the original DNA loci of the neoantigens in the perspective of 3D genome which may provide key information for inferring neoantigens’ immunogenicity.ResultsIn this study, we discovered that DNA loci of the immunopositive and immunonegative MHC-I neoantigens have distinct spatial distribution patterns across the genome. We therefore used the 3D genome information along with an ensemble pMHC-I coding strategy, and developed a group feature selection-based deep sparse neural network model (DNN-GFS) that is optimized for neoantigen prioritization. DNN-GFS demonstrated increased neoantigen prioritization power comparing to existing sequence-based approaches. We also developed a webserver named deepAntigen (http://yishi.sjtu.edu.cn/deepAntigen) that implements the DNN-GFS as well as other machine learning methods. We believe that this work provides a new perspective toward more accurate neoantigen prediction which eventually contribute to personalized cancer immunotherapy.Availability and implementationData and implementation are available on webserver: http://yishi.sjtu.edu.cn/deepAntigen.Supplementary informationSupplementary data are available at Bioinformatics online.

Wenzhou virus (WENV) was first identified in rodents and Asian house shrews in Wenzhou, Zhejiang province, China. However, little is known about the prevalence of WENV infections in humans in China. To determine the threat that WENV may pose to humans, we determine the seroprevalence of WENV in healthy individuals in China in this study. Cross-reactivities of nucleoprotein (NP) were detected between Lymphocytic choriomeningitis virus (LCMV) and WENV using Western blot and ELISA assy. The prevalence of specific IgG antibodies against WENV NP was investigated in different age groups of 830 healthy individuals aged 0–70 years old in China using a competition ELISA assay. The results indicate that WENV and LCMV share cross-reactive epitopes between NPs. The total seroprevalence of WENV in healthy adults was 4.6%, with 3.6% (8/221) for individuals 15–44 years of age, 5.4% (17/317) for individuals 45–59 years of age, and 4.1% (4/98) for older adults over 60. The total seroprevalence of WENV in children under age 15 was 1.5%, with 2.9% (1/34) in children aged 2–5 years, and 2.2% in 5–14 years (2/91). The finding suggests that WENV or WENV-like virus may sporadically infect humans of China., Highlights • Scientific question: Wenzhou virus (WENV) is a newly identified virus has human-infection potential. However, its transmission risk in human population has not been well addressed. • Evidence before this study: Rodents can carry and transmit viruses to humans and display little or no ill. WENV was first isolated from rodents and Asian house shrews in Wenzhou, Zhejiang Province, China in 2014, and then in rodents in Southeast. Some patients with respiratory symptoms tested positive for the WENV and anti-WENV IgG antibodies were detected in some healthy individuals in Southeast. Broader studies are warranted to evaluate the frequency of WENV infection in the human population. • New findings: In this study, cross-reactivity between WENV and lymphocytic choriomeningitis virus (LCMV), another well-known Arenavirus, was assessed and competitive ELISAs based on the WENV nucleoprotein (NP) were developed. Anti-NP IgG antibodies in sera from 830 healthy individuals were screened. Cross-reactivities of NP exist between LCMV and WENV. Low level seroprevalence of WENV were determined in healthy individuals, which suggests that WENV or WENV-like virus may sporadically infect humans. • Significance of the study: The seroprevalence data in this study indicate the possibility that WENV or WENV-like viruses can jump the species barrier to infect the human population sporadically. Our findings are informative for understanding the cross-species transmission potential and pathologic roles of WENV.

BackgroundKrüppel-like factor 8 (KLF8), a cancer-promoting factor that regulates critical gene transcription and cellular cancer-related events, has been implicated in tumor development and progression. However, the functional role of KLF8 in the pathogenesis of hepatocellular carcinoma (HCC) remains largely unknown.MethodsThe gene expression patterns and genome-wide regulatory profiles of HCC cells after KLF8 knockout were analyzed by using RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) of histone H3 lysine 27 acetylation (H3K27ac) combined with bioinformatics analysis. Transcription factor-binding motifs that recognized by KLF8 were evaluated by motif analysis. For the predicted target genes, transcriptional changes were examined by ChIP, and loss of function experiments were conducted by siRNA transfection.ResultsKLF8 functioned as a transcription repressor in HCC and mainly regulated apoptotic-related genes directly. A total of 1,816 differentially expressed genes after KLF8 knockout were identified and significantly corresponded to global changes in H3K27ac status. Furthermore, two predicted target genes, high-mobility group AT-hook 2 (HMGA2) and matrix metalloproteinase 7 (MMP7), were identified as important participants in KLF8-mediated anti-apoptotic effect in HCC. Knockout of KLF8 enhanced cell apoptosis process and caused increase in the associated H3K27ac, whereas suppression HMGA2 or MMP7 attenuated these biological effects.ConclusionsOur work suggests a novel role and mechanism for KLF8 in the regulation of cell apoptosis in HCC and facilitates the discovery of potential therapeutic targets for HCC treatment.

