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Abstract: Protein-ligand interactions are necessary for majority protein functions. Adenosine- 5’-triphosphate (ATP) is one such ligand that plays vital role as a coenzyme in providing energy for cellular activities, catalyzing biological reaction and signaling. Knowing ATP binding residues of proteins is helpful for annotation of protein function and drug design. However, due to the huge amounts of protein sequences influx into databases in the post-genome era, experimentally identifying ATP binding residues is costineffective and time-consuming. To address this problem, computational methods have been developed to predict ATP binding residues. In this review, we briefly summarized the application of machine learning methods in detecting ATP binding residues of proteins. We expect this review will be helpful for further research.

Summary The immature characteristics and metabolic phenotypes of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) restrict their applications for disease modeling, drug discovery, and cell-based therapy. Leveraging on the metabolic shifts from glycolysis to fatty acid oxidation as CMs mature, a human hexokinase1-GFP metabolic reporter cell line (H7 HK1-GFP) was generated to facilitate the isolation of fetal or more matured hPSC-CMs. RNA sequencing of fetal versus more matured CMs uncovered a potential role of interferon-signaling pathway in regulating CM maturation. Indeed, IFN-γ-treated CMs resulted in an upregulation of the JAK-STAT pathway, which was found to be associated with increased expression of CM maturation genes, shift from MYH6 to MYH7 expression, and improved sarcomeric structure. Functionally, IFN-γ-treated CMs exhibited a more matured electrophysiological profile, such as increased calcium dynamics and action potential upstroke velocity, demonstrated through calcium imaging and MEA. Expectedly, the functional improvements were nullified with a JAK-STAT inhibitor, ruxolitinib., Highlights • RNA-seq revealed upregulation of IFN-signaling pathways during CM maturation • IFN-γ-treated PSC-derived fetal CMs display increased MYH7:MYH6 ratio • IFN-γ-treated PSC-derived fetal CMs exhibited improved electrophysiological profile, In this article, Soh and colleagues utilize a metabolic reporter to identify a novel role of JAK-STAT signaling in hPSC-CM maturation. IFN-γ treatment activates the JAK-STAT pathway and upregulates STAT1 expression in hPSC-derived fetal CMs, thereby enhancing the expression of CM maturation genes including MYH7, which subsequently resulted in improved sarcomeric structure, and a relatively more matured electrophysiological profile in vitro.

Scavenger receptor is pattern-recognition receptor (PRR) that plays a crucial function in host defense against pathogens. Scavenger receptor C (SR-C) is present only in invertebrates and its function has not been studied in detail. In this study, an SR-C homologous gene from the silkworm, Bombyx mori, was identified and characterized. SR-C was largely expressed in hemocytes and Malpighian tubules, with continuous expression in hemocytes. The peak expression was observed in hemocytes during molting and wandering stages both at mRNA and protein levels. Furthermore, immunofluorescence demonstrated it to be mainly distributed in the cell membranes of hemocytes, including oenocytoids and granulocytes. The recombinant SR-C protein (rSR-C) could bind to different types of bacteria and pathogen-associated molecular patterns (PAMPs), with strong binding to gram-positive bacteria and Lys-type peptidoglycans. The overexpression of SR-C induced the expression of genes related to the Toll pathway and antibacterial peptides. While the knockdown of SR-C reduced the expression of AMPs and inhibited the Toll pathway, it impaired the bacterial clearance ability of silkworm larvae, thus decreasing silkworm larvae's survival rate. Altogether, SR-C is a PRR that protect silkworms against bacterial pathogens by enhancing the expression of AMPs expression via the Toll pathway in hemocytes.

Microglial activation and neuroinflammation induced by amyloid β (Aβ) play pivotal roles in Alzheimer's disease (AD) pathogenesis. Astragaloside IV (AS-IV) is one of the major active compounds of the traditional Chinese medicine Astmgali Radix. It has been reported that AS-IV could protect against Aβ-induced neuroinflammation and cognitive impairment, but the underlying mechanisms need to be further clarified. In this study, the therapeutic effects of AS-IV were investigated in an oligomeric Aβ (oAβ) induced AD mice model. The effects of AS-IV on microglial activation, neuronal damage and reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase expression were further studied. Different doses of AS-IV were administered intragastrically once a day after intracerebroventricularly oAβ injection. Results of behavioral experiments including novel object recognition (NOR) test and Morris water maze (MWM) test revealed that AS-IV administration could significantly ameliorate oAβ-induced cognitive impairment in a dose dependent manner. Enzyme linked immunosorbent assay (ELISA) results showed that increased levels of reactive oxygen species (ROS), tumor necrosis factor α (TNF-α), interleukin-1β (IL-1β) and IL-6 in hippocampal tissues induced by oAβ injection were remarkably inhibited after AS-IV treatment. OAβ induced microglial activation and neuronal damage was significantly suppressed in AS-IV-treated mice brain, observed in immunohistochemistry results. Furthermore, oAβ upregulated protein expression of NADPH oxidase subunits gp91phox, p47phox, p22phox and p67phox were remarkably reduced by AS-IV in Western blotting assay. These results revealed that AS-IV could ameliorate oAβ-induced cognitive impairment, neuroinflammation and neuronal damage, which were possibly mediated by inhibition of microglial activation and down-regulation of NADPH oxidase protein expression. Our findings provide new insights of AS-IV for the treatment of neuroinflammation related diseases such as AD.

