De novo transcriptome sequencing of marine-derived Aspergillus glaucus and comparative analysis of metabolic and developmental variations in response to salt stress

Shaomei Liu,Jiaxin Li,Yuan Wu,Yanna Ren,Qi Liu,Qiyao Wang,Xiangshan Zhou,Menghao Cai,Yuanxing Zhang 한국유전학회 2017 Genes & Genomics Vol.39 No.3

Aspergillus glaucus HB1-19 is a typical marinederived fungus preferring the dependence on sea water for its growth, asexual development and polyketides biosynthesis. Therein, salt stress greatly functions even in superior to light illumination, which is also a critical regulation signal for fungi. Here, comparative RNA-seq analysis of this strain was performed under conditions of saltstress ? dark (group A), non salt-stress ? dark (group B), salt-stress ? light (group C). The RNA-seq generated a total of 19,024 unigenes with an average length of 1415 bp. Differentially expressed genes were very similar between group A and group C but greatly differed between group A and group B, proving that salt stress functioned superior to light illumination globally. Salt stress highly enhanced primary metabolism and activated Ras and MAPK signaling pathways. There seems no direct interaction between asexual development and polyketides biosynthesis. Salt stress inhibited terpenoids biosynthesis but showed little influences on polyketide pathway as well as other secondary metabolism pathways. These findings provide a better understanding of marine fungi adapting to marine environment. Also, it indicates that the so-called ‘salt stress-induced’ may truly be a ‘metal ions-induced’ for biosynthesis of secondary metabolites in marine fungi.

Multiple-Shot Person Re-identification by Features Learned from Third-party Image Sets

( Yanna Zhao ),( Lei Wang ),( Xu Zhao ),( Yuncai Liu ) 한국인터넷정보학회 2015 KSII Transactions on Internet and Information Syst Vol.9 No.2

Person re-identification is an important and challenging task in computer vision with numerous real world applications. Despite significant progress has been made in the past few years, person re-identification remains an unsolved problem. This paper presents a novel appearance-based approach to person re-identification. The approach exploits region covariance matrix and color histograms to capture the statistical properties and chromatic information of each object. Robustness against low resolution, viewpoint changes and pose variations is achieved by a novel signature, that is, the combination of Log Covariance Matrix feature and HSV histogram (LCMH). In order to further improve re-identification performance, third-party image sets are utilized as a common reference to sufficiently represent any image set with the same type. Distinctive and reliable features for a given image set are extracted through decision boundary between the specific set and a third-party image set supervised by max-margin criteria. This method enables the usage of an existing dataset to represent new image data without time-consuming data collection and annotation. Comparisons with state-of-the-art methods carried out on benchmark datasets demonstrate promising performance of our method.

RUNX1 Upregulation Causes Mitochondrial Dysfunction via Regulating the PI3K-Akt Pathway in iPSC from Patients with Down Syndrome

Jingbin Yan,Yanna Liu,Yuehua Zhang,Zhaorui Ren,Fanyi Zeng 한국분자세포생물학회 2023 Molecules and cells Vol.46 No.4

Down syndrome (DS) is the most common autosomal aneuploidy caused by trisomy of chromosome 21. Previous studies demonstrated that DS affected mitochondrial functions, which may be associated with the abnormal development of the nervous system in patients with DS. Runt-related transcription factor 1 (RUNX1) is an encoding gene located on chromosome 21. It has been reported that RUNX1 may affect cell apoptosis via the mitochondrial pathway. The present study investigated whether RUNX1 plays a critical role in mitochondrial dysfunction in DS and explored the mechanism by which RUNX1 affects mitochondrial functions. Expression of RUNX1 was detected in induced pluripotent stem cells of patients with DS (DS-iPSCs) and normal iPSCs (N-iPSCs), and the mitochondrial functions were investigated in the current study. Subsequently, RUNX1 was overexpressed in N-iPSCs and inhibited in DS-iPSCs. The mitochondrial functions were investigated thoroughly, including reactive oxygen species levels, mitochondrial membrane potential, ATP content, and lysosomal activity. Finally, RNA-sequencing was used to explore the global expression pattern. It was observed that the expression levels of RUNX1 in DS-iPSCs were significantly higher than those in normal controls. Impaired mitochondrial functions were observed in DS-iPSCs. Of note, overexpression of RUNX1 in N-iPSCs resulted in mitochondrial dysfunction, while inhibition of RUNX1 expression could improve the mitochondrial function in DS-iPSCs. Global gene expression analysis indicated that overexpression of RUNX1 may promote the induction of apoptosis in DS-iPSCs by activating the PI3K/Akt signaling pathway. The present findings indicate that abnormal expression of RUNX1 may play a critical role in mitochondrial dysfunction in DS-iPSCs.

