Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3

Abstract: Recent investigations of extreme environments have revealed numerous bioactive natural products. However, biosurfactant-producing strains from deep sea extreme environment are largely unknown. Here, we show that Dietzia maris As-13-3 isolated from deep sea hydrothermal field could produce di-rhamnolipid as biosurfactant. The critical micelle concentration (CMC) of the purified di-rhamnolipid was determined to be 120 mgL-1, and it lowered the surface tension of water from 74±0.2 mN m-1 to 38±0.2 mN m-1. Further, the alkane metabolic pathway-related genes and di-rhamnolipid biosynthesis-related genes were also analyzed by the sequencing genome of D. maris As-13-3 and quantitative real-time PCR (Q-PCR), respectively. Q-PCR analysis showed that all these genes were induced by n-Tetradecane, n-Hexadecane and pristane. To the best of our knowledge, this is first report about the complete pathway of the di-rhamnolipid synthesis process in the genus Dietzia. Thus, our study provided the insights into Dietzia in respects of oil degradation and biosurfactant production, and will help to evaluate the potential of Dietzia in marine oil removal

An Advanced Quantum-Resistant Signature Scheme for Cloud Based on Eisenstein Ring

The authors wish to express their appreciation to the reviewers for their helpful suggestions which greatly improved the presentation of this paper. This work was supported by the Major Program of National Natural Science Foundation of China (11290141).Peer reviewe

miR-499-5p Attenuates Mitochondrial Fission and Cell Apoptosis via p21 in Doxorubicin Cardiotoxicity

Doxorubicin (DOX) is a broad-spectrum anti-tumor drug, but its cardiotoxicity limits its clinical application. A better understanding of the molecular mechanisms underlying DOX cardiotoxicity will benefit clinical practice and remedy heart failure. Our present study observed that DOX caused cardiomyocyte (H9c2) apoptosis via the induction of abnormal mitochondrial fission. Notably, the expression levels of p21 increased in DOX-treated cardiomyocytes, and the silencing of p21 using siRNA greatly attenuated mitochondrial fission and apoptosis in cardiomyocytes. We also found that miR-499-5p could directly target p21 and attenuated DOX-induced mitochondrial fission and apoptosis. The role of the miR-499-5p-p21 axis in the prevention of DOX cardiotoxicity was also validated in the mice model. DOX treatment induced an upregulation of p21, which induced subsequent abnormal mitochondrial fission and myocardial apoptosis in mouse heart. Adenovirus-harboring miR-499-5p-overexpressing mice exhibited significantly reduced p21 expression, mitochondrial fission and myocardial apoptosis in hearts following DOX administration. The miR-499-5p-overexpressing mice also exhibited improved cardiomyocyte hypertrophy and cardiac function after DOX treatment. However, miR-499-5p was not involved in the DOX-induced apoptosis of cancer cells. Taken together, these findings reveal an emerging role of p21 in the regulation of mitochondrial fission program. miR-499-5p attenuated mitochondrial fission and DOX cardiotoxicity via the targeting of p21. These results provide new evidence for the miR-499-5p-p21 axis in the attenuation of DOX cardiotoxicity. The development of new therapeutic strategies based on the miR-499-5p-p21 axis is a promising path to overcome DOX cardiotoxicity as a chemotherapy for cancer treatment

Recessive Antimorphic Alleles Overcome Functionally Redundant Loci to Reveal TSO1 Function in Arabidopsis Flowers and Meristems

Arabidopsis TSO1 encodes a protein with conserved CXC domains known to bind DNA and is homologous to animal proteins that function in chromatin complexes. tso1 mutants fall into two classes due to their distinct phenotypes. Class I, represented by two different missense mutations in the CXC domain, leads to failure in floral organ development, sterility, and fasciated inflorescence meristems. Class II, represented by a nonsense mutation and a T-DNA insertion line, develops wild-type–like flowers and inflorescences but shows severely reduced fertility. The phenotypic variability of tso1 alleles presents challenges in determining the true function of TSO1. In this study, we use artificial microRNA, double mutant analysis, and bimolecular fluorescence complementation assay to investigate the molecular basis underlying these two distinct classes of phenotypes. We show that the class I mutants could be converted into class II by artificial microRNA knockdown of the tso1 mutant transcript, suggesting that class I alleles produce antimorphic mutant proteins that interfere with functionally redundant loci. We identified one such redundant factor coded by the closely related TSO1 homolog SOL2. We show that the class I phenotype can be mimicked by knocking out both TSO1 and its homolog SOL2 in double mutants. Such antimorphic alleles targeting redundant factors are likely prevalent in Arabidopsis and maybe common in organisms with many sets of paralogous genes such as human. Our data challenge the conventional view that recessive alleles are always hypomorphic or null and that antimorphic alleles are always dominant. This study shows that recessive alleles can also be antimorphic and can produce a phenotype more severe than null by interfering with the function of related loci. This finding adds a new paradigm to classical genetic concepts, with important implications for future genetic studies both in basic research as well as in agriculture and medicine