To further understand the effect of Kuroshio intrusion on phytoplankton community structure in the northeastern South China Sea (NSCS, 14°-23°N, 114°-124°E), one targeted cruise was carried out from July to August, 2017. A total of 79 genera and 287 species were identified, mainly including Bacillariophyta (129 species), Pyrrophyta (150 species), Cyanophyta (4 species), Chrysophyta (3 species) and Haptophyta (1 species). The average abundance of phytoplankton was 2.14×103 cells/L, and Cyanobacterium was dominant species accounting for 86.84% of total phytoplankton abundance. The abundance and distribution of dominant Cyanobacterium were obviously various along the flow of the Kuroshio, indicating the Cyanobacterium was profoundly influenced by the physical process of the Kuroshio. Therefore, Cyanobacterium could be used to indicate the influence of Kuroshio intrusion. In addition, the key controlling factors of the phytoplankton community were nitrogen, silicate, phosphate and temperature, according to Canonical Correspondence Analysis. However, the variability of these chemical parameters in the study water was similarly induced by the physical process of circulations. Based on the cluster analysis, the similarity of phytoplankton community is surprisingly divided by the regional influence of the Kuroshio intrusion, which indicated Kuroshio intrusion regulates phytoplankton community in the NSCS.

Wheat root rot caused by Gaeumannomyces graminis var. tritici (Ggt) results in severe yield losses in wheat production worldwide. However, little is known about the molecular mechanism that regulates systemic symptom development in infected wheat. Fluorescent microscopy observation of the stained wheat roots infected by Ggt showed that lesions were visible when the fungus could be detected in the endodermis, pericycle and phloem at 5 days post inoculation (dpi), and rust symptoms were visible when there was extensive fungal colonization in the root cortex at 6 dpi. Transcriptome sequencing of Ggt-inoculated wheat roots and healthy control root samples was performed at 5 dpi to identify Ggt-induced gene expression changes in wheat roots at the time of lesion formation. A total of 3973 differentially expressed genes (DEGs) were identified, of which 1004 (25.27%) were up-regulated and 2969 (74.73%) were down-regulated in Ggt-inoculated wheat roots compared with those in control roots. GO annotation and KEGG pathway analysis of these DEGs revealed that many of them were associated with pathogen resistance, such as those involved in oxidation-reduction process, tryptophan biosynthesis process, and phenylpropanoid biosynthesis process. Analysis of DEGs revealed that 15 DEGs were involved in cellular regulation, 57 DEGs in signal transduction pathways, and 75 DEGs in cell wall reorganization, and 23 DEGs are pathogenesis-related proteins. Reverse transcription quantitative PCR (RT-qPCR) of 13 of those DEGs showed that these genes may play roles in wheat resistance against Ggt. Overall, this study represents the first transcriptional profiling of wheat roots in response to Ggt infection and further characterization of DEGs identified in this study may lead to better understanding of resistance against take-all in wheat.

Summary A major challenge to the development of therapies for human retinal degenerative diseases is the lack of an ideal preclinical model because of the physiological differences between humans and most model animals. Despite the successful generation of a primate model through germline knockout of a disease-causing gene, the major issues restricting modeling in nonhuman primates (NHPs) are their relatively long lifespan, lengthy gestation, and dominant pattern of singleton births. Herein, we generated three cynomolgus macaques with macular in situ knockout by subretinal delivery of an adeno-associated virus (AAV)-mediated CRISPR-Cas9 system targeting CNGB3, the gene responsible for achromatopsia. The in vivo targeting efficiency of CRISPR-Cas9 was 12%–14%, as shown by both immunohistochemistry and single-cell transcriptomic analysis. Through clinical ophthalmic examinations, we observed a reduced response of electroretinogram in the central retina, which corresponds to a somatic disruption of CNGB3. In addition, we did not detect CRISPR-Cas9 residue in the heart, liver, spleen, kidney, brain, testis, or blood a year after administration. In conclusion, we successfully generated a NHP model of cone photoreceptor dysfunction in the central retina using an in situ CNGB3-knockout strategy., Graphical Abstract, Jin and colleagues delivered AAV-mediated CRISPR-cas9 targeting a cone-specific gene, CNGB3, to rapidly generate a non-human primate model with achromatopsia. This study provides a new approach and insights to establish a non-human primate model recapitulating human macular degeneration.

