Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato

Jinhua Li,Xiaoxing Su,Yinlei Wang,Wei Yang,Yu Pan,Chenggang Su,Xingguo Zhang 한국유전학회 2018 Genes & Genomics Vol.40 No.1

BTB (broad-complex, tramtrack, and bric-abrac) family proteins are characterized by the presence of a protein–protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies. The SlBTB proteins contains 1–3 BTB domains, and several other types of functional domains, including KCTD (Potassium channel tetramerization domain-containing), the MATH (meprin and TRAF homology), ANK (Ankyrin repeats), NPR1 (nonexpressor of pathogenesis-related proteins1), NPH3 (Nonphototropic Hypocotyl 3), TAZ zinc finger, C-terminal Kelch, Skp1 and Arm (Armadillo/betacatenin- like repeat) domains are also found in some tomato BTB proteins. Moreover, their expression patterns in tissues/ stages, in response to different abiotic stress treatments and hormones were also investigated. This study provides the first comprehensive analysis of BTB gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of BTB genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

Improved Sliding Shapes for Instance Segmentation of Amodal 3D Object

( Jinhua Lin ),( Yu Yao ),( Yanjie Wang ) 한국인터넷정보학회 2018 KSII Transactions on Internet and Information Syst Vol.12 No.11

State-of-art instance segmentation networks are successful at generating 2D segmentation mask for region proposals with highest classification score, yet 3D object segmentation task is limited to geocentric embedding or detector of Sliding Shapes. To this end, we propose an amodal 3D instance segmentation network called A3IS-CNN, which extends the detector of Deep Sliding Shapes to amodal 3D instance segmentation by adding a new branch of 3D ConvNet called A3IS-branch. The A3IS-branch which takes 3D amodal ROI as input and 3D semantic instances as output is a fully convolution network(FCN) sharing convolutional layers with existing 3d RPN which takes 3D scene as input and 3D amodal proposals as output. For two branches share computation with each other, our 3D instance segmentation network adds only a small overhead of 0.25 fps to Deep Sliding Shapes, trading off accurate detection and point-to-point segmentation of instances. Experiments show that our 3D instance segmentation network achieves at least 10% to 50% improvement over the state-of-art network in running time, and outperforms the state-of-art 3D detectors by at least 16.1 AP.

Genetic diversity analysis in Chinese miniature pigs using swine leukocyte antigen complex microsatellites

Wu, Jinhua,Liu, Ronghui,Li, Hua,Yu, Hui,Yang, Yalan Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.11

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

Tuning the Surface Properties of Graphene Oxide by Surface-Initiated Polymerization of Epoxides: An Efficient Method for Enhancing Gas Separation

Wu, Yu,Jia, Pan,Xu, Linli,Chen, Zhangyan,Xiao, Linhong,Sun, Jinhua,Zhang, Jun,Huang, Yong,Bielawski, Christopher W.,Geng, Jianxin American Chemical Society 2017 ACS APPLIED MATERIALS & INTERFACES Vol.9 No.5

<P>Here, we describe an in situ approach for growing polyepoxides from the surfaces of graphene oxide (GO) using a surface-initiated polymerization reaction. The polymerization methodology is facile and general as a broad range of epoxides carrying various functional groups have been successfully polymerized by simply adding GO powders in the epoxide monomers. The resultant polyepoxide grafted GO are found to show enhanced dispersibility in various common solvents and to exhibit increased d-spacing between the basal planes. In particular, grafting poly(2,3-epoxy-1-propanol) (PEP) to GO results in a composite (i.e., GO-g-PEP) that is dispersible in water and miscible with polyether block amide, i.e., Pebax MH 1657. Preliminary studies have indicated the membranes prepared using Pebax/GO-g-PEP composites exhibit enhanced CO2 permeabilities and selectivities in comparison to H-2, O-2, or N-2. The excellent performance in gas separation is attributed to the layered structure of the GO-g-PEP sheets with enlarged d-spacing and the functional groups present on the PEP chains grafted to the surfaces of GO sheets.</P>

<i>S</i>-Adenosyl-<small>L</small>-methionine Activates Actinorhodin Biosynthesis by Increasing Autophosphorylation of the Ser/Thr Protein Kinase AfsK in <i>Streptomyces coelicolor</i> A3(2)

