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Engineered T cell therapies, mainly chimeric antigen receptor (CAR)-T and T cell receptor (TCR)-T, have become the new frontier of cancer treatment. CAR-T and TCR-T therapies differ in many aspects, including cell persistence and toxicity, leading to different therapeutic outcomes. Both TCR and CAR recognize antigens and trigger T cell mediated antitumor response, but they have distinct molecular structures and signaling properties. TCR represents one of the most complex receptors, while CAR is a single-chain chimera integrating modules from multiple immune receptors. Understanding the mechanisms underlying the strengths and limitations of both systems can pave the way for the development of next-generation T cell therapy. This review synthesizes recent findings on TCR and CAR signaling and highlights the potential strategies of T cell engineering by signaling refinement.

CD19-targeting chimeric antigen receptor (CAR) T cells have become an important therapeutic option for patients with relapsed and refractory B cell malignancies. However, a significant portion of patients still do not benefit from the therapy owing to various resistance mechanisms, including high expression of multiple inhibitory immune checkpoint receptors. Here, we report a lentiviral two-in-one CAR T approach in which two checkpoint receptors are downregulated simultaneously by a dual short hairpin RNA cassette integrated into a CAR vector. Using this system, we evaluated CD19-targeting CAR T cells in the context of four different checkpoint combinations—PD-1/TIM-3, PD-1/LAG-3, PD-1/CTLA-4, and PD-1/TIGIT—and found that CAR T cells with PD-1/TIGIT downregulation uniquely exerted synergistic antitumor effects. Importantly, functional and phenotypic analyses suggested that downregulation of PD-1 enhances short-term effector function, whereas downregulation of TIGIT is primarily responsible for maintaining a less differentiated/exhausted state, providing a potential mechanism for the observed synergy. The PD-1/TIGIT-downregulated CAR T cells generated from diffuse large B cell lymphoma patient-derived T cells also showed robust antitumor activity and significantly improved persistence in vivo. The efficacy and safety of PD-1/TIGIT-downregulated CD19-targeting CAR T cells are currently being evaluated in adult patients with relapsed or refractory large B cell lymphoma (ClinicalTrials.gov: NCT04836507 ).

Gastric cancer (GC) has a dismal prognosis and is also one of the most commonly diagnosed malignancies worldwide. circRNAs are covalently closed circular RNA molecules without 5'-cap and a 3'-tail, currently listed among the broad noncoding RNA family. circRNAs participate in a variety of pathophysiological processes relevant to human diseases, especially malignancies, including GC. Compelling evidence has shown that circRNAs can function by sponging miRNAs, interacting with RNA binding proteins, and encoding proteins or peptides. Yet, our current understanding of these RNA circles remains very limited. Here, we overview the biogenesis, characteristics, functions, and degradation of circRNAs. Moreover, we give an account of the circRNAs that have been linked with GC, describing their functions and mechanisms of action in the context of GC. Next, we discuss the potential value of circRNAs as diagnostic or prognostic GC biomarkers and summarize future prospects, important questions, and challenges of circRNA-based therapeutics.

Marine microalgae are a promising sustainable source of lipids, omega-3 fatty acids, and carbohydrates. Selected microalgae species belonging to the Bacillariophyceae, Haptophyceae, Eustigmatophyceae, and Prasinophyceae were characterised for cellular content of carbon and nitrogen, and for production yields of lipids, fatty acids, total carbohydrates, and β-glucans. Carbon and nitrogen content showed a hyperbolic decrease with increasing cell numbers for Chaetoceros calcitrans, C. muelleri, Skeletonema costatum, Tetraselmis sp., and Nannochloropsis oculata. Cultures of Pavlova lutheri and Tisochrysis lutea showed an increase in carbon content per cell, but a decrease in nitrogen content. The total lipid content of C. muelleri, C. calcitrans, N. oculata, and T. lutea increased with decreasing relative growth rate; however, the highest productivity of lipids was found in T. lutea grown at 40% of the maximum specific growth rate. The highest content of eicosapentaenoic acid was found in C. muelleri, C. calcitrans, and N. oculata, and the highest content of docosahexaenoic acid was found in T. lutea. The β-glucan fraction of the carbohydrates was highest in C. muelleri and C. calcitrans and was very low in N. oculata. Out of the species investigated, C. muelleri had the highest production yield of β-glucans, obtained when cultivated at a 40% relative growth rate.

The chaperone-assisted soluble expression and characterization of high molecular weight chitinase chiZJ408 in Escherichia coli BL21 were investigated. Chitin degradation products by chitinase chiZJ408 were analyzed. The results indicated that the introduction of the chaperone GroELS promoted the correct folding of chitinase chiZJ408 and increased its soluble expression by 14.9% (p < 0.05) in E. coli BL21. The optimal pH and temperature of chitinase chiZJ408 were respectively 6.0 and 50 °C. Chitinase chiZJ408 was stable at pHs of 4.0 ∼ 7.0 and at below 40 °C. Mg2+and Ca2+ had a significant impact on improving the activity of chitinase chiZJ408. Chitinase chiZJ408 was demonstrated to be exochitinase that cleaved the β-1,4-glycosidic bond of the chitin chain to generate only N,N'-diacetylchitobiose. This study broadens our understanding of chitinase and provides a basis for solving the problem of inclusion body formed by long fragment gene expression in E. coli.

DNA methylation is a prevalent epigenetic modification in vertebrates, and it has been shown to be involved the regulation of gene expression and embryo development. However, it remains unclear how DNA methylation regulates sexual development, especially in species without sex chromosomes. To determine this, we utilized zebrafish to investigate DNA methylation reprogramming during juvenile germ cell development and adult female-to-male sex transition. We reveal that primordial germ cells (PGCs) undergo significant DNA methylation reprogramming during germ cell development, and the methylome of PGCs is reset to an oocyte/ovary-like pattern at 9 days post fertilization (9 dpf). When DNA methyltransferase (DNMT) activity in juveniles was blocked after 9 dpf, the zebrafish developed into females. We also show that Tet3 is involved in PGC development. Notably, we find that DNA methylome reprogramming during adult zebrafish sex transition is similar to the reprogramming during the sex differentiation from 9 dpf PGCs to sperm. Furthermore, inhibiting DNMT activity can prevent the female-to-male sex transition, suggesting that methylation reprogramming is required for zebrafish sex transition. In summary, DNA methylation plays important roles in zebrafish germ cell development and sexual plasticity.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease, characterized by phosphorylated TDP-43 (pTDP-43)-positive inclusions in neurons and glial cells. However, the pathogenic mechanism that underlies ALS remains largely unknown. To investigate the effects of autophagy deficiency in the formation and spreading of pathological TDP-43 along corticospinal tract axons, TDP-43 preformed fibrils (PFFs) were prepared and unilaterally injected into the fifth layer of the left primary motor cortex (M1) or the left anterior horn of the seventh cervical spinal cord segment (C7) of Atg5+/- mice. After the injection of TDP-43 PFFs, the elevated levels of pTDP-43 were present in several pyramidal tract-associated regions of Atg5+/- mice. Additionally, the occurrence of spontaneous potentials detected by electromyography demonstrates evidence of lower motor neuron dysfunction in M1-TDP-43 PFFs-injected Atg5+/- mice, and prolonged central motor conduction time detected by motor evoked potentials provides evidence of upper motor neuron dysfunction in C7-TDP-43 PFFs-injected Atg5+/- mice. These results show that injection of TDP-43 PFFs into the M1 or C7 of Atg5+/- mice induces the spreading of pathological TDP-43 along corticospinal tract axons in both an anterograde and retrograde manner. Importantly, TDP-43 PFFs-injected Atg5+/- mice also display ALS-like motor dysfunction. Taken together, our findings provide direct evidence that TDP-43 PFFs-injected Atg5+/- mice exhibited ALS-like neuropathology and motor phenotypes, suggesting that autophagy deficiency promotes the formation and spreading of pathological TDP-43 in vivo.