X-linked ubiquitin-specific peptidase 9 (USP9X) serves important roles in the development and progression of various human cancers. However, its role and molecular mechanism in liver cancer require further elucidation. In the present study, USP9X was found to be upregulated in liver cancer tissues. At the same time, overexpression of USP9X promoted the proliferation, invasiveness and migration of liver cancer cells, which were subsequently suppressed by USP9X silencing. On a molecular level, the results revealed that USP9X knockdown suppressed elements of the Janus kinase 2 (JAK2)/STAT3 signaling pathway, including JAK2, STAT3, matrix metalloproteinase-2 and c-Myc. By contrast, overexpression of USP9X had the opposite effect. In conclusion, the results of the present study suggest that USP9X is upregulated in patients with liver cancer, which may accelerate the proliferation, invasiveness and migration of liver cancer cells by regulating the JAK2/STAT3 signaling pathway.

The rapid wide-scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses34 globally. However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood. Here we report the assembly of a 390.38-M chromosome-level genome of fall armyworm using Pacific Bioscience (PacBio) and Hi-C sequencing technologies with scaffold N50 of 12.7 M consisting of 22260 annotated protein-coding genes. Genome-wide resequencing of 103 samples from 16 provinces in China revealed that the fall armyworm population comprises a complex inter-strain hybrid, mainly with the corn-strain genetic background and less of the rice-strain, which highlights the inaccuracy of strain identification using mitochondrial or Triosephosphate isomerase (Tpi) genes. Analysis of genes related to pesticide- and Bt-resistance showed that the risk of fall armyworm developing resistance to conventional pesticides is very high. Laboratory bioassay results showed that insects invading China carry resistance to organophosphate and pyrethroid pesticides, but are sensitive to genetically modified maize expressing Bacillus thuringiensis (Bt) toxins Cry1Ab in field experiments. Additionally, two mitochondrial fragments are inserted into the nuclear genome, and the insertion event occurred after the differentiation of the two strains. This study represents a valuable advance toward improving management strategies for fall armyworm.

Introduction Pancreatic cancer, or pancreatic duct adenocarcinoma (PDAC), remains one of the most lethal cancers and features insidious onset, highly aggressive behavior and early distant metastasis. The dense fibrotic stroma surrounding tumor cells is thought to be a shield to resist the permeation of chemotherapy drugs in the treatment of PDAC. Thus, we synthesized a pancreas-targeting paclitaxel-loaded PEGylated liposome and investigated its antitumor efficacy in the patient-derived orthotopic xenograft (PDOX) nude mouse models of PDAC. Methods The PTX-loaded PEGylated liposomes were prepared by film dispersion-ultrasonic method and modified by an N,N-dimethyl tertiary amino residue. Morphology characteristics of the PTX-loaded liposomes were observed by transmission electron microscope (TEM). The PDOX models of PDAC were established by orthotopic implantation and imaged by a micro positron emission tomography/computed tomography (PET/CT) imaging system. The in vivo distribution and antitumor study were then carried out to observe the pancreas-targeting accumulation and the antitumor efficacy of the proposed PTX liposomes. Results PTX loaded well into both modified (PTX-Lip2N) and unmodified (PTX-Lip) PEGylated liposomes with spherical shapes and suitable parameters for the endocytosis process. The PDOX nude mouse models were successfully created in which high 18F-FDG intaking regions were observed by micro-PET/CT. In addition to higher cellular uptakes of PTX-Lip2N by the BxPC-3 cells, the proposed nanoparticle had a notable penetrating ability towards PDAC tumor tissues, and consequently, the antitumor ability of PTX-Lip2N was significantly superior to the unmodified PTX-Lip in vivo PDOX models and even more effective than nab-PTX in restraining tumor growth. Conclusion The modified pancreas-targeting PTX-loaded PEGylated liposomes provide a promising platform for the treatment of pancreatic cancer.

