Lysobacter lactosilyticus sp. nov., a Novel ß-Galactosidase Producing Bacterial Strain Isolated from Farmland Soil Applied with Amino Acid Fertilizer.

To isolate ß-galactosidase producing bacterial resources, a novel Gram-stain-negative, strictly aerobic bacterial strain designated as A6T was obtained from a farmland soil sample. Cells of the strain were rod-shaped (0.4-0.7 µm × 1.8-2.2 µm) without flagella and motility. Strain A6T grew optimally at 30 °C, pH 7.0 with 0% (w/v) NaCl. Based on phylogenetic analysis, strain A6T clustered within the genus Lysobacter clade and branched with Lysobacter dokdonensis KCTC 12822T (99.5%, 16S rRNA gene sequence similarity) and Lysobacter caseinilyticus KACC 19816T (98.5%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain A6T and Lysobacter dokdonensis KCTC 12822T were 82.7% and 26.2%, and the values for strain A6T and KACC 19816T were 81.4% and 23.8%, respectively. Iso-C16:0, iso-C15:0, summed feature 9 (C17:1 iso ω9c and/or C16:0 10-methyl) and summed feature 3 (C16:1ω7c and/or C16:1 ω6c) were the major fatty acids, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, and ubiquinone 8 (Q-8) was the major ubiquinone. The genomic DNA G+C content was 67.2 mol%. Furthermore, under the condition of 30 °C, pH 7.0, 4% inoculation with 10.0 g L-1 lactose, the ß-galactosidase activity produced by strain A6T was highest, reaching 95.3 U mL-1, indicating that this strain could be applied as a potential strain for ß-galactosidase production. Strain A6T represents a novel species of the genus Lysobacter, and Lysobacter lactosilyticus sp. nov. is proposed on the basis of phenotypic, genotypic, and chemotaxonomic analysis. The type strain is A6T (=KCTC 82184T=CGMCC 1.18582T).

Comprehensive analysis of an immune infiltrate-related competitive endogenous RNA network reveals potential prognostic biomarkers for non-small cell lung cancer.

Globally, non-small cell lung cancer (NSCLC) is the most common malignancy and its prognosis remains poor because of the lack of reliable early diagnostic biomarkers. The competitive endogenous RNA (ceRNA) network plays an important role in the tumorigenesis and prognosis of NSCLC. Tumor immune microenvironment (TIME) is valuable for predicting the response to immunotherapy and determining the prognosis of NSCLC patients. To understand the TIME-related ceRNA network, the RNA profiling datasets from the Genotype-Tissue Expression and The Cancer Genome Atlas databases were analyzed to identify the mRNAs, microRNAs, and lncRNAs associated with the differentially expressed genes. Weighted gene co-expression network analysis revealed that the brown module of mRNAs and the turquoise module of lncRNAs were the most important. Interactions among microRNAs, lncRNAs, and mRNAs were prognosticated using miRcode, miRDB, TargetScan, miRTarBase, and starBase databases. A prognostic model consisting of 13 mRNAs was established using univariate and multivariate Cox regression analyses and validated by the receiver operating characteristic (ROC) curve. The 22 immune infiltrating cell types were analyzed using the CIBERSORT algorithm, and results showed that the high-risk score of this model was related to poor prognosis and an immunosuppressive TIME. A lncRNA-miRNA-mRNA ceRNA network that included 69 differentially expressed lncRNAs (DElncRNAs) was constructed based on the five mRNAs obtained from the prognostic model. ROC survival analysis further showed that the seven DElncRNAs had a substantial prognostic value for the overall survival (OS) in NSCLC patients; the area under the curve was 0.65. In addition, the high-risk group showed drug resistance to several chemotherapeutic and targeted drugs including cisplatin, paclitaxel, docetaxel, gemcitabine, and gefitinib. The differential expression of five mRNAs and seven lncRNAs in the ceRNA network was supported by the results of the HPA database and RT-qPCR analyses. This comprehensive analysis of a ceRNA network identified a set of biomarkers for prognosis and TIME prediction in NSCLC.

Aquamicrobium zhengzhouense sp. nov., a Bacterium Isolated from Farmland Soil Applied with Amino Acid Fertilizer.