Significance Clathrin-mediated endocytosis (CME), the major pathway for uptake into cells, is a multistep process involving a myriad of endocytic accessory proteins (EAPs). Although the biochemical activities of many EAPs have been extensively studied, their stage-specific role(s) during clathrin-coated pit (CCP) initiation, stabilization, and/or maturation are poorly defined. Here, using quantitative total internal reflection fluorescence microscopy and a rigorous experimental and multiparametric analytical pipeline, we study the effect of CRISPR interference (CRISPRi)- or small interfering RNA (siRNA)-mediated knockdown of 67 individual EAPs on CCP dynamics. Our comprehensive analyses combined with unsupervised phenotypic clustering reveal the complex and overlapping roles of EAPs during early, critical stages of CME, providing a valuable resource to spur further research into their function., Clathrin-mediated endocytosis (CME) begins with the nucleation of clathrin assembly on the plasma membrane, followed by stabilization and growth/maturation of clathrin-coated pits (CCPs) that eventually pinch off and internalize as clathrin-coated vesicles. This highly regulated process involves a myriad of endocytic accessory proteins (EAPs), many of which are multidomain proteins that encode a wide range of biochemical activities. Although domain-specific activities of EAPs have been extensively studied, their precise stage-specific functions have been identified in only a few cases. Using single-guide RNA (sgRNA)/dCas9 and small interfering RNA (siRNA)-mediated protein knockdown, combined with an image-based analysis pipeline, we have determined the phenotypic signature of 67 EAPs throughout the maturation process of CCPs. Based on these data, we show that EAPs can be partitioned into phenotypic clusters, which differentially affect CCP maturation and dynamics. Importantly, these clusters do not correlate with functional modules based on biochemical activities. Furthermore, we discover a critical role for SNARE proteins and their adaptors during early stages of CCP nucleation and stabilization and highlight the importance of GAK throughout CCP maturation that is consistent with GAK’s multifunctional domain architecture. Together, these findings provide systematic, mechanistic insights into the plasticity and robustness of CME.

Periphytic algae is a useful indicator of aquatic ecological conditions. We investigated the periphytic algae on natural substrate and the environmental variables at 44 sites on three river systems in the Weihe River Basin (WRB). A total of 84 species are identified, representing 37 genera. The most common genera were Navicula, Oscillatoria, Nitzschia, Scenedesmus, Cymbell, and Fragilaria. One-way analysis of variance (ANOVA) indicated significant differences among the three river systems in environmental variables (p < 0.05). Non-metric multidimensional scaling (NMDS) analyses also showed differences in periphytic algae communities in the three river systems (p < 0.05) and identified different dominant species in each river system. Canonical correspondence analysis (CCA) and Monte Carlo permutation tests revealed that nutrient concentration, WT, and altitude were the most important variables affecting the structure and distribution of periphytic algae communities. Chemical variables were the most accounted for environmental variables (12.5%), while physical variable and geographical factors (5.8% in total) play a relevant minor role. Our results demonstrate that Navicula pupula, Navicula radiosq, Nitzschia palea, and Nitzschia denticula, exhibiting wide ecological amplitude, are tolerant of high concentrations of nutrient pollution. Variation of periphytic algae communities in WRB is due to the combination of anthropogenic and natural factors including agricultural and domestic wastes water inputting, land use patterns, geology, climatic changes, and river hydrology. HIGHLIGHTS Structure and distribution of periphytic algae communities were investigated in the Weihe River Basin.; The gradient of organic pollution detected in environmental variables was the main gradient, and the periphytic algae responded to this gradient.; The types of substrates in river impact periphytic algae abundance, causing higher periphytic algae abundance in cobbles substrate.; The variation of periphytic algae communities is attributed to the combination of anthropogenic factors and natural factors.; The results support the periphytic algae as ecological indicators in the Weihe River Basin.

The bed nucleus of the stria terminalis (BNST) plays a critical role in regulating anxiety, yet the involved specific cell types and their connections functioning in anxiety-related behaviors remains elusive. Here we identified two cell subpopulations—corticotropin-releasing hormone-positive (CRH+) and protein kinase C-δ-positive (PKC-δ+) neurons—each displayed discrete emotionally valenced behaviors in the anterior-dorsal BNST (adBNST). Using whole-cell patch-clamp recordings and virus-assisted circuit tracing techniques, we delineated the local and long-range connectivity networks in a cell-type-specific manner. The results show that the CRH+ and PKC-δ+ neurons received inputs from similar brain regions and exhibited significant differences in the downstream projection density. In addition, in vivo calcium imaging as well as gain- and loss-of-function studies characterized the physiological response properties and the functional heterogeneities in modulating anxiety, further suggesting the similarity and individuality between the two adBNST cell types. These results provide novel insights into the circuit architecture of adBNST neurons underlying the functionally specific neural pathways that relate to anxiety disorders.

Background The dysregulation of microRNA (miRNAs) is broadly participated in cancer progression, resulting in sustained cell proliferation by directly targeting various targets. This study investigated the expression of miR-582 in GC and its association with liver metastasis. Methods Firstly, differentially expressed miRNAs in gastric cancer (GC) tissues were predicted by microarray. Then, the relationship between miR-582 and clinical characteristics of GC patients was analyzed. By silencing of miR-582 in GC cells, the change in malignant biological behaviors of GC cells was detected. The upstream lncRNA, downstream targeting genes of miR-582 and the corresponding signaling pathway were predicted by online databases and verified by luciferase reporter assays, RT-qPCR and Western blot analysis. Finally, the effects of miR-582 on the growth and metastasis of GC cells were detected by in vivo tumorigenesis and metastasis tests. Results MiR-582 was highly expressed in GC tissues and related to the metastasis of patients with GC. Silencing of miR-582 expression blocked malignant biological behaviors of GC cells in vitro and in vivo. MiR-582 inhibited forkhead box protein O3 (FOXO3) to upregulate the PI3K/AKT/Snail signaling pathway in GC cells. Besides, GATA6-AS1 was found as an upstream lncRNA to modulate the expression of miR-582. Conclusion MiR-582 induced by GATA6-AS1 silencing promotes the growth and metastasis of GC cells by targeting FOXO3 to induce the activation of the PI3K/AKT/Snail signaling pathway. MiR-582 could be a potential molecular therapy target for patients with GC.