From August to November 2019, 11 were set up in the Three Gorges Reservoir area and its tributaries (Taiping River, Xiangxi River, Wanzhou, Fuling, Fengdu, Fujiang, Jialing River, Jiantan River, Banan, Yunyang, Xiaojiang) At the sampling point, the selected fishing gears were ground cages (mesh 1.2cm), seal nets (diameter 1m, length 3m) and gill nets. The specifications of the gillnet are multi-mesh composite gillnets, including 12 mesh specifications: 2a=8.5cm, 4.0cm, 12.5cm, 2.0cm, 11.0cm, 1.6cm, 2.5cm, 4.8cm, 3.1cm, 1.0cm , 7.5cm and 6.0cm, each mesh gillnet is 2.5m long and 2m wide, spliced ​​into a composite gillnet with a total length of 30m. Field fishing was carried out at each sampling point, on-site identification, and biological traits such as fish body length and weight were collected. During the sampling period of this study, 18,466 fish samples were recorded in the Three Gorges Reservoir area. The samples were preliminarily identified as 64 species, and the species were morphologically identified with reference to "Chinese Cyprinidae (Volume 1)", "Sichuan Fish Chronicles" and "Fishes of the World". All samples were preserved in 10% formaldehyde solution in intact individual form for further morphological identification, and were preserved in our laboratory (Laboratory of Animal Genetics, Jianghan University), and tissue samples were preserved in 95% ethanol. About 100 mg of fish muscle tissue or fin rays were taken, and genomic DNA was extracted by high-salt method. The COI gene sequence amplification primer sequence was: F1:5'-TCAACCAACCACAAAGACATTGGCAC3'R1:5'-TAGACTTCTGGGTGGGCCAAAGAATC3'. The PCR reaction system was 30 μL, including 10.3 μL of 2×Taq Master Mix, 1.5 μL of upstream and downstream primers (10 mM), 1.5 μL of DNA template, and 15.2 μL of double-distilled water. The PCR reaction program was as follows: 95°C high temperature pre-denaturation for 5 min; 95°C denaturation for 30s; 56°C annealing for 45s; 72°C extension for 45s, a total of 31 cycles; final extension at 72°C for 10 min; °C in the refrigerator. Finally, the results of PCR products were detected by electrophoresis. PCR products were detected by 1% agarose gel electrophoresis and then sent to a biological company for sequencing. BioEdit software was used to manually correct the forward and reverse sequencing peaks, and the DNA sequences were aligned and spliced ​​using the splicing program SEQMAN in DNASTAR, and all sequences containing missing information and degenerate bases were eliminated. Finally, 946 COI sequences from fish were obtained in this study, and the 639bp mitochondrial COI gene sequence after homology alignment was used for barcode analysis. No deletion or insertion of bases was found in all sequences., 2019年8月-11月，在三峡库区及各支流(太平溪，香溪河，万州，涪陵，丰都，涪江，嘉陵江，箭滩河，巴南，云阳，小江)设置11个采样点，选取的渔具为地笼(网目1.2cm)、篆网(直径1m，长度3m)和刺网等。刺网的规格为多网目复合刺网，包括12种网目规格：2a=8.5cm、4.0cm、12.5cm、2.0cm、11.0cm、1.6cm、2.5cm、4.8cm、3.1cm、1.0cm、7.5cm和6.0cm，每个网目的刺网长2.5m，宽2m，拼接成总长30m的复合刺网。在各采样点进行实地捕捞，现场鉴定，采集鱼类体长及重量等生物学性状。本研究采样期间记录三峡库区鱼类样本18466尾。样品初步鉴定为64种，参考《中国鲤科鱼类志(上卷)》、《四川鱼类志》和《Fishes of the world》等对物种进行形态学鉴定。所有样本均以完整个体形式保存在10%甲醛溶液中进行进一步形态学鉴定，保存于本实验室(江汉大学动物遗传学实验室)，组织样本保存在95%乙醇中。取约100mg的鱼类肌肉组织或鳍条，采用高盐法提取基因组DNA，COI基因序列扩增引物序列为：F1:5’-TCAACCAACCACAAAGACATTGGCAC3’R1:5’-TAGACTTCTGGGTGGGCCAAAGAATC3’。PCR反应体系为30 μL, 其中包括2×Taq Master Mix 10.3 μL , 上下游引物(10 mM)各1.5 μL和 DNA模板1.5μL, 和双蒸水15.2 μL。PCR反应程序为: 95℃高温预变性 5min；95℃变性30s；56℃退火 45s；72℃延伸45s，共31个循环；最后72℃延伸 10min；16℃保存20分钟，或者结束后置于4℃冰箱中。最后经电泳检测 PCR产物结果。PCR产物经1%琼脂糖凝胶电泳检测后送生物公司测序。利用BioEdit软件对正反向的测序峰图进行人工校正，利用DNASTAR中的拼接程序SEQMAN对DNA序列进行比对和拼接，剔除所有含缺失信息、兼并碱基的序列。最后本研究获取鱼类946条COI序列，同源比对后639bp的线粒体COI基因序列用于条形码分析，所有序列均未发现碱基的缺失、插入。

BackgroundGinseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with soil environmental degradation, which may involve changes in soil microbiology and physicochemical properties.ResultsIn this study, GRS and healthy ginseng (HG) samples were used as experimental materials for comparative analysis of transcriptome and metabolome. Compared with those in HG samples, 949 metabolites and 9451 genes were significantly changed at the metabolic and transcriptional levels in diseased samples. The diseased tissues’ metabolic patterns changed, and the accumulation of various organic acids, alkaloids, alcohols and phenols in diseased tissues increased significantly. There were significant differences in the expression of genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the peroxidase pathway, and the plant-pathogen interaction pathway.ConclusionThe current study involved a comparative metabolome and transcriptome analysis of GRS and HG samples. Based on the findings at the transcriptional and metabolic levels, a mechanism model of the ginseng response to GRS was established. Our results provide new insights into ginseng’s response to GRS, which will reveal the potential molecular mechanisms of this disease in ginseng.

Glioblastoma multiforme (GBM) is an aggressive malignant brain tumour that is resistant to existing therapeutics. Identifying signalling pathways deregulated in GBM that can be targeted therapeutically is critical to improve the present dismal prognosis for GBM patients. In this report, we have identified that the BRG1 (Brahma‐Related Gene‐1) catalytic subunit of the SWI/SNF chromatin remodelling complex promotes the malignant phenotype of GBM cells. We found that BRG1 is ubiquitously expressed in tumour tissue from GBM patients, and high BRG1 expression levels are localized to specific brain tumour regions. Knockout (KO) of BRG1 by CRISPR‐Cas9 gene editing had minimal effects on GBM cell proliferation, but significantly inhibited GBM cell migration and invasion. BRG1‐KO also sensitized GBM cells to the anti‐proliferative effects of the anti‐cancer agent temozolomide (TMZ), which is used to treat GBM patients in the clinic, and selectively altered STAT3 tyrosine phosphorylation and gene expression. These results demonstrate that BRG‐1 promotes invasion and migration, and decreases chemotherapy sensitivity, indicating that it functions in an oncogenic manner in GBM cells. Taken together, our findings suggest that targeting BRG1 in GBM may have therapeutic benefit in the treatment of this deadly form of brain cancer.

Background: Colorectal cancer (CRC) is one of the most frequent digestive tract tumors in the world with an increasing incidence. Currently, surgical resection and chemotherapy are the main therapeutic options; however, their effects are limited by various adverse reactions. Rauwolfia vomitoria extract (Rau) has been shown to repress the progression of multiple human cancers; however, whether Rau plays a role in CRC remains undetermined. Methods: Influences of Rau treatment on HCT-116 and LoVo cells were estimated via MTT and colony formation experiments. Flow cytometry analysis was adopted to evaluate the apoptosis rate of HCT-116 and LoVo cells. Apoptosis-related proteins (Bcl-2, Bax, and caspase-3) and autophagy-related proteins (LC3 and P62) were assessed by Western blotting. Effects of Rau on autophagy of HCT-116 and LoVo cell were evaluated through GFP-LC3 analysis. In vivo xenograft tumor assay was conducted to further examine the role of Rau in CRC tumor growth. Results: Rau remarkably repressed HCT-116 and LoVo cell viability and promoted HCT-116 and LoVo cell apoptosis in vitro in a dose-dependent manner. Rau increased the expression of caspase-3 and Bax and decreased the expression of Bcl-2 in HCT-116 and LoVo cells. Moreover, Rau was demonstrated to decrease the LC3||/LC3| ratio and increase the level of P62 in HCT-116 and LoVo cells. In addition, we found that Rau repressed xenograft tumor growth and also repressed autophagy in vivo. Conclusion: Our findings revealed that Rau repressed CRC cell viability and autophagy in vitro and in vivo, suggesting that Rau might be a potent therapeutic agent of CRC.

Transcription factors play key roles in cell-fate decisions by regulating 3D genome conformation and gene expression. The traditional view is that methylation of DNA hinders transcription factors binding to them, but recent research has shown that many transcription factors prefer to bind to methylated DNA. Therefore, identifying such transcription factors and understanding their functions is a stepping-stone for studying methylation-mediated biological processes. In this paper, a two-step discriminated method was proposed to recognize transcription factors and their preference for methylated DNA based only on sequences information. In the first step, the proposed model was used to discriminate transcription factors from non-transcription factors. The areas under the curve (AUCs) are 0.9183 and 0.9116, respectively, for the 5-fold cross-validation test and independent dataset test. Subsequently, for the classification of transcription factors that prefer methylated DNA and transcription factors that prefer non-methylated DNA, our model could produce the AUCs of 0.7744 and 0.7356, respectively, for the 5-fold cross-validation test and independent dataset test. Based on the proposed model, a user-friendly web server called TFPred was built, which can be freely accessed at http://lin-group.cn/server/TFPred/., Graphical Abstract, Transcription factors binding to methylated DNA perform special and unclear functions. Lin and colleagues developed a machine-learning-based method to predict transcription factors and their preference for methylated DNA, which will help the discovery of methylated DNA-bound transcription factors and the study of their functions.