A novel Gram-stain-negative, rod-shaped, strictly aerobic, non-motile bacterium, designated strain cd-1T, was isolated from a farmland soil applied with amino acid fertilizer in Zhengzhou, Henan province, China. The optimum growth of strain cd-1T occurred at 30 °C, pH 7.0 in Luria-Bertani (LB) broth without NaCl supplement. Phylogenetic analysis based on 16S rRNA gene sequences indicated that cd-1T is member of the genus Aquamicrobium, and formed a separate branch with Aquamicrobium aerolatum DSM 21857T (96.5%) and Aquamicrobium soli KCTC 52165T (95.7%). The draft genome sequencing revealed a DNA G + C content of 59.2 mol% and Q-10 was the predominant respiratory quinone. The major cellular fatty acids were identified as C18:1 ω7c (35.8%), C19:0 cyclo ω8c (32.1%), and C18:1 ω7c 11-methyl (5.2%). The polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (dDDH) for draft genomes between strain cd-1T and KCTC 52165T were 71.0% and 19.9%, respectively, the values for strain cd-1T and DSM 21857T were 73.4% and 20.6%. Based on the physiological and biochemical characteristics, phylogenetic and chemotaxonomic analysis, strain cd-1T is considered to represent a novel species of the genus Aquamicrobium, for which the name Aquamicrobium zhengzhouense sp. nov. is proposed. The type strain is cd-1T (= KCTC 82182T = CCTCC M 2018904T).

The ancestral duplicated DL/CRC orthologs, PeDL1 and PeDL2, function in orchid reproductive organ innovation.

Orchid gynostemium, the fused organ of the androecium and gynoecium, and ovule development are unique developmental processes. Two DROOPING LEAF/CRABS CLAW (DL/CRC) genes, PeDL1 and PeDL2, were identified from the Phalaenopsis orchid genome and functionally characterized. Phylogenetic analysis indicated that the most recent common ancestor of orchids contained the duplicated DL/CRC-like genes. Temporal and spatial expression analysis indicated that PeDL genes are specifically expressed in the gynostemium and at the early stages of ovule development. Both PeDLs could partially complement an Arabidopsis crc-1 mutant. Virus-induced gene silencing (VIGS) of PeDL1 and PeDL2 affected the number of protuberant ovule initials differentiated from the placenta. Transient overexpression of PeDL1 in Phalaenopsis orchids caused abnormal development of ovule and stigmatic cavity of gynostemium. PeDL1, but not PeDL2, could form a heterodimer with Phalaenopsis equestris CINCINNATA 8 (PeCIN8). Paralogous retention and subsequent divergence of the gene sequences of PeDL1 and PeDL2 in P. equestris might result in the differentiation of function and protein behaviors. These results reveal that the ancestral duplicated DL/CRC-like genes play important roles in orchid reproductive organ innovation.

Aconitine attenuates mitochondrial dysfunction of cardiomyocytes via promoting deacetylation of cyclophilin-D mediated by sirtuin-3.

ETHNOPHARMACOLOGICAL RELEVANCE: Aconite is a processed product of seminal root of perennial herbaceous plant Aconitum Carmichaclii Debx. of Ranunculaceae. It has the effects of warming and tonifying heart yang and restoring yang to save from collapse. Aconitine is the main effective constituent of aconite and used to prevent and treat heart disease. However, how aconitine exerts myocardial protection is still poorly understood. AIM OF THE STUDY: The present study aimed to investigate the effects of aconitine on mitochondrial dysfunction and explore its mechanism of action. MATERIALS AND METHODS: The model of myocardial injury was induced by Angiotensin II (Ang II) (1 × 10-6 mol L-1), and H9c2 cells were incubated with different concentrations of aconitine. The effect of aconitine on mitochondrial was determined by flow cytometry, transmission electron microscopy, luciferase, Seahorse technique and Western blot. The effects of aconitine on sirtuin-3 (Sirt3) activity and Cyclophilin D (CypD) acetylation were detected by immunofluorescence, RT-PCR and co-immunoprecipitation. RESULTS: We demonstrate that aconitine alleviates the energy metabolic dysfunction of H9c2 cells by activating Sirt3 to deacetylate CypD and inhibiting mitochondrial permeability transition pore (mPTP) opening. In cardiomyocytes, aconitine significantly reduced mitochondrial fragmentation, inhibited acetylation of CypD, suppressed the mPTP opening, mitigated mitochondrial OXPHOS disorders, and improved the synthesis ability of ATP. In contrast, Sirt3 deficiency abolished the effects of aconitine on mPTP and OXPHOS, indicating that aconitine improves mitochondrial function by activating Sirt3. CONCLUSIONS: These results showed that aconitine attenuated the energy metabolism disorder by promoting Sirt3 expression and reducing CypD-mediated mPTP excess openness, rescuing mitochondrial function. Improve mitochondrial function may be a therapeutic approach for treating heart disease, which will generate fresh insight into the cardioprotective of aconitine.