Despite intensive efforts, a considerable proportion of colorectal cancer (CRC) patients develop local recurrence and distant metastasis. Stomatin-like protein 2 (SLP-2), a member of the highly conserved stomatin superfamily, is upregulated across cancer types. However, the biological and functional roles of SLP-2 remain elusive in CRC. Here, we report that high SLP-2 expression was found in CRC tissues and was linked to tumor progression and tumor cell differentiation. Additionally, high SLP-2 expression correlated with poor overall survival (OS) in CRC patients (p < 0.001). SLP-2 knockout (SLP-2KO), generated by CRISPR/Cas9, reduced cell growth, migration, and invasion; induced apoptosis in CRC cells; and reduced tumor xenograft growth in vivo. A 181-compound library screening showed that SLP-2KO produced resistance to JAK2 inhibitors (NVP-BSK805 and TG-101348) and a PIM1 inhibitor (SGI-1776), revealing that the JAK2-STAT3-PIM1 oncogenic pathway was potentially controlled by SLP-2 in CRC. In vitro and in vivo, TG-101348 combined with SGI-1776 was synergistic in CRC (combination index [CI] < 1). Overall, our findings suggest that SLP-2 controls the JAK2-STAT3-PIM1 oncogenic pathway, offering a rationale for a novel therapeutic strategy with combined SGI-1776 and TG-101348 in CRC. Additionally, SLP-2 may be a prognostic marker and biomarker for sensitivity to JAK2 and PIM1 inhibitors., Graphical Abstract, Liu and colleagues show that enhanced SLP-2 expression correlates with tumor progression in CRC. SLP-2 knockout by CRISPR/Cas9 inhibits CRC cell growth. PIM1i SGI-1776 and JAK2i TG-101348 are successfully identified as SLP-2-linked drugs after compound library screening. Co-treatment with the two drugs produces synergistic effect, which provides a promising therapy in CRC.

The expression of C-terminal phosphorylated Smad3 (pSmad3C) is down-regulated with the progression of liver disease. Thus, we hypothesized that pSmad3C expression may be negatively related to liver disease. To develop novel therapeutic strategies, a suitable animal model is required that will allow researchers to study the effect of Smad3 domain-specific phosphorylation on liver disease progression. The current study aimed to construct a new mouse model with the Smad3 C-terminal phosphorylation site mutation and to explore the effects of this mutation on CCl4 -induced inflammation. Smad3 C-terminal phosphorylation site mutant mice were generated using TetraOne™ gene fixed-point knock-in technology and embryonic stem cell microinjection. Resulting mice were identified by genotyping, and the effects on inflammation were explored in the presence or absence of CCl4 . No homozygous mice were born, indicating that the mutation is embryonic lethal. There was no significant difference in liver phenotype and growth between the wild-type (WT) and heterozygous (HT) mice in the absence of reagent stimulation. After CCl4 -induced acute and chronic liver damage, liver pathology, serum transaminase (ALT/AST) expression and levels of inflammatory factors (IL-6/TNF-α) were more severely altered in HT mice than in WT mice. Furthermore, pSmad3C protein levels were lower in liver tissue from HT mice. These results suggest that Smad3 C-terminal phosphorylation may have a protective effect during the early stages of liver injury. In summary, we have generated a new animal model that will be a novel tool for future research on the effects of Smad3 domain-specific phosphorylation on liver disease progression.

B cell hyperactivation and functional impairment were identified from patients with chronic hepatitis B virus (CHB) infection; however, the underlying mechanism remains unknown. Here, we aim to elucidate the mechanisms responsible for B cell hyperactivation during HBV infection. Peripheral CD19+ B cells isolated from 4 CHB patients and 4 healthy volunteers were analysed by RNA sequencing. A total of 1401 differentially expressed genes were identified from B cell transcriptome of CHB patients vs healthy volunteers. We found that B cells from CHB patients were functional impaired, with increased TLR4 expression, activated NF‐κB pathway and altered mitochondrial function. The expression of B cell activation‐related genes, including TLR4, was further validated using additional clinical samples. To further verify the role of TLR4 in B cell activation during CHB, B cell phenotypes were determined in wild‐type (WT) and TLR4−/− HBV‐carrier mice. Hyperactivated B cell and TLR4 signalling pathway were observed in WT HBV‐carrier mice, while TLR4 ablation failed to induce B cell hyperactivation, and downstream MyD88 and NF‐κB were also not altered. Taken together, TLR4 pathway plays a pivotal role in B cell hyperactivation during CHB, which might serve as a promising target for B cell function restoration.

