Interplay between nuclear factor erythroid 2-related factor 2 and inflammatory mediators in COVID-19-related liver injury.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 is a global pandemic and poses a major threat to human health worldwide. In addition to respiratory symptoms, COVID-19 is usually accompanied by systemic inflammation and liver damage in moderate and severe cases. Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that regulates the expression of antioxidant proteins, participating in COVID-19-mediated inflammation and liver injury. Here, we show the novel reciprocal regulation between NRF2 and inflammatory mediators associated with COVID-19-related liver injury. Additionally, we describe some mechanisms and treatment strategies.

A Novel Hemoglobin Variant Hb Liaobu [α107(G14)Val→Leu, HBA2: c.322G>C] Detected by Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry.

We here describe a novel hemoglobin (Hb) variant, Hb Liaobu [α107(G14)Val→Leu, HBA2: c.322G>C], in a Chinese family. The structurally abnormal α chain variant could not be detected using capillary electrophoresis (CE) and was subsequently characterized by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS), and further confirmed by reversed phase high performance liquid chromatography (HPLC). Sanger sequencing revealed a novel base mutation on the α2-globin gene and RNA analysis by reverse transcription polymerase chain reaction (RT-PCR) showed the presence of an abnormal HBA transcript. The isopropanol stability test indicated the stable state of this structural Hb variant. In conclusion, a new Hb variant, Hb Liaobu, was discovered and characterized. It was proven to be a nonpathogenic variant. Our study resolved the confusion in the clinical diagnosis of individuals with this novel Hb variant in this family.

Transcriptome profiling analysis reveals metabolic changes across various growth phases in Bacillus pumilus BA06.

BACKGROUND: Bacillus pumilus can secret abundant extracellular enzymes, and may be used as a potential host for the industrial production of enzymes. It is necessary to understand the metabolic processes during cellular growth. Here, an RNA-seq based transcriptome analysis was applied to examine B. pumilus BA06 across various growth stages to reveal metabolic changes under two conditions. RESULTS: Based on the gene expression levels, changes to metabolism pathways that were specific to various growth phases were enriched by KEGG analysis. Upon entry into the transition from the exponential growth phase, striking changes were revealed that included down-regulation of the tricarboxylic acid cycle, oxidative phosphorylation, flagellar assembly, and chemotaxis signaling. In contrast, the expression of stress-responding genes was induced when entering the transition phase, suggesting that the cell may suffer from stress during this growth stage. As expected, up-regulation of sporulation-related genes was continuous during the stationary growth phase, which was consistent with the observed sporulation. However, the expression pattern of the various extracellular proteases was different, suggesting that the regulatory mechanism may be distinct for various proteases. In addition, two protein secretion pathways were enriched with genes responsive to the observed protein secretion in B. pumilus. However, the expression of some genes that encode sporulation-related proteins and extracellular proteases was delayed by the addition of gelatin to the minimal medium. CONCLUSIONS: The transcriptome data depict global alterations in the genome-wide transcriptome across the various growth phases, which will enable an understanding of the physiology and phenotype of B. pumilus through gene expression.

Using the CRISPR/Cas9 system to eliminate native plasmids of Zymomonas mobilis ZM4.

The CRISPR/Cas system can be used to simply and efficiently edit the genomes of various species, including animals, plants, and microbes. Zymomonas mobilis ZM4 is a highly efficient, ethanol-producing bacterium that contains five native plasmids. Here, we constructed the pSUZM2a-Cas9 plasmid and a single-guide RNA expression plasmid. The pSUZM2a-Cas9 plasmid was used to express the Cas9 gene cloned from Streptococcus pyogenes CICC 10464. The single-guide RNA expression plasmid pUC-T7sgRNA, with a T7 promoter, can be used for the in vitro synthesis of single-guide RNAs. This system was successfully employed to knockout the upp gene of Escherichia coli and the replicase genes of native Z. mobilis plasmids. This is the first study to apply the CRISPR/Cas9 system of S. pyogenes to eliminate native plasmids in Z. mobilis. It provides a new method for plasmid curing and paves the way for the genomic engineering of Z. mobilis.

Daily rhythm variations of the clock gene PER1 and cancer-related genes during various stages of carcinogenesis in a golden hamster model of buccal mucosa carcinoma.