Tongxinluo Ameliorates Myocardial Ischemia-Reperfusion Injury Mainly via Activating Parkin-Mediated Mitophagy and Downregulating Ubiquitin-Proteasome System.

OBJECTIVE: To investigate the protective effects and mechanism of Chinese herbal compound Tongxinluo Capsule (, TXL) on the Parkin-mediated mitophagy and the ubiquitin-proteasome system in a rat model of myocardial ischemia-reperfusion injury (MIRI). METHODS: Seventy adult male Sprague-Dawley rats were randomly divided into 7 groups: sham group, MIRI group, low- and high-dose TXL (0.5 and 1 g·kg-1·d-1, respectively) groups, atorvastatin (ATV) group (7.2 g·kg-1·d-1), chloroquine (CQ) group (10 g·kg-1·d-1), and highdose TXL + CQ group. After pharmacological administration for 7 days, rats underwent left anterior descending artery ligation surgery to establish the MIRI models with 50 min ischemia followed by 4 h reperfusion. Blood was taken for cardiac troponin I (cTnI) detection and hearts were harvested for infarct staining and apoptosis detection. The autophagy or mitophagy proteins and ubiquitinated proteins were detected by Western blotting. RESULTS: Compared with the sham group, the MIRI group exhibited a larger infarcted area (27.13%±0.01%, P<0.01), a higher apoptotic index (34.33%±2.03% vs.1.81%±0.03%, P<0.01), and higher cTnI expression (14.18±1.01 vs. 7.96±0.32, P<0.01). The mitochondrial integrity was damaged in the MIRI group, while TXL and ATV alleviated the damage of MIRI. More autophagosomes were observed in the high-dose TXL group than in the MIRI group (7.00±0.58 vs. 4.33±1.15, P<0.05). More amounts of PTEN-induced putative kinase protein 1 (PINK1) and Parkin translocated onto the mitochondria were detected in the high-dose TXL group than in the MIRI group (P<0.05). The ubiquitin response was signifificantly downregulated in the high-dose TXL group relative to the MIRI group (P<0.05). CQ administration abolished the activation of autophagy flux and the PINK1/ Parkin pathway induced by high-dose of TXL. CONCLUSIONS: TXL ameliorates MIRI via activating Parkin-mediated mitophagy in rats. The downregulation of the ubiquitin-proteasome system is also involved.

Mechanistic target of rapamycin-mediated autophagy is involved in the alleviation of lipopolysaccharide-induced acute lung injury in rats.

Acute lung injury (ALI) is a complex clinical syndrome with high morbidity and mortality rates. Autophagy is an adaptive process that plays a complex role in ALI. The aim of this study was to investigate the effects of autophagy on lipopolysaccharide (LPS)-induced lung injury by establishing a rat ALI model and to further explore the possible mechanisms involved. Rats were pretreated with the autophagy inhibitor 3-methyladenine (3-MA) or the autophagy activator rapamycin before they were challenged with the intratracheal instillation of LPS (5 mg/kg). The level of autophagy in the lung tissue was detected. Lung injury and vascular permeability were assessed. The role of the mechanistic target of rapamycin (mTOR)-mediated Unc-51-like kinase 1 (ULK1) and the class III PI3 kinase VPS34 in autophagy regulation was examined. LPS challenge induced autophagy and rapamycin pretreatment enhanced autophagy activity in LPS-induced ALI rats. LPS caused severe lung injury and high pulmonary vascular permeability, which could be alleviated by enhancing autophagy. In addition, the inhibition of mTOR upregulated the expression of ULK1 and VPS34 and thus increased LPS-induced autophagy. Autophagy plays a protective role in LPS-induced ALI, and enhancing autophagy via the inhibition of mTOR alleviates lung injury and pulmonary barrier function. Moreover, mTOR negatively mediates ULK1 and VPS34 to regulate LPS-induced autophagy in rats.