N-7 methylguanosine (m7G) modification is a ubiquitous post-transcriptional RNA modification which is vital for maintaining RNA function and protein translation. Developing computational tools will help us to easily predict the m7G sites in RNA sequence. In this work, we designed a sequence-based method to identify the modification site in human RNA sequences. At first, several kinds of sequence features were extracted to code m7G and non-m7G samples. Subsequently, we used mRMR, F-score, and Relief to obtain the optimal subset of features which could produce the maximum prediction accuracy. In 10-fold cross-validation, results showed that the highest accuracy is 94.67% achieved by support vector machine (SVM) for identifying m7G sites in human genome. In addition, we examined the performances of other algorithms and found that the SVM-based model outperformed others. The results indicated that the predictor could be a useful tool for studying m7G. A prediction model is available at https://github.com/MapFM/m7g_model.git.

Cryopreservation of ovarian tissues (OTs) has become the most effective way to preserve the fertility of female cancer patients. However, cryopreservation of OTs is still relatively at an experimental stage. The aim of study is to examine the effect of melatonin (MTL) on cryopreserved-thawed OTs. Fragments of OTs were cryopreserved in medium containing different concentrations (0 mM, 0.001 mM, 0.01 mM, 0.1 mM and 1 mM) of MLT. The endogenous enzymes (GSH-PX, GSH, SOD, CAT and T-AOC), MDA and ROS levels were all evaluated after cryopreservation. Our results showed that the 0.1 mM of MLT significantly improved the survival and diameter of follicles (P 0.001). Meanwhile, the antioxidant enzymes activities (including GSH-PX, GSH, SOD, CAT and T-AOC) were enhanced and MDA content were significantly decreased in 0.1 mM of MLT group compared to other groups (P 0.001). Additionally, compared to the control group, MTL of 0.1 mM resulted in a significantly lower ROS level. In conclusion, MLT protects the quality of cryopreserved OTs by decreasing oxidative stress level and the optimal concentration is 0.1 mM.

Spore production of bryophytes is common in subalpine ecosystems, but how spore banks of bryophytes vary with elevations is unknown. We used peat cores from two Sphagnum dominated peatlands, a low- (780 m a.s.l.) and a high-elevation (1480 m a.s.l.) site to test the hypotheses that spore concentration, accumulation rate, germinability and longevity are lower at a high-elevation peatland than those at lower elevation due to the assumed climatic limitations at high elevation. Along the cores, Sphagnum spores were extracted, burial time of spores was dated and spore germinability was tested layer by layer. Sphagnum spore concentration, accumulation rate and germinability were greater at the high-elevation peatland than at the low-elevation site. Both peatlands had long-term persistent Sphagnum spore banks with a predicted longevity (the burial time when 1% spores are viable) of c. 390 and 140 years for the low- and high-elevation sites, respectively. Our study suggests that Sphagnum, the ecological engineer of peatlands, by regulating spore production and longevity can maintain relatively constant spore banks which may be of great importance in population regeneration and persistence in a changing world.

Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.

Ginseng rusty root (GRR) symptom is one of the primary diseases of ginseng. There has been a problem of ginseng rusty root, leading to a severe decline in the quality of ginseng. To clarify the relationship between root symptoms of ginseng rust and soil, the physical and chemical properties, enzyme activity, community structure and microbial diversity of GRR and healthy ginseng (HG) rhizosphere soil were analyzed and compared. The pH and redox potential (Eh) of GRR soil decreased, and the contents of total phosphorus (TP), available phosphorus (AP), and available potassium (AK) decreased. The activity of catalase and phosphatase and invertase was lower than that of HG groups. Besides, the microbial community of GRR rhizosphere soil changes much, and its abundance and diversity are significantly reduced. The community structure of GRR rhizosphere soil also shows apparent differences, and the samples of the HG group gathered together, and the samples of the GRR group were dispersed. In general, GRR was closely associated with decreases in soil pH and Eh; decreases in TP, AP, and AK; decreases in the activity of several enzymes. Additionally, it is strongly associated with an increase in pathogenic microorganisms such as Ilyonectria and a reduction of beneficial microorganisms such as Tremellomycetes Acidobacteria subgroup 6 and Gemmatimonadetes.

Background and Objectives The effective use of MSCs for the treatment of some B cell-mediated immune diseases is quite limited. The main reason is that the immunomodulatory effects of mesenchymal stem cells (MSCs) on B cells are unclear, and their underlying mechanisms have not been fully explored. Methods and Results By co-culturing B cells with MSCs without (MSC/CTLsh) or with suppressor of cytokine signaling 1 (SOCS1) knockdown (MSC/SOCS1sh), we found that MSCs inhibited B cell proliferation, activation and terminal differentiation. Remarkably, the highest inhibition of B cell proliferation was observed in MSC/SOCS1sh co-culture. Besides, MSC/SOCS1sh reversed the inhibitory effect of MSCs in the last stage of B cell differentiation. However, MSC/SOCS1sh had no effect on inhibiting B cell activation by MSCs. We also showed that IgA+ B cell production was significantly higher in MSC/SOCS1sh than in MSC/CTLsh, although no difference was observed when both MSCs co-cultures were compared to isolated B cells. In addition, MSCs increased PGE2 production after TNF-α/IFN-γ stimulation, with the highest increase observed in MSC/SOCS1sh co-culture. Conclusions Our results highlighted the role of SOCS1 as an important new mediator in the regulation of B cell function by MSCs. Therefore, these data may help to develop new treatments for B cell-mediated immune diseases.

Circadian clock genes are crucial for generating and sustaining most rhythmic daily functions in the animal kingdom, which entrain the rhythms of biochemical, physiological, and behavioural processes. To better understand the molecular oscillations of the circadian rhythms in darkbarbel catfish (Pelteobagrus vachellii), we isolated and characterized two circadian clock genes in P. vachellii, period 1 (per1), and period 3 (per3). The circadian clock gene per1 was found to encode a 1 428-amino acid polypeptide, including PER-ARNT-SIM (PAS) dimerisation domains, a PAS-associated C-terminal motif (PAC), a short mutable domain (S/M), and a nuclear export signal (NES). The 4 902-bp per3 cDNA includes an open reading frame encoding a 1 292-amino acid residue polypeptide with a PER-ARNT-SIM (PAS) domain, cytoplasmic localisation domain (CLD), interaction site (TIS), and a nuclear localisation signal (NLS). The per1 and per3 gene was constitutively expressed in all examined tissues. Moreover, per1 expression within a light/dark cycles showed rhythmic expression in the diencephalon, brain, liver and intestine, with the acrophase at 15:15, 12:52, 7:51, and 12:55, respectively. Daily expression of per3 was rhythmic in the diencephalon, brain, liver and intestine, with the acrophase at 8:15, 9:54, 10:39, and 10:25 h, respectively. These findings expand our understanding of circadian mechanism at the molecular level in this species.