BACKGROUND: Recent studies have demonstrated that the clock gene PER1 regulates various tumor-related genes. Abnormal expressions and circadian rhythm alterations of PER1 are closely related to carcinogenesis. However, the dynamic circadian variations of PER1 and tumor-related genes at different stages of carcinogenesis remain unknown. This study was conducted to investigate the daily rhythm variation of PER1 and expression of tumor-related genes VEGF, KI67, C-MYC, and P53 in different stages of carcinogenesis. MATERIALS AND METHODS: Dimethylbenzanthracene was used to establish a golden hamster model of buccal mucosa carcinogenesis. Hamsters with normal buccal mucosa, precancerous lesion, and cancerous lesion were sacrificed at six different time points during a 24-hour period of a day. Pathological examination was conducted using routine hematoxylin and eosin staining. PER1, VEGF, KI67, C-MYC, and P53 mRNAs were detected by real-time reverse transcriptase polymerase chain reaction, and a cosinor analysis was applied to analyze the daily rhythm. RESULTS: PER1, VEGF, C-MYC, and P53 mRNA exhibited daily rhythmic expression in three carcinogenesis stages, and KI67 mRNA exhibited daily rhythmic expression in the normal and precancerous stages. The daily rhythmic expression of KI67 was not observed in cancerous stages. The mesor and amplitude of PER1 and P53 mRNA expression decreased upon the development of cancer (P<0.05), whereas the mesor and amplitude of VEGF, KI67, and C-MYC mRNA increased upon the development of cancer (P<0.05). Compared with the normal tissues, the acrophases of PER1, VEGF, and C-MYC mRNA occurred earlier, whereas the acrophases of P53 and KI67 mRNA lagged remarkably in the precancerous lesions. In the cancer stage, the acrophases of VEGF and C-MYC mRNA occurred earlier and later, respectively, compared with the normal stage. CONCLUSION: Variations in the daily rhythm characteristics of the clock gene PER1 and tumor-related genes VEGF, KI67, C-MYC, and P53 correlate with the development of cancer. Additional studies might provide new insights and methods to explore carcinogenic mechanisms and cancer treatment.

Circadian variations of clock gene Per2 and cell cycle genes in different stages of carcinogenesis in golden hamster buccal mucosa.

Previous studies have suggested that the expression of clock genes have circadian rhythms, and many cell cycle genes are regulated by clock genes. The disruption of circadian rhythms appears to be associated with the acceleration of cancer development. To investigate the circadian patterns of the clock gene Per2 and of cell cycle genes p53, Cyclin D1, CDK1 and Cyclin B1 in different stages of carcinogenesis, the daily mRNA profiles of these genes were detected by real-time RT-PCR in dimethylbenzanthracene-induced cancer, in precancerous lesions and in normal tissues. Per2, p53, Cyclin D1 and CDK1 showed circadian rhythms in the 3 different stages of carcinogenesis, whereas the circadian rhythm of Cyclin B1 was absent in the precancerous lesions. The mesors and amplitudes of Per2 and p53 were decreased (P < 0.05), but the mesors of Cyclin D1, CDK1 and Cyclin B1 were increased with the development of cancer (P < 0.05). Compared with the normal tissues, the acrophases of Per2 and CDK1 were earlier in precancerous lesions, and the acrophases of Cyclin D1, CDK1 and Cyclin B1 occurred later in the cancer cells. Our study represents the first demonstration of the circadian pattern variations of these genes in different stages of carcinogenesis.

Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].

BACKGROUND: Transposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs. METHODOLOGY/PRINCIPAL FINDINGS: We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1-3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification. CONCLUSIONS/SIGNIFICANCE: Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction. It contributes to elucidating the roles of TEs in genome evolution.

Draft genome sequence of Enterobacter cloacae subsp. cloacae strain 08XA1, a fecal bacterium of giant pandas.

Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1 from the feces of a giant panda in China. Genes encoding a ß-lactamase and efflux pumps, as well as other factors, have been found in the genome.

[Research on the degradation of BaP with potassium ferrate characterized by fluorescence].