Camptothecin (CPT) has unique anti-tumor activities, and its analogs such as irinotecan and topotecan are clinically used as anti-cancer drugs. Recently, CPT biosynthesis pathway is gradually being resolved. However, few studies have been conducted on transcription factors (TFs), which regulate CPT biosynthesis in Ophiorrhiza pumila. In this study, we cloned and functionally identified a new OpWRKY1 TF from O. pumila that was preferentially expressed in stems and responded to exogenous elicitors such as gibberellin, acetylsalicylic acid, salicylic acid, abscisic acid and 1-aminocyclopropane-carboxylic acid. Subcellular localization assay showed that OpWRKY1 was specifically expressed in the nucleus. Transgenic results revealed that over-expression of OpWRKY1 significantly repressed CPT accumulation in the hairy roots by inhibiting the expression of several CPT biosynthesis genes, especially OpCPR. Furthermore, Dual-Luciferase assay and yeast-one-hybrid assay showed that OpCPR was a target of OpWRKY1. The above results elucidated how OpWRKY1 directly down-regulated the transcription of OpCPR and inhibited CPT biosynthesis in O. pumila. Our findings indicate that OpWRKY1 acts as a negative regulator of CPT biosynthesis in O. pumila and provide new insights on metabolic engineering of CPT metabolism in the future. Overexpression of OpWRKY1 inhibits CPT accumulation in transgenic O. pumila hairy roots by reducing the expression of CPT biosynthetic gene OpCPR.

Shewanella oneidensis MR-1 is a potent hydrogen producer in the deficiency of exogenous electron acceptors. The electron transfer pathway for hydrogen production remains unclear, although enzymes for hydrogen production have been identified in S. oneidensis MR-1. In this study, we investigated the electron transfer pathway from formate to hydrogen, given that formate is commonly a key chemical for bacterial hydrogen production. We revealed that two formate dehydrogenases FdhA1B1C1 and FdhA2B2C2, rather than FdnGHI, played a dominant role in formate-driven hydrogen production. Menaquinone was indispensable for the electron transfer from formate to hydrogen, which excluded the presence of formate hydrogen-lyase in S. oneidensis MR-1. A previously proposed formate dehydrogenase subunit HydC was identified as a menaquinone-binding subunit of [FeFe] hydrogenase HydAB, and the hydABC operon is conserved in bacteria living in diverse environments. A formate exporter FocA and transcriptional regulator FhlA were identified for their effect on formate metabolism and hydrogen production. FhlA positively affected the metabolism of formate and hydrogen by regulating the expression of fdhA2B2C2, fdnGHI, focA, and dld-II. Overall, the electron transfer pathway deciphered in this work will facilitate the improvement of biohydrogen production by S. oneidensis MR-1.Key Points• The electron transfer pathway from formate to hydrogen in MR-1 is deciphered.• Menaquinone is indispensable for hydrogen production.• A cytochrome b subunit transfers electrons from menaquinone to [FeFe] hydrogenase.

Liver fibrosis is a common pathological process of chronic hepatic injury, preceded by the chronic inflammation. The homeobox B13 (HOXB13) gene, a member of HOX family, plays diverse biological roles in embryonic development, carcinogenesis, and many inflammatory diseases. However, the expression of HOXB13 in chronic liver diseases including hepatic fibrosis remains to be defined. In present study, 55 patients with hepatic fibrosis, 15 patients of hepatocellular carcinoma, and 17 healthy controls were enrolled in this study. Pathological specimens were collected through liver biopsy or surgical resection. The degree of hepatic inflammation (G0–G4) and fibrosis (S0–S4) of hepatic fibrosis was scored based on the modified histology activity index. Intrahepatic HOXB13 expression was analyzed using immunohistochemistry analysis. Compared with healthy subjects, both patients with hepatic fibrosis and patients with hepatocellular carcinoma exhibited significant accumulations of HOXB13+ cells in the liver (p

Circular RNAs (circRNAs) represent a class of noncoding RNAs with a wide expression pattern, and they constitute an important layer of the genome regulatory network. To date, the expression pattern and regulatory potency of circRNAs in the retina, a key part of the central nervous system, are not yet well understood. In this study, RNAs from five stages (E18.5, P1, P7, P14, and P30) of mouse retinal development were sequenced. A total of 9,029 circRNAs were identified. Most circRNAs were expressed in different stages with a specific signature, and their expression patterns were different from those of their host linear transcripts. Some circRNAs could act as sponges for several retinal microRNAs (miRNAs). Furthermore, circTulp4 could function as a competitive endogenous RNA (ceRNA) to regulate target genes. Remarkably, silencing circTulp4 in vivo led to mice having a thin outer nuclear layer (ONL) and defective retinal function. In addition, we found that circRNAs were dysregulated at a much earlier time point than that of disease onset in a retinal degeneration model (rd8 mice). In summary, we provide the first circRNA expression atlas during retinal development and highlight a key biological role for circRNAs in retinal development and degeneration.