Background An accumulating amount of evidence has suggested that there is a contributive role of sympathetic nervous hyperactivity in the pathogenesis of chronic kidney disease (CKD). α1-AR promotes an increase in calcium levels in podocytes and adjusts podocyte contraction. Changes in TRPC6 expression and function can directly affect the podocyte cytoskeleton, which is a key component in podocyte injury. This study proposed to clarify the correlation between α1-AR activation-induced signal cascade reaction and TRPC6 in human podocytes. Methods Human podocytes were incubated with the calcium probe Fluo-3/AM. Next, the effects of the α1-AR agonists or antagonists and nonselective TRPC6 blockers on intracellular calcium were observed under laser confocal microscopy. FITC-phalloidin was employed to stain podocytes, and the change of F-actin under the α1-AR activation condition was observed. Results The α1-AR agonist PE (phenylephrine hydrochloride) induced an increase in intracellular Ca2+ ([Ca2+]i) in human podocytes. Moreover, the downregulation of TRPC6 by siRNA or TRPC blocker could attenuate the PE-induced [Ca2+]i elevation in a phospholipase C (PLC)-dependent pattern. When podocytes were stimulated to the PE, their F-actin fiber cytoskeletal structure was lost. PE subsequently increased the expression of RhoA, and the TRPC6-dependent Ca2+ influx was involved in this process. The abnormal activation of RhoA could result in disturbance of the podocyte skeleton structure, thus leading to podocyte injury. Conclusions We concluded that TRPC6 is involved in α1-AR activation-induced calcium signal changes in podocytes. Meanwhile, the α1-AR agonists can destroy the cell's cytoskeletal structure, which is mediated by TRPC6 via the RhoA/ROCK pathway.

Background Lung adenocarcinoma is one of the malignant tumors in the world. This study aimed to explore the biological mechanism of GINS2 in lung adenocarcinoma. Materials and methods Raw data were downloaded from GEO. WGCNA co-expression network and PPI network were established to identify the hub gene. The expression profile and clinical features of GINS2 were collected from TCGA-LUAD cohort. Survival analysis in TCGA-LUAD cohort was plotted by R package. GSEA was analyzed via GSEA software. MTS, Transwell and apoptosis assays were used to detect the proliferation, migration and apoptotic abilities of lung adenocarcinoma cells. Results GINS2 was identified as the hub gene via WGCNA co-expression network and PPI network. Higher GINS2 expressions were observed in TCGA-LUAD cohort, GSE32863 and clinical samples dataset. Overexpression of GINS2 had a significantly negative connection with poor survival outcome. GSEA results revealed that GINS2 could be enriched in "HALLMARK_G2M_CHECKPOINT", "HALLMARK_E2F_TARGETS", "HALLMARK_DNA_REPAIR" and "HALLMARK_MYC_TARGETS_V2". Overexpression of GINS2 promoted tumor cell proliferation and migration and suppressed cell apoptosis. Conclusion Our results explored that GINS2 functioned as an oncogene in lung adenocarcinoma, and suggested that GINS2 could act as a promising prognosis biomarker for lung adenocarcinoma.

Background Astrocytes are crucial regulators in the central nervous system. Abnormal activation of astrocytes contributes to some behavior deficits. However, mechanisms underlying the effects remain unclear. Here, we studied the activation of A1 astrocytes and their contribution to murine behavior deficits. Methods A1 astrocytes were induced by treatment with lipopolysaccharide (LPS) in vitro. The functional phenotype of astrocytes was determined by quantitative RT-PCR, ELISA, and immunohistochemistry. To assess the role of A1 astrocytes in vivo, mice were injected intraperitoneally with LPS. Then, murine behaviors were tested, and the hippocampus and cortex were analyzed by quantitative RT-PCR, ELISA, and immunohistochemistry. The function of IL-10 and fluorocitrate on A1 astrocyte activation was also examined. Results Our results show that astrocytes isolated from B6.129S6-Il10tm1Flv/J homozygotes (IL-10tm1/tm1) were prone to characteristics of A1 reactive astrocytes. Compared with their wild-type counterparts, IL-10tm1/tm1 astrocytes exhibited higher expression of glial fibrillary acidic protein (GFAP). Whether or not they were stimulated with LPS, IL-10tm1/tm1 astrocytes exhibited enhanced expression of A1-specific transcripts and proinflammatory factors IL-1β, IL-6, and TNFα. In addition, IL-10tm1/tm1 astrocytes demonstrated hyperphosphorylation of STAT3. Moreover, astrocytes from IL-10tm1/tm1 mice showed attenuated phagocytic ability and were neurotoxic. IL-10tm1/tm1 mice demonstrated increased immobility time in the forced swim test and defective learning and memory behavior in the Morris water maze test. Moreover, enhanced neuroinflammation was found in the hippocampus and cortex of IL-10tm1/tm1 mice, accompanying with more GFAP-positive astrocytes and severe neuron loss in the hippocampus. Pretreatment IL-10tm1/tm1 mice with IL-10 or fluorocitrate decreased the expression of proinflammatory factors and A1-specific transcripts in the hippocampus and cortex, and then alleviated LPS-induced depressive-like behavior. Conclusion These results demonstrate that astrocytes isolated from B6.129S6-Il10tm1Flv/J homozygotes are prone to A1 phenotype and contribute to the depression-like behavior and memory deficits. Inhibiting A1 astrocyte activation may be an attractive therapeutic strategy in some neurodegenerative diseases.

In aquaculture, it is necessary to determine of the diurnal biological variations in the intestines to determine an appropriate feeding schedule. The present study aimed to examine the transcriptomes of the

Three prokaryotic predator strains, BL9T, BL10 and BL28, were isolated with Vibrio alginolyticus from coastal seawater of PR China. Cells of the strains were Gram-negative, vibrioid-shaped and motile with a single sheathed flagellum (25–28 nm wide). Cells were around 0.3×0.5–1.0 µm in size. The three strains were obligate predators that exhibited a biphasic life cycle: a free-swimming attack phase and an intraperiplasmic growth phase within the prey. Bdelloplasts were formed. NaCl was required for growth. Optimum growth occurred at ~37 °C, with 2–4 % (w/v) NaCl and at pH 7.0–8.0. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains shared 99.9 % similarity to each other, were affiliated with the genus Halobacteriovorax in the class Oligoflexia, and represented the same new species. Strain BL9T (=MCCC 1K03527T=JCM 32962T) was designated as the type strain. Genome sequencing of strain BL9T revealed a genome size of 3.14 Mb and a G+C content of 35.8 mol%. The estimated digital DNA–DNA hybridization (dDDH) values and the whole genome average nucleotide identity (gANI) values between the genome of strain BL9T and those of Bdellovibrionales and Bacteriovoracales were 12.5–19 and 63.49–76.15 %, respectively. On the basis of life cycle features, results of physiological analyses, gANI data and dDDH data, strain BL9T represents a new species within the genus Halobacteriovorax , for which the name Halobacteriovorax vibrionivorans sp. nov. is proposed.

Soil fungistasis is a phenomenon in which the germination and growth of fungal propagules is widely inhibited in soils. Although fungistatic compounds are known to play important roles in the formation of soil fungistasis, how such compounds act on soil fungi is little studied. In this study, it was found that ammonia (NH3) induced global protein misfolding marked by increased ubiquitination levels of proteins (ubiquitylome data and Western blot verification). The misfolded proteins should trigger the endoplasmic reticulum (ER) stress, which was indicated by electron microscope image and proteome data. Results from the mutants of BiP and proteasome subunit alpha 7 suggested that ER stress played a mechanistic role in inhibiting conidial germination. Results from proteome data indicated that, to survive ammonia fungistasis, conidia first activated the unfolded protein response (UPR) to decrease ER stress and restore ER protein homeostasis, and the function of UPR in surviving ammonia was confirmed by using mutant strains. Second, ammonia toxicity could be reduced by upregulating carbon metabolism-related proteins, which benefited ammonia fixation. The results that metabolites (especially glutamate) could relieve the ammonia fungistasis confirmed this indirectly. Finally, results from gene knockout mutants also suggested that the fungistatic mechanism of ammonia is common for soil fungistasis. This study increased our knowledge regarding the mechanism of soil fungistasis and provided potential new strategies for manipulating soil fungistasis. IMPORTANCE Soil fungistasis is a phenomenon in which the germination and growth of fungal propagules is widely inhibited in soil. Although fungistatic compounds are known to play important roles in the formation of soil fungistasis, how such compounds act on soil fungi remains little studied. This study revealed an endoplasmic reticulum stress-related fungistatic mechanism with which ammonia acts on Arthrobotrys oligospora and a survival strategy of conidia under ammonia inhibition. Our study provides the first mechanistic explanation of how ammonia impacts fungal spore germination, and the mechanism may be common for soil fungistasis. This study increases our knowledge regarding the mechanism of soil fungistasis in fungal spores and provides potential new strategies for manipulating soil fungistasis.