Oral lichen planus (OLP) is an inflammatory disease. It is believed that infection and immune dysfunction play a key role in its pathogenesis, but the specific mechanism of action remains unclear. The 16s rRNA high-throughput sequencing technique was used to analyze the microbial flora structure in the saliva of OLP patients and healthy controls. The relative abundance of Derxia, Haemophilus, and Pseudomonas in the saliva of the OLP group was lower than that of the healthy control group, but there was no significant difference in the overall structure of the microbial population. In addition, we measured the protein expression levels of toll-like receptor 4 (TLR4) and nuclear factor-kappab p65 (NF-κB p65) in the tissues of OLP patients, and found that there was a significant increase and positive correlation between them (r = 0.907, P = 0.034). The expression levels of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in the OLP group were consistent with those of NF-κB p65. Therefore, we believe that changes in the composition ratio of microbialflora break the original balance state of flora, promote the occurrence of immune inflammatory reaction, and then lead to the generation or aggravation of OLP disease. This discovery provides new ideas for further research on OLP initiation and immune regulation mechanism.

Vigilance is an important antipredation technique that can be affected by many factors, such as body size and group size. Small animals are more vulnerable than large ones, so the former are expected to behave more vigilantly than the latter. This effect of body size on vigilance may occur inter- or intraspecifically. We studied the vigilance behavior of two sympatric wild ungulates, Tibetan antelopes (Pantholops hodgsonii) and Tibetan gazelles (Procapra picticaudata). Tibetan antelopes, with a body size of 33 kg are much larger than Tibetan gazelles, with a body size of approximately 14 kg. Tibetan antelopes are sexually and body-size dimorphic; that is, males are much heavier than females. Alternately, Tibetan gazelles are sexually dimorphic but the sexes do not differ in weight. Tibetan gazelles scanned their environment more frequently than Tibetan antelopes did. Small female Tibetan antelopes scanned their environment more frequently than males did, whereas male Tibetan gazelles scanned their environment more frequently than females did. Group size did not affect the vigilance of Tibetan gazelle, but its negative effect on the vigilance of male Tibetan antelopes was marginally significant. In female Tibetan antelopes, vigilance in large groups was high probably because of scramble competition and social monitoring. Our results suggested that body mass and group size play an important role in shaping the vigilance of these two rare Tibetan ungulates.

Sequential encoding of motor programs is essential for behavior generation. However, whether it is critical for instinctive behavior is still largely unknown. Mouse hunting behavior typically contains a sequential motor program, including the prey search, chase, attack, and consumption. Here, we reveal that the neuronal activity in the lateral periaqueductal gray (LPAG) follows a sequential pattern and is time-locked to different hunting actions. Optrode recordings and photoinhibition demonstrate that LPAGVgat neurons are required for the prey detection, chase and attack, while LPAGVglut2 neurons are selectively required for the attack. Ablation of inputs that could trigger hunting, including the central amygdala, the lateral hypothalamus, and the zona incerta, interrupts the activity sequence pattern and substantially impairs hunting actions. Therefore, our findings reveal that periaqueductal gray neuronal ensembles encode the sequential hunting motor program, which might provide a framework for decoding complex instinctive behaviors., Hunting behavior typically contains a sequential motor program, including search, chase, attack, and consumption. Here, the authors show that periaqueductal gray neuronal ensembles encode the sequential hunting motor program, which might provide a framework for decoding complex instinctive behaviors.

Background Gastric cancer (GC) is the fifth most commonly diagnosed cancer worldwide. Due to the dismal prognosis, identifying novel therapeutic targets in GC is urgently needed. Evidences have shown that miRNAs played critical roles in the regulation of tumor initiation and progression. GLI family zinc finger 2 (GLI2) has been reported to be up-regulated and facilitate cancer progression in multiple malignancies. In this study, we focused on identifying GLI2-targeted miRNAs and clarifying the underlying mechanism in GC. Methods Paired fresh gastric cancer tissues were collected from gastrectomy patients. GLI2 and miRNAs expression were detected in gastric cancer tissues and cell lines. Bioinformatics analysis was used to predict GLI2-targeted miRNAs and dual-luciferase reporter assay was applied for target verification. CCK-8, clone formation, transwell and flow cytometry were carried out to determine the proliferation, migration, invasion and cell cycle of gastric cancer cells. Tumorsphere formation assay and flow cytometry were performed to detail the stemness of gastric cancer stem cells (GCSCs). Xenograft models in nude mice were established to investigate the role of the miR-144-3p in vivo. Results GLI2 was frequently upregulated in GC and indicated a poor survival. Meanwhile, miR-144-3p was downregulated and negatively correlated with GLI2 in GC. GLI2 was a direct target gene of miR-144-3p. MiR-144-3p overexpression inhibited proliferation, migration and invasion of gastric cancer cells. Enhanced miR-144-3p expression inhibited tumorsphere formation and CD44 expression of GCSCs. Restoration of GLI2 expression partly reversed the suppressive effect of miR-144-3p. Xenograft assay showed that miR-144-3p could inhibit the tumorigenesis of GC in vivo. Conclusions MiR-144-3p was downregulated and served as an essential tumor suppressor in GC. Mechanistically, miR-144-3p inhibited gastric cancer progression and stemness by, at least in part, regulating GLI2 expression.

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations., An examination of motor cortex in humans, marmosets and mice reveals a generally conserved cellular makeup that is likely to extend to many mammalian species, but also differences in gene expression, DNA methylation and chromatin state that lead to species-dependent specializations.

The mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2–6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans., A comprehensive analysis of gene regulatory elements in 160 distinct cell types from the mouse cerebrum.

Root exudates determine plant’s ability to acquire nutrients through influencing plant’s interactions with soil microorganisms. Recent studies suggest that plant’s associations with beneficial soil microorganisms explain variation in root exudation as plants opt to minimize the exudation cost through such symbiosis. Yet, we have a poor understanding of whether plants change their exudation rates through mycorrhizal symbiosis in soil environments with varying resource availability. Here, we report the effects of plant-mycorrhizal symbiosis on root exudation rates across a gradient of soil phosphorous (P) availability from a field experiment in subtropical forests. Root exudation rates were higher in plants partnering with arbuscular mycorrhizal fungi than those with ectomycorrhizal fungi, but this difference disappeared in soils with high P. Specific root surface area, specific root length and fine root vitality explained high root exudation in P-limited soils. These findings demonstrate that mycorrhizal symbiosis and root functional traits collectively determine the variation in root exudation in Plimited environments.