JIN, Ying-Yu,CHENG, Jinhua,YANG, Seung Hwan,MENG, Lingzhu,PALANIYANDI, Sasikumar Arunachalam,ZHAO, Xin-Qing,SUH, Joo-Won Japan Society for Bioscience, Biotechnology, and A 2011 Bioscience, biotechnology, and biochemistry Vol.75 No.5

<P><I>S</I>-Adenosyl-<SMALL>L</SMALL>-methionine (SAM) is one of the major methyl donors in all living organisms. The exogenous treatment with SAM leads to increased actinorhodin production in <I>Streptomyces coelicolor</I> A3(2). In this study, mutants from different stages of the AfsK-AfsR signal transduction cascade were used to test the possible target of SAM. SAM had no significant effect on actinorhodin production in <I>afsK</I>, <I>afsR</I>, <I>afsS</I>, or <I>act</I>II-open reading frame 4 (ORF4) mutant. This confirms that <I>afsK</I> plays a critical role in delivering the signal generated by exogenous SAM. The <I>afsK-pHJL-KN</I> mutant did not respond to SAM, suggesting the involvement of the C-terminal of AfsK in binding with SAM. SAM increased the <I>in vitro</I> autophosphorylation of kinase AfsK in a dose-dependent manner, and also abolished the effect of decreased actinorhodin production by a Ser/Thr kinase inhibitor, K252a. In sum, our results suggest that SAM activates actinorhodin biosynthesis in <I>S. coelicolor</I> M130 by increasing the phosphorylation of protein kinase AfsK.</P>

Application of the French Codes to the Pressurized Thermal Shocks Assessment

Mingya Chen,Guian Qian,Jinhua Shi,Rongshan Wang,Weiwei Yu,Feng Lu,Guodong Zhang,Fei Xue,Zhilin Chen 한국원자력학회 2016 Nuclear Engineering and Technology Vol.48 No.6

The integrity of a reactor pressure vessel (RPV) related to pressurized thermal shocks (PTSs)has been extensively studied. This paper introduces an integrity assessment of an RPVsubjected to a PTS transient based on the French codes. In the USA, the “screening criterion”for maximum allowable embrittlement of RPV material is developed based on theprobabilistic fracture mechanics. However, in the French RCC-M and RSE-M codes, whichare developed based on the deterministic fracture mechanics, there is no “screening criterion”. In this paper, the methodology in the RCC-M and RSE-M codes, which are used forPTS analysis, are firstly discussed. The bases of the French codes are compared with ASMEand FAVOR codes. A case study is also presented. The results show that the method in theRCC-M code that accounts for the influence of cladding on the stress intensity factor (SIF)may be nonconservative. The SIF almost doubles if the weld residual stress is considered. The approaches included in the codes differ in many aspects, which may result in significantdifferences in the assessment results. Therefore, homogenization of the codes inthe long time operation of nuclear power plants is needed.

Research on the Rotational Accuracy Measurement of an Aerostatic Spindle in a Rolling Bearing Performance Analysis Instrument

Zhaohui Yang,Jun Hong,JinHua Zhang,Michael Yu Wang 한국정밀공학회 2014 International Journal of Precision Engineering and Vol. No.

An ultra-precision instrument is developed to measure the rotational accuracy of a rolling bearing under working conditions. Thisinstrument uses a high-precision aerostatic spindle, which has high-stiffness to support a test bearing under large axial loading. Thiswork demonstrates the capabilities of the double-probe error separation method for the measurement of aerostatic spindle errormotion at various axial forces and rotational speeds. The rotational performance of an aerostatic spindle is discussed. The resultsindicate that the error motion and the form of the error of the measurement surface are reliably separated at various axial forces androtational speeds. In addition, the error motion of the aerostatic spindle is very stable, increasing slightly and smoothly as therotational speed increases. The error motion is less than 0.18 um when the speed reaches 1920 rpm. In the future, it will be possibleto separate the error motion of an aerostatic spindle from the measurement results of a test bearing.