Phoenix canariensis Chabaud is a vital ornamental and widely planted in the urban landscape of China. In this study, we reported the complete chloroplast genome (cpDNA) of P. canariensis, which is ...

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (∼80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.One-sentence summaryMultiomics analysis reveals the regulatory plasticity of plants in response to beneficial and antagonistic microbes, resulting in distinct phenotypes and rewired transcriptional networks.

Background Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control. Results We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens. Conclusion Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens.

Purpose: Diabetic retinopathy (DR) is one of the most common diabetic microvascular complications. However, the pathogenesis of DR has not yet been fully elucidated. This study aimed to discover novel and key molecules involved in the pathogenesis of DR, which could potentially be targets for therapeutic DR intervention.Methods: To identify potential genes involved in the pathogenesis of DR, we analyzed the public database of neovascular membranes (NVMs) from patients with proliferative diabetic retinopathy (PDR) and healthy controls (HCs) (GSE102485, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102485). Further, we compared these findings by performing RNA-sequencing analysis of peripheral blood mononuclear cells (PBMC) from patients with DR, control patients with non-complicated diabetes mellitus (DMC), and HCs. To determine the critical role of candidate genes in DR, knockdown or knockout was performed in human retinal vascular endothelial cells (HRVECs). The oxidative stress pathway, as well as tight junction integrity, was analyzed.Results: Transcriptional profiles showed distinct patterns between the NVMs of patients with DR and those of the HCs. Those genes enriched in either extracellular matrix (ECM)-receptor interaction or focal adhesion pathways were considerably upregulated. Both pathways were important for maintaining the integrity of retinal vascular structure and function. Importantly, the gene encoding the matricellular protein CCN1, a key gene in cell physiology, was differentially expressed in both pathways. Knockdown of CCN1 by small interfering RNA (siRNA) or knockout of CCN1 by the CRISPR-Cas9 technique in HRVECs significantly increased the levels of VE-cadherin, reduced the level of NADPH oxidase 4 (NOX4), and inhibited the generation of reactive oxygen species (ROS).Conclusion: The present study identifies CCN1 as an important regulator in the pathogenesis of DR. Increased expression of CCN1 stimulates oxidative stress and disrupts tight junction integrity in endothelial cells by inducing NOX4. Thus, targeting the CCN1/NOX4 axis provides a therapeutic strategy for treating DR by alleviating endothelial cell injury.

In this paper, a novel and ultrasensitive lateral flow assay (LFA) based on aptamer–magnetic separation, and multifold Au nanoparticles (AuNPs) was developed for visual detecting Salmonella enterica ser. Typhimurium (S. Typhimurium). The method realized magnetic enrichment and signal transduction via magnetic separation and achieved signal amplification through hybridizing AuNPs–capture probes and AuNPs–amplification probes to form multifold AuNPs. Two different thiolated single-strand DNA (ssDNA) on the AuNPs–capture probe played different roles. One was combined with the AuNPs–amplification probe on the conjugate pad to achieve enhanced signals. The other was connected to transduction ssDNA1 released by aptamer–magnetic capture of S. Typhimurium, and captured by the T-line, forming a positive signal. This method had an excellent linear relationship ranging from 8.6 × 102 CFU/mL to 8.6 × 107 CFU/mL with the limit of detection (LOD) as low as 8.6 × 100 CFU/mL in pure culture. In actual samples, the visual LOD was 4.1 × 102 CFU/mL, which did not carry out nucleic acid amplification and pre-enrichment, increasing three orders of magnitudes than unenhanced assays with single–dose AuNPs and no magnetic separation. Furthermore, the system showed high specificity, having no reaction with other nontarget strains. This visual signal amplificated system would be a potential platform for ultrasensitive monitoring S. Typhimurium in milk samples.

In the course of screening for bacterial predator, a Gram-negative, non-flagellated, gliding, long rod-shaped and yellow-pigmented bacterium, designated strain HICWT, was isolated from coastal seawater of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HICWT represented a member of the genus Muricauda and showed the highest sequence similarity to M. aquimarina JCM11811T (98.8%) and M. ruestringensis DSM13258T (98.1%). NaCl was required for growth. Optimum growth occurred at 25–30 oC, 2.0–3.0% (w/v) NaCl with pH 7.0. Strain HICWT showed some similar characteristics to the nonobligate bactertal predators, the cells can attach the prey cells. Strain HICWT contained MK-6 as the predominant respiratory quinone and had iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major cellular fatty acids. The polar lipids contained phosphatidylethanolamine (PE), three unknown phospholipids (PL1–PL3), one unknown aminolipids (AL) and three unknown polar lipids (L1–L3). The genome size of strain HICWT was approximately 3.8 Mbp, with a G+C content of 41.4%. On the basis of the polyphasic evidence, strain HICWT is proposed as representing a new species of the genus Muricauda, for which the name Muricauda chongwuensis sp. nov. is proposed. The type strain is HICWT (=JCM 33643T=MCCC 1K03769T).

Cutaneous blastomycosis is endemic to North America and is often caused by dimorphic fungi with spores that are inhaled, inoculated spores, or hyphae that infect immunosuppressed and healthy people. It is sporadic and described as a universal imitator with morphological manifestations as erythema, nodules, and ulcers. Our case demonstrated a 69-year-old female bitten by her pet dog who was then diagnosed with cutaneous blastomycosis through social history and detailed laboratory examinations. She experienced a prolonged failure with antibacterial treatment, negative stool and tissue culture, and chronic inflammatory cell infiltrates on tissue pathology. High-throughput sequencing was performed and showed evidence of Blastomyces dermatitidis aetiology. Photodynamic therapy combined with oral itraconazole was administered, and the patient recovered in a short time. Our case presents inoculated cutaneous blastomycosis and a treatment approach in which photodynamic therapy combined with oral itraconazole significantly reduced the duration of disease treatment and affords a promising choice for the treatment of cutaneous blastomycosis.

The tumor microenvironment plays an important role in tumor progression. Hyaluronic acid (HA), an important component of the extracellular matrix in the tumor microenvironment, abnormally accumulates in a variety of tumors. However, the role of abnormal HA accumulation in glioma remains unclear. The present study indicated that HA, hyaluronic acid synthase 3 (HAS3), and a receptor of HA named CD44 were expressed at high levels in human glioma tissues and negatively correlated with the prognosis of patients with glioma. Silencing HAS3 expression or blocking CD44 inhibited glioma cell proliferation in vitro and in vivo. The underlying mechanism was attributed to the inhibition of autophagy flux and maintaining glioma cell cycle arrest in G1 phase. More importantly, 4-methylumbelliferone (4-MU), a small competitive inhibitor of Uridine diphosphate (UDP) with the ability to penetrate the blood-brain barrier (BBB), also inhibited glioma cell proliferation in vitro and in vivo. Thus, approaches that interfere with HA metabolism by altering the expression of HAS3 and CD44 and the administration of 4-MU potentially represent effective strategies for glioma treatment.