Transcriptome analysis to identify candidate genes related to mammary gland development of Bactrian camel (Camelus bactrianus)

IntroductionThe demand for camel milk, which has unique therapeutic properties, is increasing. The mammary gland is the organ in mammals responsible for the production and quality of milk. However, few studies have investigated the genes or pathways related to mammary gland growth and development in Bactrian camels. This study aimed to compare the morphological changes in mammary gland tissue and transcriptome expression profiles between young and adult female Bactrian camels and to explore the potential candidate genes and signaling pathways related to mammary gland development.MethodsThree 2  years-old female camels and three 5  years-old adult female camels were maintained in the same environment. The parenchyma of the mammary gland tissue was sampled from the camels using percutaneous needle biopsy. Morphological changes were observed using hematoxylin-eosin staining. High-throughput RNA sequencing was performed using the Illumina HiSeq platform to analyze changes in the transcriptome between young and adult camels. Functional enrichment, pathway enrichment, and protein–protein interaction networks were also analyzed. Gene expression was verified using quantitative real-time polymerase chain reaction (qRT-PCR).ResultsHistomorphological analysis showed that the mammary ducts and mammary epithelial cells in adult female camels were greatly developed and differentiated from those in young camels. Transcriptome analysis showed that 2,851 differentially expressed genes were obtained in the adult camel group compared to the young camel group, of which 1,420 were upregulated, 1,431 were downregulated, and 2,419 encoded proteins. Functional enrichment analysis revealed that the upregulated genes were significantly enriched for 24 pathways, including the Hedgehog signaling pathway which is closely related to mammary gland development. The downregulated genes were significantly enriched for seven pathways, among these the Wnt signaling pathway was significantly related to mammary gland development. The protein–protein interaction network sorted the nodes according to the degree of gene interaction and identified nine candidate genes: PRKAB2, PRKAG3, PLCB4, BTRC, GLI1, WIF1, DKK2, FZD3, and WNT4. The expression of fifteen genes randomly detected by qRT-PCR showed results consistent with those of the transcriptome analysis.DiscussionPreliminary findings indicate that the Hedgehog, Wnt, oxytocin, insulin, and steroid biosynthesis signaling pathways have important effects on mammary gland development in dairy camels. Given the importance of these pathways and the interconnections of the involved genes, the genes in these pathways should be considered potential candidate genes. This study provides a theoretical basis for elucidating the molecular mechanisms associated with mammary gland development and milk production in Bactrian camels

Patterns and mechanisms of coseismic and postseismic slips of the 2011 M W 7.1 Van (Turkey) earthquake revealed by multi-platform synthetic aperture radar interferometry

On 23rd October 2011, a MW 7.1 reverse slip earthquake occurred in the Bardakçı-Saray thrust fault zone in the Van region, Eastern Turkey. Earlier geodetic studies have found different slip distributions in terms of both magnitude and pattern. In this paper, we present several COSMO-SkyMED (CSK), Envisat ASAR and RADARSAT-2 interferograms spanning different time intervals, showing that significant postseismic signals can be observed in the first three days after the mainshock. Using observations that combine coseismic and postseismic signals is shown to significantly underestimate coseismic slip. We hence employed the CSK pair with the minimum postseismic signals to generate one conventional interferogram and one along-track interferogram for further coseismic modelling. Our best-fit coseismic slip model suggests that: (1) this event is associated with a buried NNW dipping fault with a preferable dip angle of 49° and a maximum slip of 6.5 m at a depth of 12 km; and (2) two unequal asperities can be observed, consistent with previous seismic solutions. Significant oblique aseismic slip with predominant left-lateral slip components above the coseismic rupture zone within the first 3 days after the mainshock is also revealed by a postseismic CSK interferogram, indicating that the greatest principal stress axis might have rotated due to a significant stress drop during the coseismic rupture