The genus Didymocorypha Wood-Mason, 1877 (Eremiaphilidae, Iridinae) has only been recorded in South Asia, including a sole species D. lanceolata (Fabricius). Here, we firstly extend its distribution to China, with description of one new species D. libaiisp. nov.Didymocorypha libaiisp. nov. lives in an area about 3000 meters above sea level on the southern slope of the Himalayas (Tibet in China), one of the highest-altitude inhabited areas of mantis in the Northern Hemisphere. It is also the first recorded Oriental mantis species in which both sexes are wingless. Life history of the new species, necessary illustrations and ecological images are provided. The distribution of the new Didymocorypha species is discussed and mapped.

Noninvasive tests (NITs) for liver fibrosis are highly needed for chronic hepatitis B (CHB) patients. We aimed to investigate whether plateletcrit (PCT) could be used as a NIT in predicting liver fibrosis for CHB patients. Five hundred and sixty-seven treatment-naive CHB patients with available liver biopsies were included. Patients were randomly divided into a derivation cohort (n = 378) and a validation cohort (n = 189). The diagnostic accuracy of PCT was evaluated using receiver operating characteristic (ROC) curves. In the derivation cohort, PCT in CHB patients with S2-S4 (0.14%), S3-S4 (0.13%) and S4 (0.12%) was lower than patients with S0-S1 (0.17%, P < .001), S0-S2 (0.17%, P < .001) and S0-S3 (0.16%, P < .001), respectively. PCT was an independent predictor of significant fibrosis (≥S2), advanced fibrosis (≥S3) and cirrhosis (S4). The area under the ROC curve (AUROC) of PCT in predicting significant fibrosis, advanced fibrosis and cirrhosis was 0.645, 0.709 and 0.714, respectively. The AUROC of PCT was higher than the aspartate transaminase to platelet ratio index (APRI) in identifying advanced fibrosis and cirrhosis, while this was comparable with APRI in identifying significant fibrosis. The diagnostic value of PCT was comparable with fibrosis-4 score (FIB-4) in predicting significant fibrosis, advanced fibrosis and cirrhosis. In the validation cohort, PCT could also identify significant fibrosis, advanced fibrosis and cirrhosis with similar diagnostic accuracy as in the derivation cohort. PCT represents a simple and inexpensive indictor for liver fibrosis in CHB patients. PCT is just as good or better than other more complex tools for staging liver fibrosis in CHB patients.

Background Mitochondrial dynamics plays an important role in tumour progression. However, how these dynamics integrate tumour metabolism in hepatocellular carcinoma (HCC) metastasis is still unclear. Methods The mitochondrial fusion protein mitofusin-1 (MFN1) expression and its prognostic value are detected in HCC. The effects and underlying mechanisms of MFN1 on HCC metastasis and metabolic reprogramming are analysed both in vitro and in vivo. Results Mitochondrial dynamics, represented by constant fission and fusion, are found to be associated with HCC metastasis. High metastatic HCC displays excessive mitochondrial fission. Among genes involved in mitochondrial dynamics, MFN1 is identified as a leading downregulated candidate that is closely associated with HCC metastasis and poor prognosis. While promoting mitochondrial fusion, MFN1 inhibits cell proliferation, invasion and migration capacity both in vitro and in vivo. Mechanistically, disruption of mitochondrial dynamics by depletion of MFN1 triggers the epithelial-to-mesenchymal transition (EMT) of HCC. Moreover, MFN1 modulates HCC metastasis by metabolic shift from aerobic glycolysis to oxidative phosphorylation. Treatment with glycolytic inhibitor 2-Deoxy-d-glucose (2-DG) significantly suppresses the effects induced by depletion of MFN1. Conclusions Our results reveal a critical involvement of mitochondrial dynamics in HCC metastasis via modulating glucose metabolic reprogramming. MFN1 may serve as a novel potential therapeutic target for HCC.