Sphingobacterium chuzhouense sp. nov., isolated from farmland soil.

A novel Gram-staining-negative bacterium, designated DH-5T, was isolated from a farmland soil in Chuzhou, Anhui province, China. Cells of strain DH-5T were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 20-37 °C, pH 6.0-9.0 and with 0-5 % NaCl (w/v). The DNA G+C content was 42.8 mol%. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and C16 : 0. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DH-5T was a member of the genus Sphingobacterium and shared the highest similarity with Sphingobacterium gobiense H7T (96.0 %), followed by Sphingobacterium arenae H-12T (94.5 %). Strain DH-5T exhibited low DNA-DNA relatedness with S. gobiense H7T (35.1±1.4 %) and S. arenae H-12T (21.4±1.0 %). On the basis of phenotypic, genotypic and phylogenetic evidence, DH-5T is considered to represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium chuzhouense sp. nov. is proposed. The type strain is DH-5T (=ACCC 19856T=KCTC 42746T).

Luteimonas soli sp. nov., isolated from farmland soil.

A yellow-pigmented bacterial strain, designated Y2T, was isolated from farmland soil in Bengbu, Anhui province, China. Cells of strain Y2T were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Strain Y2T grew optimally at pH 7.0, 30 °C and in the presence of 2 % (w/v) NaCl. The DNA G+C content was 68.9 mol%. The major fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C11 : 0 3-OH and iso-C11 : 0. The major respiratory quinone was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain Y2T was most closely related to Luteimonas mephitis B1953/27.1T (99.1 % 16S rRNA gene sequence similarity), followed by Luteimonas lutimaris G3T (98.6 %), Luteimonas abyssi XH031T (96.2 %) and Luteimonas aquatica RIB1-20T (96.0 %). Strain Y2T exhibited low DNA-DNA relatedness with Luteimonas mephitis B1953/27.1T (43.6 ± 0.5 %) and Luteimonas lutimaris G3T (43.9 ± 2.1 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain Y2T represents a novel species of the genus Luteimonas, for which the name Luteimonas soli sp. nov. is proposed. The type strain is Y2T ( = ACCC 19799T = KCTC 42441T).

Fluviicola hefeinensis sp. nov., isolated from the wastewater of a chemical factory.

A Gram-negative, strictly aerobic, yellow-orange-pigmented, motile, short rod-shaped, catalase-positive, oxidase-negative bacterium, strain MYL-8(T), was isolated from wastewater of the Jin Tai Chemical Factory in Hefei, China. Strain MYL-8(T) grew optimally at 30 °C, in the absence of NaCl and at pH 7. Menaquinone 6 (MK-6) was the sole respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile was composed predominantly of unidentified polar lipids and aminolipids. Minor amounts of phosphatidylethanolamine and unidentified phospholipids were also detectable. The DNA G+C content of strain MYL-8(T) was 43.5 mol%. The 16S rRNA gene sequence of strain MYL-8(T) showed the highest similarity to that of Fluviicola taffensis RW 262(T) (97.03 %), followed by Wandonia haliotis Haldis-1-1(T) (92.05 %), Lishizhenia caseinilytica UST040201-001(T) (91.43 %) and Lishizhenia tianjinensis JCM 15141(T) (90.61 %). DNA-DNA relatedness between strain MYL-8(T) and F. taffensis RW 262(T) was 21.35±0.90 %. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic data, strain MYL-8(T) is considered to represent a novel species of the genus Fluviicola, for which the name Fluviicola hefeinensis sp. nov. is proposed. The type strain is MYL-8(T) ( = KACC 16597(T) = CCTCC AB 2013168(T)).