The degradation of Benzo(a)pyrene (BaP) by potassium ferrate was researched by means of multiple fluorescence spectroscopic methods such as synchronous, time-scan, excitation emission matrix (EEM) and photometry, under the optimal condition. Within the degradation process, the characteristics of the BaP's concentration at different time-intervals, and the kinetics of the degradation of BaP by potassium ferrate were discussed. From the experimental data, both synchronous and EEM spectra's results showed that the concentration of BaP was reduced 90% by potassium ferrate within 20 s after degradation, and the reaction process was very slow after 60 s. The degradation kinetic equation, ln(F0/Ft) = 0.563 2t + 0.171 2, (R2 = 0.994 2), was obtained through a convenient and fast way combining the time-scan fluorescence data and photometry data, and the photometry included the synchronous photometry and emission photometry. According to the kinetic equation, the degradation of BaP by potassium ferrate was in accord with the order of the first order reaction. So this article could provide a very useful conference for the research on the pollutant degradation by potassium ferrate, especially for the degradation process and the degradation mechanisms.

4,7,8-Trimethyl-2H-chromen-2-one.

The mol-ecule of the title compound, C(12)H(12)O(2), is essentially planar, with a maximum deviation from the mean plane of all non-H atoms of 0.038 (1) Šfor the methyl C atom in the 8-position. The crystal structure is characterized by anti-parallel π-π stacking along the c axis, with centroid-centroid distances as short as 3.866 (1) Å. In the crystal, C-H⋯O hydrogen bonds connect the mol-ecules across the stacks into ribbons in the a-axis direction.

An effective method of RNA isolation from Fallopia multiflora tuberous roots.

To isolate high-quality total RNA from Fallopia multiflora tuberous roots is difficult because of the presence of high levels of carbohydrates, phenolics, and other secondary metabolites. Since several procedures specialized for RNA isolation from polysaccharides and phenols rich tissues have resulted in poor yields, in this study, we developed a modified protocol that was derived from the traditional CTAB method. The protocol was able to produce high-quality and intact RNA from the tuberous roots of F. multiflora. The yield of total RNA was more than 0.15 mg/g fresh weight, with an A260/A280 ratio of 1.9-2.0. The obtained RNA was of sufficient quality and suitable for downstream application such as reverse-transcription polymerase chain reaction (RT-PCR), Northern hybridization, and cDNA library construction. The protocol may also have wider applicability for total RNA isolation from other plant species with tuberous roots.

2-(3-Oxo-2,3-dihydro-1,2-benzothia-zol-2-yl)acetic acid.

In the title compound, C(9)H(7)NO(3)S, the benzoisothia-zolone ring system is essentially planar, with a maximum deviation of 0.013 (2) Å. In the crystal, mol-ecules are linked via O-H⋯O hydrogen bonds, forming chains along [010]. In addition, weak inter-molecular C-H⋯O hydrogen bonds are present.

Butyl 3-oxo-2,3-dihydro-benzo[d][1,2]thia-zole-2-carboxyl-ate.

The title compound, C(12)H(13)NO(3)S, was synthesised by the reaction of benzo[d]isothia-zol-3(2H)-one with butyl alcohol in toluene. The benzoisothia-zolone ring system is almost planar with a mean deviation of 0.041 (1) Å. In the crystal, mol-ecules are linked by weak inter-molecular C-H⋯O hydrogen bonds.

[Study of vibrational spectra of humic substance in soils from the three Gorges Reservoir Area].

The six typical different parts of soils and sediments along the bank of the Three Gorges Reservoir Area (TGRA) were collected, and the humic substance isolated from the six parts of the soils and sediments' samples was separated to humic acid and fulvic acid, purified, and characterized with the combination of the Raman and IR vibrational spectroscopic technologies after cool-dried separation; through assigning the vibrational peaks in each part of the Raman and IR spectra of each sample part, the vibrational characteristics of the structures and the groups that belonged to the molecules of the humic acids and the fulvic acids in the soils and sediments of the TGRA were obtained; the changing features of the groups and structures in the humic acid and the fulvic aicd's molecules from the different soils and sediments in the TGRA were discussed with the environmental impact factors such as soil humic degree, the conditions of different soils conference, using and/or cultivating models and water level fluctuations. From the experimental results, the vibrations about C-O, C-C, and poly-hydrogen bonds dominate in the structures and the groups of each part' humic substance; the active vibration numbers in the upstream are more than in the downstream; the soil's humic degree has great effect on the formation of the humic substances' structures in soil's humic substance; the soil used as agricultural cultivating mode showed higher humic degrees in the upstream parts of the TGRA. The effect of the water level's fluctuation on the formation of the humic acid and fulvic aicd in the sediments of the TGRA is not obvious in the short time.

[Study of the fluorescence characteristics of DOM from the Yangtze River and Jialing River around Chongqing's urban areas].