Cell walls are at the front line of interactions between walled-organisms and their environment. They support cell expansion, ensure cell integrity and, for multicellular organisms such as plants, they provide cell adherence, support cell shape morphogenesis and mediate cell-cell communication. Wall-sensing, detecting perturbations in the wall and signaling the cell to respond accordingly, is crucial for growth and survival. In recent years, plant signaling research has suggested that a large family of receptor-like kinases (RLKs) could function as wall sensors partly because their extracellular domains show homology with malectin, a diglucose binding protein from the endoplasmic reticulum of animal cells. Studies of several malectin/malectin-like (M/ML) domain-containing RLKs (M/MLD-RLKs) from the model plant Arabidopsis thaliana have revealed an impressive array of biological roles, controlling growth, reproduction and stress responses, processes that in various ways rely on or affect the cell wall. Malectin homologous sequences are widespread across biological kingdoms, but plants have uniquely evolved a highly expanded family of proteins with ML domains embedded within various protein contexts. Here, we present an overview on proteins with malectin homologous sequences in different kingdoms, discuss the chromosomal organization of Arabidopsis M/MLD-RLKs and the phylogenetic relationship between these proteins from several model and crop species. We also discuss briefly the molecular networks that enable the diverse biological roles served by M/MLD-RLKs studied thus far.

Ginseng rusty root symptom (GRS) is one of the primary diseases of ginseng. It leads to a severe decline in the quality of ginseng and significantly affects the ginseng industry. The regulatory mechanism of non-coding RNA (ncRNA) remains unclear in the course of disease. This study explored the long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) in GRS tissues and healthy ginseng (HG) tissues and performed functional enrichment analysis of the screened differentially expressed ncRNAs. Considering the predictive and regulatory effects of ncRNAs on mRNAs, we integrated ncRNA and mRNA data to analyze and construct relevant regulatory networks. A total of 17,645 lncRNAs, 245 circRNAs, and 299 miRNAs were obtained from HG and GRS samples, and the obtained ncRNAs were characterized, including the classification of lncRNAs, length and distribution of circRNA, and the length and family affiliations of miRNAs. In the analysis of differentially expressed ncRNA target genes, we found that lncRNAs may be involved in the homeostatic process of ginseng tissues and that lncRNAs, circRNAs, and miRNAs are involved in fatty acid-related regulation, suggesting that alterations in fatty acid-related pathways may play a key role in GRS. Besides, differentially expressed ncRNAs play an essential role in regulating transcriptional translation processes, primary metabolism such as starch and sucrose, and secondary metabolism such as alkaloids in ginseng tissues. Finally, we integrated the correlations between ncRNAs and mRNAs, constructed corresponding interaction networks, and identified ncRNAs that may play critical roles in GRS. These results provide a basis for revealing GRS's molecular mechanism and enrich our understanding of ncRNAs in ginseng.

Toxoplasma gondii and Neospora caninum are protozoan parasites that infect warm-blooded animals, and cause major economic losses in livestock industries worldwide. However, little is known about the genotypes of T. gondii and N. caninum in domestic ducks in China. Herein, brain samples from 588 domestic ducks from Hunan province in China were examined for the presence of T. gondii and N. caninum. Polymerase chain reaction (PCR) was used to detect T. gondii B1 gene and N. caninum NC-5 gene. Forty-five DNA samples (7.7%; 95% CI: 5.5–9.9) were positive for B1 gene, and two (0.3%; 95% CI: 0–0.7) were positive for NC-5 gene. The risk factors significantly associated with T. gondii infection were age and sex. The 45 samples positive for T. gondii were genotyped using multi-locus PCR-RFLP analysis and only one sample was fully genotyped as ToxoDB#9 (Chinese I). These results provide new information about the epidemiology of T. gondii and N. caninum in ducks in Hunan province in China. The data also highlight the importance of a “One Health” approach to dealing with toxoplasmosis.

Biocontrol of root-knot nematode has attracted increasing attention over the past two decades. The inconsistent field performance of biocontrol agents, which is caused by soil fungistasis, often restricts their commercial application. There is still a lack of research on the genes involved in biocontrol fungi response to soil fungistasis, which is important for optimizing practical applications of biocontrol fungi. In this study, the lactoylglutathione lyase-encoding AOL_s00004g335 in the nematophagous fungi Arthrobotrys oligospora was knocked out, and three mutant strains were obtained. The hyphal growth of mutants on the three media was almost the same as that of the wild-type strain, but mutants had slightly higher resistance to NaCl, SDS, and H2O2. Methylglyoxal (MG) significantly increased the resistance of A. oligospora to ammonia, but decreased the resistance to benzaldehyde. Furthermore, the resistance of the mutants to soil fungistasis was largely weakened and MG could not increase the resistance of A. oligospora to soil fungistasis. Our results revealed that MG has different effects on the fungistatic roles of ammonia and benzaldehyde and that lactoylglutathione lyase is very important for A. oligospora to resist soil fungistasis.

Two new diketopiperazines (1, 2), one new polyprenol (3), together with 19 known compounds (4-22) were obtained from the EtOAc extract of Bionectria sp. Y1085, an endophytic fungus isolated from the plant Huperzia serrata. Their structures were elucidated by extensive NMR and MS analysis. Bionectin D (1) is a rare diketopiperazine with a single methylthio substitution at the α-carbon of cyclized amino acid residue. The antibacterial activity of compounds was assayed against Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium ATCC 6539, and some metabolites (1, 2, 10, 11, and 14) exhibited evident antibacterial activity.

Researches have shown that mice lacking the metabotropic glutamate receptor 1 (mGluR) showed albuminuria, remodeling of F-actin, with loss of stress fibers. Selective group I mGluRs agonist (S)-3,5-dihydroxyphenylglycine (DHPG) attenuated albuminuria in several rodent models of nephrotic syndrome. However, the molecular mechanism is obscure. Using a human podocyte cell line, we here investigated the molecular mechanisms of group I mGluRs-induced calcium influx and the formation of stress fibers. Our data showed that group I mGluRs activation by DHPG induced a significant calcium influx, and promoted cytoskeletal stress fiber formation and focal adhesions in podocytes. Pre-incubating podocytes with non-selective inhibitor of transient receptor potential channels (TRPC), or the knockdown of TRPC6 attenuated the calcium influx and the stress fiber formation induced by DHPG. Further, DHPG resulted in an increase of active RhoA expression. However, the knockdown of RhoA by siRNA abolished the DHPG-induced increase in stress fibers. Additionally, nonselective inhibitors of TRPC or TRPC6 knockdown clearly inhibited RhoA activation induced by DHPG, as assessed by Glutathione-S-transferase pull-down assay followed by Western blotting. Taken together, our findings suggest TRPC6 regulates actin stress fiber formation and focal adhesions via the RhoA pathway in response to group I mGluRs activation. Our data can potentially explain the mechanism of protective action of group I mGluRs in glomerular podocyte injury.

Pigment pattern formation in economical fish remains elusive to date. Oujiang color common carp (Cyprinus carpio var. color) is a variant of common carp with different pigmentation patterns and important farm fish in China. Agouti signaling protein (ASIP) is an endogenous antagonist of melanocortin in the melanogenesis pathway. In this study, two ASIP genes (ASIP 1 and ASIP 2) were first identified in color common carp. Their expression was higher in the pale belly than in the dark dorsal skin, which was consistent with the typical dorsal–ventral expression pattern such as that of wild common carp. In comparison, an unusually higher expression was detected in the non-melanophore side skin than in the melanophore side skin of Oujiang color common carp. Thus, CRISPR/Cas9 was used to disrupt the two ASIP genes in Oujiang color common carp of red with big black patches (RB) pattern. Consequently, the black patches disappeared and the melanophores dispersed along the dorsal skin in the F0 mosaic RB individuals. The findings of this study indicate that the ASIP gene is involved in regulating melanin aggregation and distribution during black patch formation in Oujiang color common carp.