Viruses are metastable macromolecular assemblies containing a nucleic acid core packaged by capsid proteins that are primed to disassemble in host-specific environments leading to genome release and replication. The mechanism of how viruses sense environmental changes associated with host entry to prime them for disassembly is unknown. We have applied a combination of mass spectrometry, cryo-EM, and simulation-assisted structure refinement to Turnip crinkle virus (TCV), which serves as a model non-enveloped icosahedral virus (Triangulation number = 3, 180 copies/icosahedron). Our results reveal genomic RNA tightly binds a subset of viral coat proteins to form a stable RNA-capsid core which undergoes conformational switching in response to host-specific environmental changes. These changes include: i) Depletion of Ca2+which triggers viral particle expansion ii) Increase in osmolytes further disrupt interactions of outer coat proteins from the RNA-capsid core to promote complete viral disassembly. A cryo-EM structure of the expanded particle shows that RNA is asymmetrically extruded from a single 5-fold axis during disassembly. The genomic RNA:capsid protein interactions confer metastability to the TCV capsid and drive release of RNA from the disassembling virion within the plant host cell.AUTHOR SUMMARYRNA viruses including coronaviruses, dengue, influenza, and HIV are a significant threat to human health. These viral particles are finely tuned to undergo complex conformational changes that allow for response to varied environments. Turnip crinkle virus (TCV) serves as an excellent model for studying RNA virus dynamics. Since TCV is non-enveloped and has no post-translational modifications, we can specifically investigate the contributions of RNA to viral dynamics. Genomic RNA is not a passive entity but plays a crucial and previously uncharacterized role in viral disassembly. Our results reveal that the genomic RNA-capsid core serves as an environmental sensor and undergoes conformational switching in response to host cell conditions.

Background Compound kushen injection (CKI), a Chinese patent drug, is widely used in the treatment of various cancers, especially neoplasms of the digestive system. However, the underlying mechanism of CKI in pancreatic cancer (PC) treatment has not been totally elucidated. Methods Here, to overcome the limitation of conventional network pharmacology methods with a weak combination with clinical information, this study proposes a network pharmacology approach of integrated bioinformatics that applies a weighted gene co-expression network analysis (WGCNA) to conventional network pharmacology, and then integrates molecular docking technology and biological experiments to verify the results of this network pharmacology analysis. Results The WGCNA analysis revealed 2 gene modules closely associated with classification, staging and survival status of PC. Further CytoHubba analysis revealed 10 hub genes (NCAPG, BUB1, CDK1, TPX2, DLGAP5, INAVA, MST1R, TMPRSS4, TMEM92 and SFN) associated with the development of PC, and survival analysis found 5 genes (TSPOAP1, ADGRG6, GPR87, FAM111B and MMP28) associated with the prognosis and survival of PC. By integrating these results into the conventional network pharmacology study of CKI treating PC, we found that the mechanism of CKI for PC treatment was related to cell cycle, JAK-STAT, ErbB, PI3K-Akt and mTOR signalling pathways. Finally, we found that CDK1, JAK1, EGFR, MAPK1 and MAPK3 served as core genes regulated by CKI in PC treatment, and were further verified by molecular docking, cell proliferation assay, RT-qPCR and western blot analysis. Conclusions Overall, this study suggests that the optimized network pharmacology approach is suitable to explore the molecular mechanism of CKI in the treatment of PC, which provides a reference for further investigating biomarkers for diagnosis and prognosis of PC and even the clinical rational application of CKI.

YgfY(SdhE/CptB) is highly conserved while has controversial functions in bacteria. It works as an antitoxin and composes a type IV toxin–antitoxin system with YgfX(CptA) typically in Escherichia coli, while functions as an flavinylation factor of succinate dehydrogenase and fumarate reductase typically in Serratia sp. In this study, we report the contribution of YgfY in Shewanella oneidensis MR-1 to tolerance of low temperature and nitrite. YgfY deficiency causes several growth defects of S. oneidensis MR-1 at low temperature, while YgfX do not cause a growth defect or morphological change of S. oneidensis MR1-1 and E. coli. YgfY do not interact with FtsZ and MreB nor with YgfX examined by bacterial two-hybrid assay. YgfY effect on growth under low temperature is not attributed to succinate dehydrogenase (SDH) because a mutant without SDH grows comparably with the wild-type strain in the presence of succinate. The ygfY mutant shows impaired tolerance to nitrite. Transcription of nitrite reductase and most ribosome proteins is significantly decreased in the ygfY mutant, which is consistent with the phenotypes detected above. Effects of YgfY on growth and nitrite tolerance are closely related to the RGXXE motif in YgfY. In summary, this study demonstrates pleiotropic impacts of YgfY in S. oneidensis MR-1, and sheds a light on the physiological versatility of YgfY in bacteria.