Background and aims Cotton (Gossypium hirsutum L.) is an important cash fiber crop species, but its root traits related to phosphorus (P) acquisition have been poorly understood. Methods Eight cotton varieties that were released between 1950 and 2013 were grown in pots with or without arbuscular mycorrhizal fungi (AMF) at three P supply levels. Eleven root traits were measured and calculated after seven weeks of growth. Results At the lower two P levels mycorrhizal plants acquired more P and produced more biomass than non-mycorrhizal plants. At the highest P level mycorrhizal plants took up more P than non-mycorrhizal plants, but there was no difference in biomass. At the intermediate P level, root diameter was significantly positively correlated with biomass, P concentration and P content of mycorrhizal plants. More recent accessions had smaller root diameters, acquired less P and obtained less biomass, indicating (inadvertent) varietal selection for thinner roots that provided less cortical space for AMF, which increased the need for high P fertilizer. Conclusion Our study provides support for the importance of the outsourcing model of nutrient acquisition in the root economics space framework. Inadvertent varietal selection in the last decades, resulting in thinner roots and a lower benefit from mycorrhizal colonization, has caused a lower productivity of cotton varieties at moderate P supply, indicating the need to rethink cotton breeding efforts in order to achieve agricultural sustainability.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen of novel coronavirus disease 2019 (COVID-19)1. SARS-CoV-2 uses angiotensin converting enzyme 2 (ACE2) as a cellular receptor and enters cells via clathrin-mediated endocytosis (CME)2-4. However, the key molecules involved in internalizing and facilitating CME for virus entry remain unknown. Here, we found metabotropic glutamate receptor subtype 2 (mGluR2) is a key entry receptor for SARS-CoV-2 infection. mGluR2 directly interacts with the SARS-CoV-2 spike protein. Knockdown of mGluR2 decreases endocytosis of SARS-CoV-2 but not cell binding. mGluR2 cooperates with ACE2 to facilitate SARS-CoV-2 entry through CME. Knockout of the mGluR2 gene in mice abolished SARS-CoV-2 infection in the nasal turbinates and significantly reduced viral infection in the lungs. Importantly, mGluR2 also is important for severe acute respiratory syndrome coronavirus spike protein and Middle East respiratory syndrome coronavirus spike protein mediated endocytosis. Our study provides important insights into SARS-CoV-2 infection and reveals an important target for the development of novel approaches to limit coronavirus infection.

The meningeal lymphatic vessels (mLVs) in central nervous system (CNS) have been validated by rodent and human studies. The mLVs play a vital role in draining soluble molecules and trafficking lymphocytes, antigens and antibodies from CNS into cervical lymph nodes (CLNs). This indicates that mLVs may serve as a link between the CNS and peripheral immune system, perhaps involving in the neuroinflammatory disease. However, the morphology and drainage function of mLVs in patients with neuroinflammatory disease, such as neuromyelitis optica spectrum disorders (NMOSD), remains unexplored. Using the dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), we found that slower flow through mLVs along superior sagittal sinus in NMOSD patients with acute attack instead of NMOSD patients in chronic phase. The reduced flow in mLVs correlated with the disease severity evaluated by expanded disability status scale (EDSS). The receiver operating characteristic curve (ROC) indicated DCE-MRI might provide objective evidence to predict the acute relapse of NMOSD through evaluating the function of mLVs. Promoting or restoring the function of mLVs might be a new target for the treatment of NMOSD relapse.

The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47× 10-54) and is also associated with increased levels of total cholesterol (p = 1.22× 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81× 10-21) and alanine (p = 6.14× 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24× 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53× 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.

Hair follicle stem cells (HFSCs), located in the bulge region of the follicle, maintain hair follicle growth and cycling. Long non-coding RNAs (lncRNAs), non-protein coding transcripts, are widely known to play critical roles in differentiation and proliferation of stem cells. Therefore, the current study aimed to explore the regulatory roles of lncRNA5322 in HFSCs proliferation and the underlying regulatory mechanisms. Initially, the expression patterns of lncRNA5322 and microRNA-19b-3p (miR-19b-3p) in HFSCs were detected. Subsequently, gain-and loss-of-functions analyses were conducted to explore the roles of lncRNA5322, miR-19b-3p and mitogen-activated protein kinase 1 (MAPK1) in cell proliferation, colony formation and apoptosis of HFSCs, with the expression of cyclin-dependent kinase (CDK)1 and CDK2 examined. Also, the interaction relationships among lncRNA5322, miR-19b-3p and MAPK1 were explored. Furthermore, a mouse model was established to detect the roles of lncRNA5322, miR-19b-3p, and MAPK1 in wound contraction and epidermal regeneration. Over-expressed lncRNA5322 was found to promote proliferation, colony formation ability but inhibit apoptosis of HFSCs, in addition to up-regulation of the expression of CDK1 and CDK2. LncRNA5322 was found to act as a ceRNA of miR-19b-3p which directly targeted MAPK1. Furthermore, up-regulation of lncRNA5322 enhanced wound contraction and epidermal regeneration in vivo by increasing the expression of MAPK1 through functioning as a ceRNA of miR-19b-3p. In summary, the results in this study suggested that lncRNA5322 serves as a ceRNA of miR-19b-3p to elevate the expression of MAPK1, ultimately promoting HFSCs proliferation, wound contraction and epidermal regeneration of mouse model.

MicroRNAs (miRNAs) play an essential role in cancer development. Several studies have indicated that miRNAs mediate tumorigenesis processes, such as inflammation, proliferation, apoptosis and invasion. In the present study, we aimed to investigate the role of the microRNA-185 (miR-185) on the proliferation, migration and invasion of osteosarcoma (OS). MiR-185 expression was reduced in OS tissues and OS cell lines. MiR-185 inhibited OS cell proliferation, migration and invasion. Furthermore, a dual-luciferase assay validated that vesicle-associated membrane protein 2 (VAMP2) was a direct target of miR-185. Overexpression of miR-185 in OC cells reduced VAMP2 expression in protein and mRNA levels, whereas suppression of miR-185 led to an increase in VAMP2 protein and mRNA levels. In addition, we found that VAMP2 silencing inhibited the OS cell proliferation, migration and invasion. Further studies verified that introducing VAMP2 mRNA into cells over-expressing miR-185 abrogated the effects of miR-185 on OS cell proliferation, migration and invasion. Therefore, these results confirm that decreased expression of miR-185 might be regarded as a tumor marker for the early diagnosis of OS, by manipulating of its interactive factors with VAMP2, to provide an effective novel therapeutic target for treatment of the OS tumor.