Bioprospecting of Novel and Bioactive Metabolites from Endophytic Fungi Isolated from Rubber Tree Ficus elastica Leaves

( Zhuang Ding ),( Tao Tao ),( Lili Wang ),( Yanna Zhao ),( Huiming Huang ),( Demeng Zhang ),( Min Liu ),( Zhengping Wang ),( Jun Han ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 Journal of microbiology and biotechnology Vol.29 No.5

Endophytic fungi are an important component of plant microbiota, and have the excellent capacity for producing a broad variety of bioactive metabolites. These bioactive metabolites not only affect the survival of the host plant, but also provide valuable lead compounds for novel drug discovery. In this study, forty-two endophytic filamentous fungi were isolated from Ficus elastica leaves, and further identified as seven individual taxa by ITS-rDNA sequencing. The antimicrobial activity of these endophytic fungi was evaluated against five pathogenic microorganisms. Two strains, Fes1711 (Penicillium funiculosum) and Fes1712 (Trichoderma harzianum), displayed broad-spectrum bioactivities. Our following study emphasizes the isolation, identification and bioactivity testing of chemical metabolites produced by T. harzianum Fes1712. Two new isocoumarin derivatives (1 and 2), together with three known compounds (3-5) were isolated, and their structures were elucidated using NMR and MS. Compounds 1 and 2 exhibited inhibitory activity against Escherichia coli. Our findings reveal that endophytic fungi from the rubber tree F. elastica leaves exhibit unique characteristics and are potential producers of novel natural bioactive products.

Mst1/2-ALK promotes NLRP3 inflammasome activation and cell apoptosis during Listeria monocytogenes infection

Aijiao Gao,Huixin Tang,Qian Zhang,Ruiqing Liu,Lin Wang,Yashan Liu,Zhi Qi,Yanna Shen 한국미생물학회 2021 The journal of microbiology Vol.59 No.7

Listeria monocytogenes (L. monocytogenes) is a Gram-positiveintracellular foodborne pathogen that causes severe diseases,such as meningitis and sepsis. The NLR family pyrindomain-containing 3 (NLRP3) inflammasome has been reportedto participate in host defense against pathogen infection. However, the exact molecular mechanisms underlyingNLRP3 inflammasome activation remain to be fully elucidated. In the present study, the roles of mammalian Ste20-like kinases 1/2 (Mst1/2) and Anaplastic Lymphoma Kinase(ALK) in the activation of the NLRP3 inflammasome inducedby L. monocytogenes infection were investigated. Theexpression levels of Mst1/2, phospho (p)-ALK, p-JNK, Nek7,and NLRP3 downstream molecules including activated caspase-1 (p20) and mature interleukin (IL)-1β (p17), were upregulatedin L. monocytogenes-infected macrophages. TheALK inhibitor significantly decreased the expression of p-JNK,Nek7, and NLRP3 downstream molecules in macrophages infectedwith L. monocytogenes. Furthermore, the Mst1/2 inhibitormarkedly inhibited the L. monocytogenes-induced activationof ALK, subsequently downregulating the expressionof p-JNK, Nek7, and NLRP3 downstream molecules. Therefore,our study demonstrated that Mst1/2-ALK mediatedthe activation of the NLRP3 inflammasome by promotingthe interaction between Nek7 and NLRP3 via JNK duringL. monocytogenes infection, which subsequently increased thematuration and release of proinflammatory cytokine to resistpathogen infection. Moreover, Listeriolysin O played akey role in the process. In addition, we also found that the L. monocytogenes-induced apoptosis of J774A.1 cells was reducedby the Mst1/2 or ALK inhibitor. The present study reported,for the first time, that the Mst1/2-ALK-JNK-NLRP3 signalingpathway plays a vital proinflammatory role during L. monocytogenesinfection.

Phenotypic and Molecular Characteristics of Children with Progressive Familial Intrahepatic Cholestasis in South China

Wen Zhang,Ruizhu Lin,Zhikun Lu,Huiying Sheng,Yi Xu,Xiuzhen Li,Jing Cheng,Yanna Cai,Xiaojian Mao,Li Liu 대한소아소화기영양학회 2020 Pediatric gastroenterology, hepatology & nutrition Vol.23 No.6

Purpose: Progressive familial intrahepatic cholestasis (PFIC) is a rare genetic autosomal recessive disease caused by mutations in ATP8B1, ABCB11 or ABCB4. Mutational analysis of these genes is a reliable approach to identify the disorder. Methods: We collected and analyzed relevant data related to clinical diagnosis, biological investigation, and molecular determination in nine children carrying these gene mutations, who were from unrelated families in South China. Results: Of the nine patients (five males, four females) with PFIC, one case of PFIC1, four cases of PFIC2, and four cases of PFIC3 were diagnosed. Except in patient no. 8, jaundice and severe pruritus were the major clinical signs in all forms. γ-glutamyl transpeptidase was low in patients with PFIC1/PFIC2, and remained mildly elevated in patients with PFIC3. We identified 15 different mutations, including nine novel mutations (p.R470HfsX8, p.Q794X and p.I1170T of ABCB11 gene mutations, p.G319R, p.A1047P, p.G1074R, p.T830NfsX11, p.A1047PfsX8 and p.N1048TfsX of ABCB4 gene mutations) and six known mutations (p.G446R and p.F529del of ATP8B1 gene mutations, p.A588V, p.G1004D and p.R1057X of ABCB11 gene mutations, p.P479L of ABCB4 gene mutations). The results showed that compared with other regions, these three types of PFIC genes had different mutational spectrum in China. Conclusion: The study expands the genotypic spectrum of PFIC. We identified nine novel mutations of PFIC and our findings could help in the diagnosis and treatment of this disease.