BackgroundFew head-to-head evaluations of immune responses to difference vaccines have been reported.MethodsSurrogate virus neutralization test (sVNT) antibody levels of adults receiving either 2 doses of BNT162b2 (n=366) or CoronaVac (n=360) vaccines in Hong Kong were determined. An age-matched subgroup (BNT162b2 (n=49) vs CoronaVac (n=49)) were tested for plaque reduction neutralizing (PRNT) and spike binding antibody and T cell reactivity in peripheral blood mononuclear cells (PBMC).FindingsOne month after the second dose of vaccine, BNT162b2 elicited significantly higher PRNT50, PRNT90, sVNT, spike receptor binding, spike N terminal domain binding, spike S2 domain binding, spike FcR binding and antibody avidity levels than CoronaVac. The geometric mean PRNT50 titres in those vaccinated with BNT162b2 and CoronaVac vaccines were 251.6 and 69.45 while PRNT90 titres were 98.91 and 16.57, respectively. All of those vaccinated with BNT162b2 and 45 (91.8%) of 49 vaccinated with CoronaVac achieved the 50% protection threshold for PRNT90. Allowing for an expected seven-fold waning of antibody titres over six months for those receiving CoronaVac, only 16.3% would meet the 50% protection threshold versus 79.6% of BNT162b2 vaccinees. Age was negatively correlated with PRNT90 antibody titres. Both vaccines induced SARS-CoV-2 specific CD4+ and CD8+ T cell responses at 1-month post-vaccination but CoronaVac elicited significantly higher structural protein-specific CD4+ and CD8+ T cell responses.ConclusionVaccination with BNT162b2 induces stronger humoral responses than CoronaVac. CoronaVac induce higher CD4+ and CD8+ T cell responses to the structural protein than BNT162b2.Summary At a GlanceThrough the head-to-head comparison, vaccination with BNT162b2 induces significantly higher levels of SARS-CoV-2 specific binding and neutralizing antibody responses when compared to CoronaVac. CoronaVac induce higher CD4+ and CD8+ T cell responses to the structural protein than BNT162b2.

Cottonseed meal (CSM) is an important protein feed source for dairy cows. Its inclusion in ruminant diets is limited due to the presence of the highly toxic gossypol though rumen microorganisms are believed to be capable of gossypol degrading and transforming. The objective of the present study was to isolate the gossypol-degrading bacteria from the rumen contents and to assess its potential for gossypol degradation in vitro. A strain named Lactobacillus agilis WWK129 was anaerobically isolated from dairy cows after mixed rumen microorganisms were grown on a substrate with gossypol as the sole carbon source. Furthermore, the strain was applied at 5% inoculum concentration in vitro to continuously ferment CSM at 39 °C for five days, and it presented gossypol degradability as high as 83%. Meanwhile, the CSM contents of crude protein, essential amino acids increased significantly along with the increase of lactic acid yield (p &lt, 0.01). Compared with the original CSM, the fermented CSM contents of neutral detergent fiber and acid detergent fiber was remarkably decreased after the anaerobic fermentation (p &lt, 0.01). In brief, the Lactobacillus strain isolated from the rumen is not only of great importance for gossypol biodegradation of CSM, but it could also be used to further explore the role of rumen microorganisms in gossypol degradation by the ruminants.

Gastric carcinoma (GC) is a severe tumor of the digestive tract with high morbidity and mortality and poor prognosis, for which novel treatment options are urgently needed. Compound Kushen injection (CKI), a classical injection of Chinese medicine, has been widely used to treat various tumors in clinical practice for decades. In recent years, a growing number of studies have confirmed that CKI has a beneficial therapeutic effect on GC, However, there are few reports on the potential molecular mechanism of action. Here, using systems pharmacology combined with proteomics analysis as a core concept, we identified the ceRNA network, key targets and signaling pathways regulated by CKI in the treatment of GC. To further explore the role of these key targets in the development of GC, we performed a meta-analysis to compare the expression differences between GC and normal gastric mucosa tissues. Functional enrichment analysis was further used to understand the biological pathways significantly regulated by the key genes. In addition, we determined the significance of the key genes in the prognosis of GC by survival analysis and immune infiltration analysis. Finally, molecular docking simulation was performed to verify the combination of CKI components and key targets. The anti-gastric cancer effect of CKI and its key targets was verified by in vivo and in vitro experiments. The analysis of ceRNA network of CKI on GC revealed that the potential molecular mechanism of CKI can regulate PI3K/AKT and Toll-like receptor signaling pathways by interfering with hub genes such as AKR1B1, MMP2 and PTGERR3. In conclusion, this study not only partially highlighted the molecular mechanism of CKI in GC therapy but also provided a novel and advanced systems pharmacology strategy to explore the mechanisms of traditional Chinese medicine formulations.

Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8–3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3–4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.