Background Multicellular organisms require precise gene regulation during ontogeny, and epigenetic modifications, such as DNA methylation and histone modification, facilitate this precise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described. However, knowledge of how histone modifications are passed on from gametes to early embryos is limited, and whether histone modification reprogramming is conserved is not clear. Results We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and found that the patterns in gene promoter regions have been largely set to either co-occupied or active states in gametes and then passed on to early embryos. Co-occupied states are partially maintained, while active states are largely restored to nearly match the sperm’s pattern prior to zygotic genome activation (ZGA). However, repressive H3K27me3 modifications in promoter regions are largely discarded in early embryos. Prior to ZGA, patterns of genes that initialize ZGA are converted to nonrepressive states to coordinate gene expression. Moreover, promoter peaks that mark stage-specific genes are hypermethylated, and histone modifications in these regions are erased independently of DNA methylation reprogramming. Furthermore, comparative analysis revealed that the functions of co-occupied and active genes passed on from gametes are conserved in vertebrates. Gene age preferences by co-occupied and active histone modifications are also confirmed in vertebrates. Conclusions Our data provide fundamental resources for understanding H3K4me3/H3K27me3 modifications in early zebrafish embryos. The data also reveal that the reprogramming progress of histone modifications is conserved in vertebrates and coordinates with gene expression during ZGA. Electronic supplementary material The online version of this article (10.1186/s12864-019-5611-7) contains supplementary material, which is available to authorized users.

Epigenetic modifications to histones dictate the differentiation of naive CD4+ T cells into different subsets of effector T helper (TH) cells. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the mechanism regulating the differentiation of TH1, TH2 and regulatory T (Treg) cells. However, whether and how EZH2 regulates follicular helper T (TFH) cell differentiation remain unknown. Using a mouse model of acute lymphocytic choriomeningitis virus (LCMV) infection, we observed abundant EZH2 expression and associated H3K27me3 modifications preferentially in the early committed virus-specific TFH cells compared to those in TH1 cells. Ablation of EZH2 in LCMV-specific CD4+ T cells leads to a selective impairment of early TFH cell fate commitment, but not late TFH differentiation or memory TFH maintenance. Mechanistically, EZH2 specifically stabilizes the chromatin accessibility of a cluster of genes that are important for TFH fate commitment, particularly B cell lymphoma 6 (Bcl6), and thus directs TFH cell commitment. Therefore, we identified the chromatin-modifying enzyme EZH2 as a novel regulator of early TFH differentiation during acute viral infection.

Prior to implementing a new kit into application, developmental validation should be conducted to demonstrate the robustness and applicability of the kit. In this study, 24 Y-STR loci from the AGCU Y SUPP STR kit were tested including 11 loci overlapping with other commercial kits (DYS385a/b, DYS635, DYS533, DYS481, DYS549, DYS460, DYS527a/b, DYS522, and DYS444) and 13 new loci (DYS531, DYS630, DYS622, DYS552, DYS510, DYS459a/b, DYS446, DYS443, DYS587, Y-GATA-A10, DYS520, and DYS557). Developmental validation including PCR-related studies, sensitivity, stability, and species specificity studies were conducted. The performance of the kit in genotyping case-type samples was also estimated. The results indicated that the kit is robust, accurate and sensitive and is able to detect male samples without being affected by female samples or other species. Population data were obtained with this kit in Chinese Xibe group as well. Totally 139 different haplotypes were obtained from 167 male samples and demonstrated that this typing system is relatively discriminative.

Complement aids in the construction of an immunosuppressive tumor microenvironment. Tumor cell–derived C3 has been previously reported, but whether and how it acts on antitumor immunity remains to be elucidated. Here, we describe a mechanism for tumor cell–derived C3 in suppressing antitumor immunity. Tumor cell–derived C3 was activated intracellularly, which results in generation of C3a. C3a modulated tumor-associated macrophages via C3a-C3aR-PI3Kγ signaling, thereby repressing antitumor immunity. Deletion of C3 in tumor cells that had high C3 expression enhanced efficacy of anti–PD-L1 treatment. Collectively, our results suggest tumor cell–derived C3 may be a useful target for cancer immunotherapy and that targeting C3 in tumor cells may enhance antitumor immunity.

Xinxin Wang,1 Diangang Chen,1 Jianbao Gao,1 Haixia Long,1 Haoran Zha,2 Anmei Zhang,1 Chi Shu,1 Li Zhou,1 Fei Yang,1 Bo Zhu,1 Wei Wu3 1Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, China; 2Department of Oncology, The General Hospital of the People’s Liberation Army Rocket Force, Beijing, China; 3Department of Cardiothoracic Surgery, Southwest Hospital, Army Medical University, Chongqing, China Purpose: Centromere protein U (CENPU) abnormally exhibits high expression in various types of human tumor tissues and participates in tumor progression; however, its expression pattern and biological function in lung cancer have not yet been elucidated. In the present study, we explored the clinical significance and biological function of CENPU in lung cancer.Materials and methods: The Cancer Genome Atlas (TCGA) data analyses, quantitative real-time PCR (RT-PCR), and Western blotting were performed to quantify CENPU and FOXM1 expression in non-small-cell lung cancer (NSCLC) samples. Survival data were obtained from Kaplan–Meier plotter or PROGgene V2 prognostic database. The function of CENPU in lung cancer cell proliferation was determined using 5-ethynyl-2′-deoxyuridine (EdU), Cell Counting Kit-8 (CCK-8), and cell cycle assays, and the underlying mechanism was determined through bioinformatic analyses and validated by in vitro siRNA or plasmid transfection experiments.Results: CENPU was abnormally overexpressed in NSCLC samples compared with matched paired normal tissues. Higher expression of CENPU predicted worse overall survival (OS) and relapse-free survival (RFS) in NSCLC patients. Knockdown of CENPU expression by siRNA significantly inhibited proliferation and delayed cell cycle progression of lung cancer cells. To figure out the mechanism, bioinformatic analyses were performed and the results showed that the transcription factor, FOXM1, positively correlated with CENPU. Further in vitro experiments indicated that FOXM1 was the possible downstream transcription factor of CENPU as the knockdown of CENPU led to lower expression of FOXM1 and the overexpression of FOXM1 significantly reversed the inhibition of proliferation caused by CENPU knockdown. Furthermore, FOXM1 was highly expressed in NSCLC. The knockdown of FOXM1 also attenuated proliferation and induced G1 arrest in lung cancer cells.Conclusion: CENPU was highly expressed in NSCLC tissues, wherein it promoted lung cancer cell proliferation via the transcription factor, FOXM1, which could be a potential target for therapeutic strategies. Keywords: CENPU, NSCLC, proliferation, FOXM1

BackgroundUreaplasmaspp.are associated with various infectious diseases in females, but there is still limited evidence regarding whether they are related to nonspecific cervicitis. The aim of this study was to develop and evaluate a digital droplet PCR (ddPCR) assay for the detection and quantification ofUreaplasmaspp. in cervical swabs.MethodsA total of 267 non-specific cervicitis (NSC) patients and 195 asymptomatic females were included in this study. We produced standard curves forUreaplasmaspp.to evaluate the analytical performance of the ddPCR assay. Then, we detected and quantified the bacterial load ofUreaplasmaspp. in cervical swabs.ResultsThe prevalences ofU. parvumwere 37.8% (101/267) and 29.7% (58/195), U. urealyticumwere 9.0% (24/267) and 8.7% (17/195) in the NSC group and control group, respectively. In addition, the median copy number ofU. parvumwas 2.5 × 104copies/ml (n = 101) in the NSC group and 9.2 × 103copies/ml (n = 58) in the control group. TheU. parvumload in the NSC group was significantly higher than that in the asymptomatic individuals (P U. urealyticumwas 8.4 × 103copies/ml (n = 24) and 1.4 × 103(n = 17) copies/ml in the two groups, respectively, , the difference was not statistically significant (P = 0.450).ConclusionsOur study is the first to develop a droplet digital PCR (ddPCR) method for the detection and quantification ofUreaplasmaspp. in clinical samples, and the method has excellent analytical performance and a wide range of clinical application prospects.