Background Disabled-2 (Dab2) is known as a tumor suppressor as well as a Wnt pathway inhibitor. We previously reported that Dab2 was down-regulated due to gene promoter hypermethylation in lung cancer. Here, we aim to study if X-ray irradiation can induce de-methylation of the Dab2 gene and subsequently up-regulate its expression, and also to attempt to suppress the malignant biological behavior of and enhance the radiosensitivity in lung cancer cells with hypermethylation of the Dab2 gene. Methods Immunostaining was performed to investigate the relationship between Dab2 expression and lung cancer clinicopathological characteristics. Bisulfite sequencing PCR (BSP) was used to evaluate the methylation status of lung cancer cells with or without X-ray treatment. Real-time PCR and western Blot were performed to investigate the expression of Dab2, Wnt pathway factors, DNMTs and methyl CpG binding protein 2 (MeCP2). Colony Formation, matrigel invasion and xenograft experiment were performed to evaluate the malignant biological behavior of lung cancer cells with irradiation. Results The result of immunostaining of Dab2 in lung cancer tissues showed that decreased Dab2 expression was positively correlated with poor differentiation, lymph node metastasis, advanced TNM stage and poor prognosis. X-ray treatment significantly up-regulated Dab2 expression and inhibited Wnt factors in LK2 cells (with hypermethylation of the Dab2 gene promoter, P

Simultaneous denitrification and anammox process are newly developed wastewater treatment processes with high-nitrogen removal efficiency, but little information is available regarding its optimal operational conditions and molecular mechanisms. In this study, a lab-scale up-flow anaerobic sludge blanket bioreactor fed with nitrate and ammonia was continuously operated for 180 days to establish the simultaneous denitrification and anammox system, so as to investigate the changing patterns of nitrogen removal efficiency and functional bacteria and genes at varying substrate loadings. Results showed that the optimal removal efficiency of total nitrogen (TN) reached 92.47%, corresponding to TN loading removal rate of 0.9 kg-N m−3 day−1 that was achieved at low influent substrate concentrations and short hydraulic retention time (HRT) (4 h). High-throughput sequencing of 16S rRNA gene amplicons revealed that the predominant denitrifying and anammox bacteria in the coupling system were Thauera (relative abundance of 25.30%) and Candidatus Brocadia (relative abundance of 6.85%), respectively. Quantitative real-time PCR showed that the anammox genes (hzsA, hzsB, and hzo) and denitrifying genes (narG, napA, and nirS) demonstrated high abundance in the optimized bioreactor. Batch experiments were also conducted to determine the temporal difference in the expression of the anammox and denitrifying genes. NarG was found to play a crucial role in nitrate reduction to produce nitrite for anammox bacteria, while nirS was identified as the key genes for nitrite reduction to produce nitric oxide, which acted as an important role in both denitrification and anammox reaction.

The diamondback moth, Plutella xylostella, is one of the most serious insect pests of cruciferous crops all over the world. Although chemical insecticides are used to control this pest, it develops resistance to almost all kinds of insecticides. In recent, triterpenoid saponins have been reported to show potent antifeedant or synergize insecticidal activity on several pests. Therefore, to assess the antifeedant activity of ginsenosides against P. xylostella is benefit to biological control of this pests. Total ginsenosides were extracted from ginseng leaves and stems, and the total content of 9 ginsenosides was 72.91 mg/mL measured by high-performance liquid chromatography (HPLC) method. Total ginsenosides extracted from ginseng leaves and stems showed significant antifeedant activity on P. xylostella larvae in both non-choice and choice assays. The concentration of median antifeedant (AFC50) of total ginsenosides for the second instar larval of P. xylostella were 4.98 and 5.03 mg/mL at 24 h and 48 h respectively in non-choice assay, and they were 2.74 and 4.14 mg/mL respectively in choice assay. The residue rate of 9 ginsenosides in the pest became gradually higher as applied concentration increased. Feeding with ginsenosides generally resulted in decrease of glutathione S-transferase (GST), acetylcholine esterase (AChE), and carboxylesterase (CarE) activities, but increase of mixed-functional oxidase (MFO) activity in P. xylostella. These results indicate that ginsenosides are suitable for developing it into a botanical pesticide.

Introduction Infantile leukemia encompasses a heterogeneous group which needs stratifying for treatment selection. Methods We collected 78 cases of infantile leukemia and retrospectively analyzed their clinicopathological data. Results Infantile leukemia featured a ratio of acute myeloid leukemia (AML) to B-lymphoblastic leukemia (B-ALL) of 1:2, with a better survival for AML than B-ALL (median survival 36 vs 24 months). When stratified by age, "early" infantile B-ALL (2-6 months) showed a high rate of KMT2A rearrangement (100%), similar to the rate seen in congenital B-ALL (1 month) (100%) and higher than seen in "late" infantile B-ALL (≥7 months) (68%). The three categories of infantile B-ALL exhibited an age-dependent increase in survival (median survival 8.5, 24, and >24 months, respectively). The age-dependent survival benefit remained after excluding the cases negative for KMT2A rearrangement. Conversely, infantile AML lacked an age-dependent pattern of survival. Conclusion The clinical outcome of infantile leukemia depends on the type of leukemia. Given the age-dependent survival, infantile B-ALL can be divided into three subcategories.

Globally, lung cancer remains one of the most prevalent malignant cancers. However, molecular mechanisms and functions involved in its pathogenesis have not been clearly elucidated. This study aimed to evaluate the specific regulatory mechanisms of exosomal miR-338-3p/CHL1/MAPK signaling pathway axis in non-small-cell lung cancer. Western blotting and qRT-PCR (reverse transcription-polymerase chain reaction) were used to determine the expression levels of CHL1 and exosomal miR-338-3p in NSCLC (non-small-cell lung cancer). The CHL1 gene was upregulated and downregulated to evaluate its functions in NSCLC progression. In vitro MTS and apoptotic assays were used to investigate the functions of CHL1 and exosomal miR-338-3p in NSCLC progression. The high-throughput sequencing was used to explore differently expressed exosomal miRNAs. The biological relationships between MAPK signaling pathway and CHL1 and exosomal miR-338-3p in NSCLC were predicted through bioinformatics analyses and verified by western blotting. Elevated CHL1 levels were observed in NSCLC tissues and cells. Upregulated CHL1 expression enhanced NSCLC cells’ progression by promoting tumor cells proliferation while suppressing their apoptosis. Conversely, the downregulation of the CHL1 gene inhibited NSCLC cells’ growth and promoted tumor cells’ apoptotic rate. Additionally, CHL1 activated the MAPK signaling pathway. Besides, we confirmed that miR-338-3p directly sponged with CHL1 to mediate tumor cells progression. Moreover, exosomal miR-338-3p serum levels in NSCLC patients were found to be low. BEAS-2B cells can transfer exosomal miR-338-3p to A549 cells and SK-MES-1 cells. In addition, elevated exosomal miR-338-3p levels significantly inhibited tumor cells proliferation and promoted their apoptosis by suppressing activation of the MAPK signaling pathway. Exosomal miR-338-3p suppresses tumor cells' metastasis by downregulating the expression of CHL1 through MAPK signaling pathway inactivation.