The fluorescence emission and excitation emission matrix (EEM) technologies were used to characterize the dissolved organic matter (DOM) in the water body of the Yangtze River and Jialing River around the Chongqing urban areas from April to August 2008. Concerning about the accidents of the Wenchuan's Earthquake in May and Tangjiashan Yansaihu's effects in June, and the high water period time in the summer in two months of July and August, from the EEM obtained from each sampling station and time, the composition, distribution and their changing features of the DOM in the two rivers were investigated as combined with the water samples' environmental parameters such as pH, DO, DOC with EEM's fingerprint features, f(450/500) etc; finally the bio-environment behavior effects of the three types of fluorescence peaks were elaborated, where humic-like, fulvic-like, and protein-like from the five sampling stations' EEMs during the five months were given detailed representation. From the experimental results obtained, the fluorescence peaks are mainly composed of two types of fluorophores: humic-like and protein-like in the two rivers around the Chongqing urban areas during the investigation in five months, the protein-like's peaks value in Jialing River is higher than the values in the Yangtze River, and all the fluorescence peaks in the two Rivers' water body decrease more or less after the two Rivers join in Chun Tan sampling station; the protein-like peak is notably higher after the "5 x 12" earthquake period time including May and June and high water period time, which mainly originated from terrestrial sources, but its intensities decreased observably while the water bodies of the two rivers joining together in the Chao Tianmen and Chun Tan's sampling station.

Cloning, sequence, and function analyses of giant panda (Ailuropoda melanoleuca) CD9 gene.

CD9 is a member of the tetraspanin family proteins and has recently been shown to be essential for sperm-oocyte fusion in mice. The giant panda (Ailuropoda melanoleuca) CD9 (gpCD9) cDNA was amplified for the first time by RT-PCR from ovary total RNA and cloned, sequenced and analyzed. The result revealed that the open reading frame (ORF) of gpCD9 was 681 bp, which has the same length as that of mouse. Sequence analysis and structure prediction displayed that the amino acid sequence of gpCD9 is over 80% identity to those of mammals with the conserved structures, including the four transmembrane domains (TM) and certain characteristic residues. The results of sperm-egg fusion experiments demonstrated that giant panda CD9 large extracellular loop (LEL) significantly inhibited (P < 0.05) the mouse gamete fusion when the recombinant protein was added. However, when three amino acid residues TVT (173-175) of the gpCD9 were mutated to AAA, the large extracellular loop (LELM) of mutated protein was rarely inhibiting the gamete fusion of mice. Our results may be useful in improving an insight into understanding the potential mechanism of gamete fusion and genetic characteristics of giant panda.

Gene cloning, sequencing, expression and biological activity of giant panda (Ailuropoda melanoleuca) interferon-alpha.

The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. In mammals, multiple subtypes of interferon-alpha (IFN-alpha) exist, most of which possess antiviral activity. Little is known about giant panda IFN-alpha genes and the role they may play in giant panda immunological responses to viruses. We have cloned genes encoding 12 giant panda IFN-alpha (AmIFN-alpha or AmIFNA) subtypes that share from 90 to 99% amino acid sequence identity. AmIFN-alpha12 has one additional amino acid at position 57, which is not present in other subtypes. Sequence identity of the AmIFN-alpha proteins encoded by the 12 genes compared to human IFN-alpha2 is approximately 58%. Unlike most of the human subtypes, each of the 12 giant panda IFN sequences has an N-glycosylation recognition site. Expression of all 12 AmIFN-alpha subtypes in 293 cells was confirmed by SDS-PAGE and Western blotting analysis. The antiviral activity and antiproliferative activity of each AmIFN-alpha subtype produced in transiently transfected 293 cell cultures were tested in vitro. All AmIFN-alpha subtypes were found to be stable at pH 2 or 65 degrees C and to exhibit antiviral activity. Some IFN subtypes (AmIFN-alpha8 and AmIFN-alpha4) showed higher biological activity levels than others, whereas AmIFN-alpha11 exhibited lower activity. AmIFN-alpha had various antiproliferative activities to different target cells. To B16 cells, AmIFN-alpha3, AmIFN-alpha4, AmIFN-alpha8 had the highest activities, while to K562 cells, AmIFN-alpha3, AmIFN-alpha7, AmIFN-alpha10 had the highest activities. The various IFN-alpha subtypes displayed a good correlation between their antiviral and antiproliferative potencies.