BackgroundPlatelet activating factor acetylhydrolase 1b catalytic subunit 3 (PAFAH1B3) is associated with a variety of human diseases. However, its function in gastric cancer remains uncertain.MethodsPAFAH1B3 expression was analyzed in The Cancer Genome Atlas (TCGA) and genotype-tissue expression pan-cancer data. The association between PAFAH1B3 expression and patient prognosis was evaluated using TCGA clinical survival data. Enrichment analysis of PAFAH1B3 was performed using the clusterProfiler R software package. Moreover, the correlation between PAFAH1B3 expression and immune cell infiltration were evaluated by analyzing TCGA database. CCK8 assay and colony-formation assay were performed to assess the effect of PAFAH1B3 on the proliferation of gastric cancer cells. Transwell assay was used to evaluate the impact of PAFAH1B3 on gastric cancer cell migration. Western blot was performed to evaluate the role of PAFAH1B3 on signaling pathways in gastric cancer cells.ResultsPAFAH1B3 was highly expressed in many types of tumors including gastric cancer. High PAFAH1B3 expression was significantly correlated with proliferation-related gene sets involved in DNA replication, the cell cycle, and cell cycle checkpoints. Further analysis showed that high PAFAH1B3 expression was associated with high M1 macrophage and CD8-positive T cell infiltration scores. PAFAH1B3 knockdown inhibited the proliferation, migration, and the activation of oncogenic signaling in gastric cancer cells.ConclusionsOur findings suggest that PAFAH1B3 may be an oncogene in gastric cancer.

Pheochromocytomas and paragangliomas (PCPGs) are catecholamine-producing neuroendocrine tumors. Accumulating evidences indicate that the blockade of antioxidative pathways might be a novel therapeutic approach to the treatment of PCPG. NIX has been confirmed to play a key role in maintaining redox homeostasis in tumors, while the function of NIX in PCPG remains unclear. In this study, the analyses of the disease-free survival (DFS) showed that high NIX protein level is related to poor prognosis in patients of PCPG. Consistent with this, high level of NIX protein upregulates the level of p-NF-κB and promotes the migration of PC12 cells. In NIX-over-expressing PC12 cells, the level of reactive oxygen species (ROS) is decreased while trolox-equivalent antioxidant capacity (TEAC) increased. But in NIX-silencing cells, ROS level is increased, while TEAC reversely reduced, consequently antioxidase and phase II enzymes of NRF2 signaling were activated, and elevated endoplasmic reticulum (ER) stress was observed. Additionally, the apoptosis induced by luminespib/NVP-AUY922, an inhibitor of heat shock protein 90 (HSP90, a cellular stress response factor), was enhanced in NIX-silencing cells but reduced in the NIX-over-expressing cells. All of these results indicated that high NIX protein level enhances antioxidant capacity of PC12 cells and reduces the apoptosis caused by cell stress, such as induced by luminespib/NVP-AUY922. Therefore, luminespib/NVP-AUY922 might be effective only for PCPG with low NIX level, while targeting NIX could be a further supplement to the therapeutic treatment strategy for PCPG patients with high NIX protein level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12192-021-01193-6.

The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

Due to insufficient mass transfer and mixing issues, cells in the industrial-scale bioreactor are often forced to experience glucose feast/famine cycles, mostly resulting in reduced commercial metrics (titer, yield and productivity). Trehalose cycling has been confirmed as a double-edged sword in the Penicillium chrysogenum strain, which facilitates the maintenance of a metabolically balanced state, but it consumes extra amounts of the ATP responsible for the repeated breakdown and formation of trehalose molecules in response to extracellular glucose perturbations. This loss of ATP would be in competition with the high ATP-demanding penicillin biosynthesis. In this work, the role of trehalose metabolism was further explored under industrially relevant conditions by cultivating a high-yielding Penicillium chrysogenum strain, and the derived trehalose-null strains in the glucose-limited chemostat system where the glucose feast/famine condition was imposed. This dynamic feast/famine regime with a block-wise feed/no feed regime (36 s on, 324 s off) allows one to generate repetitive cycles of moderate changes in glucose availability. The results obtained using quantitative metabolomics and stoichiometric analysis revealed that the intact trehalose metabolism is vitally important for maintaining penicillin production capacity in the Penicillium chrysogenum strain under both steady state and dynamic conditions. Additionally, cells lacking such a key metabolic regulator would become more sensitive to industrially relevant conditions, and are more able to sustain metabolic rearrangements, which manifests in the shrinkage of the central metabolite pool size and the formation of ATP-consuming futile cycles.

Roots of most plant species, including the roots of almost all major crops, are colonized by arbuscular mycorrhizal fungi. This relationship, which dates from the times plants conquered the land, is a beneficial nutritional symbiosis. It also increases plant tolerance or resistance against pest and diseases. Apart from the nutritional aspect (plants trade photosynthetically acquired carbon for soil nutrients, especially those of limited mobility such as phosphorus, zinc, or copper), mycorrhizal colonization is influenced by, and in turn influences, the hormonal activities in plants. This hormonal crosstalk alters plant roots traits, and this interplay between roots and fungi merits more focus. Mycorrhizal fungi confer enhanced drought tolerance, whereby both nutritional and hormonal effects play a role. Even though mycorrhizal fungi increase acquisition of nutrients, these additionally acquired nutrients are not always translated into increased plant biomass; this may result in plants with higher internal nutrient concentration (or lower nutrient-use efficiency). This effect may also have beneficial consequences in terms of enhanced food quality in specific cases. Considering the importance of the symbiosis, studies have addressed the question whether we can breed for a better symbiosis. Possibilities for genetic improvements of plants and fungi are listed, but we also indicate that under a Darwinian perspective on agriculture it is likely that such improvements are accompanied by undesired trade-offs. Management of mycorrhizal fungi is discussed, and we focus on the potential benefits of high mycorrhizal fungal diversity for plant productivity. We conclude with suggestions for future research to harness the mycorrhizal symbiosis for ecological intensification of agriculture.