INVESTIGATION OF ARABIDOPSIS TSO1, A REGULATOR OF CELL PROLIFERATION AND DIFFERENTIATION

Multicellular eukaryotic organisms build complex body structures from a single cell. Through coordinated cell proliferation and differentiation, the collective behavior of cells forms organs that achieve physiological functions. Underlying the developmental processes are the molecular machineries that integrate cell cycle regulation with cell fate acquisition. While animal organogenesis occurs early during embryogenesis, plants maintain pluripotent stem cells at the growing tips (meristems) and generate organs iteratively throughout lifespan. The amazing ability to balance stem cell self-renewal and differentiation underlies the extreme longevity of some plants species. Despite the differences, common mechanisms exist across plant and animal developmental regulation. Understanding both unique and common mechanisms of plant development has broad implications on basic science as well as agriculture and medicine. The Arabidopsis TSO1 gene is a regulator of cell proliferation and differentiation at the shoot and root meristems. TSO1 encodes a CXC domain protein and its animal homologs encode core components of a cell cycle regulatory complex, the DREAM complex. To investigate TSO1 function and identify factors that act together with TSO1, I carried out two genetic screens for suppressors and enhancers of tso1 mutants. I discovered that loss-of-function mutations in MYB3R1, which encodes the Arabidopsis ortholog of human B-Myb, can suppress tso1 mutant defects at both the shoot and root meristems. In tso1-1 mutant, MYB3R1 is over and ectopically expressed at the shoot and root meristems. Furthermore, MYB3R1 phospho mimic enhanced the tso1-3 phenotype, indicating that hyper-active MYB3R1 may mediate the tso1-1 phenotype. TSO1 physically interacts with MYB3R1 and likely forms a plant DREAM-like complex that operates in the plant meristems to balance cell proliferation with differentiation. A gain-of-function mutation of a HD-ZIP III transcription factor, REVOLUTA (REV), was identified as an enhancer of tso1 mutants. TSO1 directly represses REV transcription to balance adaxial and abaxial polarity of lateral organs and maintains the shoot apical meristem. This genetic and molecular interaction between TSO1 and the adaxial factor REV presents an integration point of cell cycle, lateral organ polarity, and meristem regulation. Together, our findings demonstrate a cell cycle regulatory module conserved across plants and animals and describe its integration into plant specific developmental context

The promising role of miRNAs in radioresistance and chemoresistance of nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor that develops in the nasopharynx. It has a distinct ethnic and geographical distribution, and emerging evidence suggests that it is an ecological disease. Most patients respond well to radiation combined with chemotherapy as the primary treatment for NPC. However, some patients will eventually develop radio resistance and chemoresistance, resulting in recurrence and metastasis, which is a primary cause of poor prognosis. The processes underlying radio resistance and chemoresistance in NPC are complex and unknown. MicroRNAs (miRNAs) are endogenic non-coding RNA molecules. They play a role in a variety of cell functions as well as development of disease such as cancer. There has been considerable data demonstrating the existence of numerous aberrant miRNAs in cancer tissues, cells, and biofluids, which indicates the importance of studying the influence of miRNAs on NPC. Therefore, this review comprehensively analyzes the elaborate mechanisms of miRNAs affecting the radio resistance and chemoresistance of NPC. Multiple tumor-specific miRNAs can be employed as therapeutic and prognostic biological indicators

Table_4_Identification of a novel immune-related gene signature for prognosis and the tumor microenvironment in patients with uveal melanoma combining single-cell and bulk sequencing data.xlsx

IntroductionUveal melanoma (UVM) is the most invasive intraocular malignancy in adults with a poor prognosis. Growing evidence revealed that immune-related gene is related to tumorigenesis and prognosis. This study aimed to construct an immune-related prognostic signature for UVM and clarify the molecular and immune classification.MethodsBased on The Cancer Genome Atlas (TCGA) database, single-sample gene set enrichment (ssGSEA) and hierarchical clustering analysis were performed to identify the immune infiltration pattern of UVM and classify patients into two immunity clusters. Then, we proposed univariate and multivariate Cox regression analysis to identify immune-related genes that related to overall survival (OS) and validated in the Gene Expression Omnibus (GEO) external validation cohort. The molecular and immune classification in the immune-related gene prognostic signature defined subgroups were analyzed.ResultsThe immune-related gene prognostic signature was constructed based on S100A13, MMP9, and SEMA3B genes. The prognostic value of this risk model was validated in three bulk RNA sequencing datasets and one single-cell sequencing dataset. Patients in the low-risk group had better OS than those in the high-risk group. The receiver-operating characteristic (ROC) analysis revealed its strong predictive ability for UVM patients. Lower expression of immune checkpoint genes was presented in the low-risk group. Functional studies showed that S100A13 knockdown via siRNA inhibited UVM cell proliferation, migration, and invasion in vitro, with the increased expression of reactive oxygen species (ROS) related markers in UVM cell lines.DiscussionThe immune-related gene prognostic signature is an independent predictive factor for the survival of patients with UVM and provides new information about cancer immunotherapy in UVM.</p