Purpose: Brain gliomas are the most common primary malignant tumors of the central nervous system and one of the leading causes of death in patients with intracranial tumors. The lncRNA RPL34-AS1 is significantly upregulated in glioma tissues. However, the biological function of RPL34-AS1, especially in proliferation in glioma, remains unclear. Methods: The role of RPL34-AS1 in proliferation and angiogenesis in glioma cells was investigated using the LN229, U87, and U251 glioma cell lines. The levels of RPL34-AS1 were detected using real-time quantitative reverse transcription polymerase chain reaction. CCK-8 and colony formation assays were performed to determine the role of RPL34-AS1 in proliferation and survival, and its role in angiogenesis was assessed by an endothelial tube formation assay. Changes in protein levels were assessed by western blotting. Results: RPL34-AS1 was upregulated in glioma tissues and was correlated with tumor grade. RPL34-AS1 expression was also higher in glioma cells than in normal astrocytes. Knockdown of RPL34-AS1 blocked glioma cell proliferation by inhibiting angiogenesis. This effect occurred through decreased ERK/AKT signaling. Conclusions: This study suggests that RPL34-AS1 affects cell proliferation and angiogenesis in glioma and therefore may potentially serve as a valuable diagnostic and prognostic biomarker and therapeutic target in patients with glioma.

Background Ginseng red skin root syndrome (GRS) is one of the most common ginseng diseases. It leads to a severe decline in ginseng quality and seriously affects the ginseng industry in China. However, as a root disease, the characteristics of GRS rhizosphere microbiome are still unclear. Methods The amplicon sequencing technology, combined with bioinformatics analysis, was used to explore the relationship between soil ecological environment and GRS. Results There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy ginseng (HG) and heavily diseased groups. We also found that bacterial communities underwent multiple changes between complex stability and simple instability in different ginseng rhizospheres through the established interaction networks. The GRS group also had more competition with each other and ecological niche separation than the HG group. The fungal community's stability decreased significantly in the early stages of the disease, followed by the formation of a stable and complex fungal community. The GRS groups significantly increased interspecies cooperation and ecological niche overlap in the fungal network than the HG group. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total P (TP), available K (AK), available P (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Conclusions This study collectively analyzed the changing characteristics in ginseng rhizosphere and provided the basis for soil improvement and biological control of field-grown ginseng.

Necrotizing enterocolitis (NEC) remains a fatal gastrointestinal disorder in neonates. Disialyllacto-N-tetraose (DSLNT), a function-unclear human milk-derived hexasaccharide, shows anti-NEC potential in previous animal studies. This study is aimed to explore the role of mast cell (MC), a fundamental cell type of mucosal immune system and protective DSLNT in regulating pathological process of NEC. For this purpose, infantile intestinal-tissues were collected from NEC neonates for examination of MCs and its proteases-positive cells. MC accumulation and MC-specific proteases (chymase, tryptase and dipeptidyl peptidase I) were firstly found in lesioned area of NEC infants in-vivo. Subsequent in-situ experiments on neonatal ileum segments showed that purified MC-chymase induced a destructive epithelial layer shedding from basement and microvascular endothelium damage in infantile intestinal segments. Human foreskin MC-activation model was established and DSLNT were applied; MC products (histamine and MC-proteases) were used as MC activation/degranulation indicators. In this in-vitro model, DSLNT pretreatment suppressed release of histamine, chymase and tryptase by MC to the tissue supernatants during lipopolysaccharide or complement C5a stimulation. Newborn rats were formula-hand-fed with or without DSLNT supplement and exposed to hypoxia/cold-stress to induce experimental-NEC-model. In NEC rats, DSLNT supplementation reduced the incidence and pathological scores of NEC, inhibited local accumulation of MC and reduced cytokines (IL-1β, IL-6 and TNF-α) levels in the ileum of rats. In conclusion, MC was causally implicated in epithelium barrier failure in pathogenesis of NEC. DSLNT favorably modulated MC homeostasis by regulating MC degranulation/accumulation, contributing to attenuated NEC. This indicated novel pathomechanisms and potential targets of NEC.

Cellular senescence is a stable state of cell cycle arrest elicited by various stresses. Hypoxia modulates senescence, but its consequences and implications in living organisms remains unknown. Here we identified the eIF4E2-GSK3β pathway regulated by hypoxia to maintain p53 proline-directed phosphorylation (S/T-P) to prevent senescence. We previously knew that GSK3β activates p53 translation through phosphorylation of RBM38 Ser195 (-Pro196). Unexpectedly, eIF4E2 directly binds to GSK3β via a conserved motif, mediating Ser195 phosphorylation. Phosphoproteomics revealed that eIF4E2-GSK3β specifically regulates proline-directed phosphorylation. Peptide e2-I or G3-I that disrupts this pathway dephosphorylates p53 at multiple S/T-P, which accelerate senescence by transcriptional suppressing TOPBP1 and TRX1. Consistently, peptides induce liver senescence that is rescued by TOPBP1 expression, and mediate senescence-dependent tumor regression. Furthermore, hypoxia inhibits eIF4E2-GSK3β. Inspiringly, eIF4E2-GSK3β is unique to mammals, which maintains mice viability and prevents liver senescence against physiological hypoxia. Interestingly, this mammalian eIF4E2 protects heart of zebrafish against hypoxia. Together, we identified a mammalian -unique eIF4E2-GSK3β pathway preventing senescence and guarding against hypoxia in vivo.

Our previous study revealed that melatonin (MLT) protected the quality of cryopreserved ovarian tissues in mice. This work was carried out to examine the role of MLT in inducing HSP90 expression of ovarian tissue for achieving cryoprotection. Pieces of ovarian tissues were obtained from 50 female rats treated with MLT at 0, 0.001, 0.01, 0.1, and 1 mM, respectively. After cryopreservation-thawing, HSP90 mRNA and protein level were evaluated using qRT-PCR and western blot. The qRT-PCR results revealed that HSP90 mRNA expression was significantly (p 0.01) upregulated in MLT-treated groups in comparison with the controls (0 mM). Western blot revealed higher HSP90 protein expression in MLT-treated groups compared to control group (0 mM), thus further confirming that MLT positively affected HSP90 expression. Moreover, 0.1 mM MLT had better effects than other concentrations of MLT. Conclusively, findings in the present work provide a feasible technology for improving cryopreserved ovarian tissue quality through the addition of MLT to elicit HSP90 expression.

Myostatin (MSTN) is a negative regulation factor involved in skeletal muscle growth and development in vertebrates. In order to understand the multi-functional roles of MSTN in crustaceans, we assessed the molting / growth characters, analyzed the tissues composition and investigated the expression levels of lipid metabolism and immune related genes in Chinese mitten crab (Eriocheir sinensis) after injection of Es-MSTN dsRNA during one molt cycle of 49 days. We found the RNAi group displayed shorter molting interval, higher specific growth rate, and lower hepatosomatic index compared with the control group, evidencing MSTN may also be a negative regulator of muscle growth and development in E. sinensis. In the RNAi group, the expression levels were upregulated for lipid metabolism-related genes of pancreatic lipase (LP), carnitine palmitoyl transferases 1β (CPT1β) and fatty acid-binding protein 3 (FABP3) in muscles, but were downregulated for these three genes and fatty acid-binding protein 9 (FABP9) in hepatopancreas. Meanwhile, the expression levels were all upregulated for immune-related genes of prophenoloxidase (PHE), anti-lipopolysaccharide factor (ALF), Lectin H (LecH), and prophenoloxidase-activating factor (PPAF) in both muscle and hepatopancreas in the RNAi group. Further tissue composition analysis showed that there were no significant differences in amino acid composition between the RNAi and control groups in muscle and hepatopancreas, but most of significant differences in fatty acid composition were detected between the two groups in both muscle and hepatopancreas. This study demonstrated that Es-MSTN is a vital muscle growth inhibition factor and displayed diverse function in participating in energy metabolism and immune response in E. sinensis.