Interest in the cultivation of Saccharina latissima is increasing in the north of Norway. In the present study, S. latissima was cultivated at two sites (Kraknes and Rotsund), 90 km apart, in Troms, northern Norway (69–70°N). The effect of site, depth, and sori origin (Kraknes and Rotsund) on S. latissima growth, biofouling, minerals, and potentially toxic elements (PTEs) content was studied. Large variations in the frond length and wet weight were observed between sites. The site with lower seawater temperature, higher nutrient levels and no freshwater influence (Kraknes) had better growth and later outbreak of epibionts. Sori origin had a significant effect on the growth only at the Kraknes site with S. latissima produced from the Kraknes sori having longer frond length and higher wet weight. The iodine content was, in general, high and increased with cultivation depth. The arsenic and cadmium content varied between sites and was lower than the recommended maximum level for food supplements in EU regulations. The present study shows that growth, biofouling, minerals, and PTEs content vary profoundly within the same geographical region and between sori origin, it thereby underlines the importance of site selection and using traits with high growth rates for seeding and cultivation to achieve maximum biomass.

E-commerce has become a crucial business model through the Internet around the world. Therefore, its transaction trend forecast can provide important information for the market planning and development in advance. For this purpose, the integrated model of enhanced whale optimization algorithm (EWOA) with support vector machine (SVM) is proposed for forecast of E-commerce transaction trend in this study. First, the global optimization ability of the whale optimization algorithm (WOA) is enhanced by the search updating strategy. Second, multiple factors that may affect the E-commerce transaction trend are analyzed and determined using the gray correlation mechanism. Third, the EWOA algorithm is employed to optimize the SVM random parameters. Finally, the EWOA-SVM model is established for forecasting E-commerce transaction trend. Two representative cases tests confirm that the EWOA-SVM model is superior to other existing methods in terms of fast convergence speed and high prediction accuracy.

The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low frequency SVs for association with 116 quantitative traits, and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including two novel loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB gene promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p=1.47×10−54), and is also associated with increased levels of total cholesterol (p=1.22×10−28) and 14 additional cholesterol-related traits, and (2) a multiallelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p=4.81×10−21) and alanine (p=6.14×10−12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs), and one linking recurrent HP gene deletion and cholesterol levels (p=6.24×10−10), which was also found to be strongly associated with increased glycoprotein level (p=3.53×10−35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.

CD19-targeting chimeric antigen receptor (CAR) T cells have become an important therapeutic option for patients with relapsed and refractory B cell malignancies. However, recent clinical data indicate that a significant portion of patients still do not benefit from the therapy owing to various resistance mechanisms, including high expression of multiple inhibitory immune checkpoint receptors on activated CAR T cells. Here, we report a lentiviral two-in-one CAR T approach in which two checkpoint receptors are downregulated simultaneously by a dual short-hairpin RNA (shRNA) cassette integrated into a CAR vector. Using this system, we evaluated CD19-targeting CAR T cells in the context of four different checkpoint combinations—PD-1/TIM-3, PD-1/LAG-3, PD-1/CTLA-4 and PD-1/TIGIT—and found that CAR T cells with PD-1/TIGIT downregulation uniquely exerted synergistic antitumor effects in mouse xenograft models compared with PD-1 single downregulation, and maintained cytolytic and proliferative capacity upon repeated antigen exposure. Importantly, functional and phenotypic analyses of CAR T cells as well as analyses of transcriptomic profiles suggested that downregulation of PD-1 enhances short-term effector function, whereas downregulation of TIGIT is primarily responsible for maintaining a less-differentiated/exhausted state, providing a potential mechanism for the observed synergy. The PD-1/TIGIT–downregulated CAR T cells generated from diffuse large B-cell lymphoma patient-derived T cells using a clinically applicable manufacturing process also showed robust antitumor activity and significantly improved persistence in vivo compared with conventional CD19-targeting CAR T cells. Overall, our results demonstrate that the cell-intrinsic PD-1/TIGIT dual downregulation strategy may prove effective in overcoming immune checkpoint-mediated resistance in CAR T therapy.

The process of fermenting tofu extends thousands of years. Despite a resurgent interest in microbial communities and fermented foods, little knowledge exists concerning microbial diversity of communities of fermented ‘hairy’ tofu known in China as Mao tofu. We used high-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA marker genes to disentangle the Mao tofu fungal and bacterial community composition and diversity across the four most important markets in the Yunnan region of China. We show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa. Significant differences in community structure were found between markets and niches. Machine learning random forest models were able to accurately classify both market and niche of sample origin. An over-abundance of yeast taxa were detected, and Geotrichum were the most abundant fungal taxa, followed by Torulaspora, Trichosporon, and Pichia. Mucor (Mucormycota) was also abundant in the LSU data and especially in the outside niche (rind), which consists of the visible ‘hairy’ mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidota, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant members. Of interest, putative fungal pathogens of plants (e.g. Cercospora, Diaporthe, Fusarium) and animal (e.g. Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora), as well as bacterial (e.g. Legionella) pathogens, were detected. Non-target eukaryotic taxa detected in by LSU amplicon sequencing included soybean (Glycine max), Protozoa, Metazoa (e.g. Nematoda and Platyhelminthes), Rhizaria and Chromista, providing evidence of additional biocomplexity and diversity in the tofu microbiome.

Programmable RNA cytidine deamination has recently been achieved using a bifunctional editor (RESCUE-S) capable of deaminating both adenine and cysteine. Here, we report the development of "CURE", the first cytidine-specific C-to-U RNA Editor. CURE comprises the cytidine deaminase enzyme APOBEC3A fused to dCas13 and acts in conjunction with unconventional guide RNAs (gRNAs) designed to induce loops at the target sites. Importantly, CURE does not deaminate adenosine, enabling the high-specificity versions of CURE to create fewer missense mutations than RESCUE-S at the off-targets transcriptome-wide. The two editing approaches exhibit overlapping editing motif preferences, with CURE and RESCUE-S being uniquely able to edit UCC and AC motifs, respectively, while they outperform each other at different subsets of the UC targets. Finally, a nuclear-localized version of CURE, but not that of RESCUE-S, can efficiently edit nuclear RNAs. Thus, CURE and RESCUE are distinct in design and complementary in utility.

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

In this present work, effects of three Euler angles (angle of attack (AOA), angle of trim (AOT), and angle of pitch (AOP)) of vertical cambered otter board on hydrodynamic characteristics (drag coefficient (Cd), lift coefficient (Cl), center-of-pressure coefficients (Cp)) were studied based on numerical simulation combined with Kriging response surface methodology (KRSM) and multi-objective genetic algorithm (MOGA). Wind tunnel experiments were carried out to validate the accuracy of the response surface based on numerical simulation. It was demonstrated that AOA had noticeable effects on Cd and Cl, while AOT and AOP had fewer effects. The working posture of the otter board was recommended to lean inward (0 deg–6 deg) and forward (−10 deg–0 deg) to improve the lift-drag ratio without sacrificing Cl. The influences of AOT and AOP on positions of center-of-pressure points were less significant than that of AOA and decreasing with the increase of AOA. Besides, the response surface of hydrodynamic coefficients around the critical AOA was a decent indicator of the occurrence of stall. Finally, three candidate cases were selected to satisfy the high working efficiency by MOGA, which was consistent with the above recommendations. This study provided a scientific reference of response surface experimental investigations methodology in the fishery engineering and the configuration of Euler angles of otter board.

Background Dual-specificity phosphatase 9 (DUSP9) belongs to the dual-specificity protein phosphatase subfamily. Recently, increasing attention has been paid on the role of DUSP9 in a variety of cancers. However, its functional role in tumor development is still unclear, especially in colorectal cancer (CRC). Methods The functional role of DUSP9 in inhibiting the progression of CRC was verified using colony formation assay, wound healing assay, nude mice xenograft model, etc. RNA-seq was performed to assess the gene expression profiling in SW480 cells with DUSP9 stable knockdown and shControl cells. Bisulfite sequencing (BSE) was performed to reveal the methylation status of CpG island in the promoter of DUSP9. Results DUSP9 was significantly downregulated in tumor tissues compared with peritumor tissues. Mechanistically, the high methylation status of CpG island in the promoter of DUSP9 may lead to the downregulation of DUSP9 in CRC. Clinically, low DUSP9 expression in CRC was closely associated with depth of invasion, metastasis (TNM) stage, and poor survival, indicating that DUSP9 may be involved in the progression of CRC. Functional study revealed that DUSP9 inhibited proliferation, migration, invasion, and epithelial-mesenchymal transition of CRC cells both in vitro and in vivo. Transcriptome profiling studies revealed that Erk signaling was involved in the tumor progression mediated by DUSP9 silencing, which is confirmed by cell experiments and clinical tissue sample staining analysis. Conclusion Our findings demonstrate that DUSP9 plays a critical role in the progression of CRC, and therapeutic intervention to increase the expression or activity of DUSP9 may be a potential target for CRC treatment in the future.

Spartina alterniflora is an aggressive invasive plant spreading along the coastal China, spanning a latitudinal range of 20°N - 39°N, and its invasion resulted in dramatic decline in both native plant diversity and ecosystem functioning. Phenology of S. alterniflora saltmarshes is a critical feature to elucidate the invasion dynamics over geographical regions but has not been well understood yet. In this study, we examined the variation of S. alterniflora saltmarsh phenology across coastal China during 2018–2020 by using time series Landsat 7/8 and Sentinel-2 images. Combined Landsat 7/8 and Sentinel-2 images provided more good-quality observations in a year, which could facilitate phenological retrieval. We applied and assessed three widely used phenology retrieval methods (i.e., NDVI-based pixel-specific statistical threshold, NDVI-based double logistic mathematical equation, and LSWI-based biological threshold) for retrieving the start and end of season (SOS and EOS) as well as the length of season (LOS) of S. alterniflora saltmarshes. The SOS and EOS dates derived from three phenology retrieval methods showed similar patterns in latitudinal phenology variation: SOS became later and LOS became shorter as latitude increased, and the latitudinal trend of EOS was not as large as that of SOS. This study shows the potential of Landsat 7/8 and Sentinel-2 to quantify land surface phenology of S. alterniflora saltmarshes, which not only enhances our understanding of the spatial-temporal dynamics of coastal saltmarshes in China but also improves the management of this plant invader that threatens native saltmarshes in the world.

Plants promote the mineralization of soil organic phosphorus by secreting phosphatase into the rhizosphere, in addition they promote the growth of bacteria which also release phosphatase to the rhizosphere. Sugars are the main component of root exudates and a key driver of soil microbial activity. In this study, we added different concentrations of a range of sugars found in root exudates to the soil during maize growth to investigate whether sugars could stimulate alkaline phosphatase activity. Sugars increased alkaline phosphatase activity in soil, while different sugars increased this activity to different extents. Small concentration of sugars did not stimulate alkaline phosphatase activity in the rhizosphere, change the bacterial community structure or select phosphatase producing species such as Saccharimonadales. However, alkaline phosphatase activity was enhanced by larger concentration of added sugars, which increased indigenous soil Saccharimonadales abundance. Notwithstanding this, Saccharimonadales were rare in the microbial taxa at the order level and their relative abundance was only 2.1%–4.9% at different sugar concentration levels. Our results suggest that addition of sugars selected for indigenous soil Saccharimonadales, enhancing alkaline phosphatase activity in the rhizosphere. These rare microbial taxa may be a key species in soil phosphorus cycling.

Background Atopic dermatitis (AD) is a worldwide chronic skin disease which burden public health. Sea buckthorn (SBT) (Hippophae rhamnoides L., Elaeagnaceae) oil, as a traditional herbal medicine, has been used for disease treatment for many years. The effects of SBT oil on AD mouse model induced by repeated administration of 2,4-dinitrochlorobenzene (DNCB) in BALB/c mice was evaluated in this study. Methods Mice were divided into four groups including the normal control group, AD model group, AD model group treated with SBT oil (5 ml/kg) and AD model group treated with SBT oil (10 ml/kg). Same volume at different concentrations of SBT oil was applied daily on the latter two groups by gavage for 15 days following AD model induction. The function of skin barrier and the production of IL-4, IFN-γ, TNF-α and TSLP were examined after animal sacrifice. The migration and mature of langerhans cell (LCs) in lymph node was further assessed by flow cytometry. Results SBT oil alleviated dermatitis scores, decreased ear thickness, prevented infiltration of mast cell, reduced lymph node weight and depressed activity of Th2 cells. SBT oil also reduced the expression of IL-4, IFN-γ, TNF-α and TSLP in ear tissue, IgE level in serum and mRNA relative expression of IL-4, IFN-γ, TNF-α in lymph node. Moreover, SBT oil inhibited the migration of LCs cells from local lesions to lymph node and it’s mature in lymph node. Conclusions These results suggest SBT oil had a beneficial effect either systemic or regional on DNCB-induced AD mice via maintain the balance of Th1/Th2 and may be a potential complementary candidate for AD treatment.

Assembling for transcription initiation Eukaryotic transcription initiation by RNA polymerase II (Pol II) requires the assembly of a preinitiation complex (PIC) on core promoters. The binding of TATA box–binding protein (TBP) to the TATA box promoter has been thought to be a general rule in PIC assembly and transcription initiation. However, most coding genes lack a TATA box, and nearly all Pol II–mediated gene transcription requires the TBP-containing multisubunit complex transcription factor IID (TFIID). Chen et al. determined the structures of human TFIID-based PIC in sequential assembly states and revealed that TFIID supports distinct PIC assembly on TATA-containing and TATA-lacking promoters. The finding resolves the long-standing mystery of how one set of general transcription machinery initiates transcription on diverse promoters. Science , this issue p. eaba8490