Quantitative analysis using intraoperative contrast-enhanced ultrasound in adult-type diffuse gliomas with isocitrate dehydrogenase mutations: association between hemodynamics and molecular features

Xiandi Zhang,Zhifeng Shi,Yuanxin Xie,Yong Wang,Chao Shen,Zengxin Qi,Liqiong Zhang,Bojie Yang,Jinhua Yu,Hong Ding 대한초음파의학회 2023 ULTRASONOGRAPHY Vol.42 No.4

Purpose: The relationship between contrast-enhanced ultrasound (CEUS) hemodynamics and the molecular biomarkers of adult-type diffuse gliomas, particularly isocitrate dehydrogenase (IDH), remains unclear. This study was conducted to provide a comprehensive description of the vascularization of adult-type diffuse gliomas using quantitative indicators. Additionally, it was designed to identify any variables with the potential to intraoperatively predict IDH mutation status. Methods: This prospective study enrolled patients with adult-type diffuse gliomas between November 2021 and September 2022. Intraoperative CEUS was performed, and CEUS videos were recorded for 90-second periods. Hemodynamic parameters, including the peak enhancement (PE) difference, were calculated based on the time-intensity curve of the region of interest. A differential analysis was performed on the CEUS parameters with respect to molecular biomarkers and grades. Receiver operating characteristic curves for various parameters were analyzed to evaluate the ability of those parameters to predict IDH mutation status. Results: Sixty patients with adult-type diffuse gliomas were evaluated. All hemodynamic parameters, apart from rising time, demonstrated significant differences between IDH-mutant and IDH-wildtype adult-type diffuse gliomas. The PE difference emerged as the optimal indicator for differentiating between IDH-wildtype and IDH-mutant gliomas, with an area under the curve of 0.958 (95% confidence interval, 0.406 to 0.785). Additionally, the hemodynamic parameters revealed significant differences across both grades and types of adult-type diffuse gliomas. Conclusion: Hemodynamic parameters can be used intraoperatively to effectively distinguish between IDHwildtype and IDH-mutant adult-type diffuse gliomas. Additionally, quantitative CEUS equips neurosurgeons with dynamic perfusion information for various types and grades of adult-type diffuse gliomas.

Effects of 7-hydroxy-3-methoxycadalene on cell cycle, apoptosis and protein translation in A549 lung cancer cells

Jin, Hua,Kim, Hyun-Woo,Xu, Cheng-Xiong,Kwon, Jung-Taek,Hwang, Soon-Kyung,Lee, Eun-Sun,Chang, Seung-Hee,Park, Sung-Jin,Noh, Mi-Suk,Woo, Min-Ah,Yu, Kyeong-Nam,Lee, Hu-Jang,Choi, Joon-Weon,Choi, Don-Ha,C IOS Press 2007 Biofactors Vol.29 No.2

<P>Previously we reported that cadalene extracted from Zelkova serrata inhibited lung tumorigenesis in mice. However, the precise mechanism has not yet investigated. Here, we examined the effects of cadalene on signal pathways important for apoptosis, cell cycle, and protein translation in lung cancer cells. Our results showed that cadalene suppressed the expression of Akt and its phosphor-forms through controlling PI3K and PTEN. Cadalene also induced apoptosis through facilitating pro-apoptotic protein expression. In addition, cadalene caused cell cycle arrest and decreased mTOR-mediated protein translation. Taken together, cadalene may be developed as a lung cancer therapeutic agent in the future.</P>

A High Inorganic Phosphate Diet Perturbs Brain Growth, Alters Akt-ERK Signaling, and Results in Changes in Cap-Dependent Translation

Jin, Hua,Hwang, Soon-Kyung,Yu, Kyungnam,Anderson, Hanjo K.,Lee, Yeon-Sook,Lee, Kee Ho,Prats, Anne-Catherine,Morello, Dominique,Beck Jr., George R.,Cho, Myung-Haing Oxford University Press 2006 TOXICOLOGICAL SCIENCES Vol.90 No.1

<P>Inorganic phosphate (Pi) plays a key role in diverse physiological functions. Recently, considerable progress has been made in our understanding of the function and regulation of the brain-specific sodium-dependent inorganic phosphate transporter 1 (NPT1), which is found to exist principally in cerebrum and cerebellum. The potential importance of Pi as a novel signaling molecule and the poor prognosis of diverse neurodegenerative diseases that involve brain-specific NPT1 have prompted us to define the pathways by which Pi affects mouse brain growth. A high phosphate diet caused an increase in serum Pi accompanied by a decrease in calcium, and a decrease in body weight coupled with a decreased relative weight of cerebellum. A high phosphate diet caused a significant increase in protein expression of NPT1, both in cerebrum and cerebellum. Additionally, the high phosphate diet increased Homo sapiens v-akt murine thymoma viral oncogene homolog 1 (Akt) phosphorylation at Ser473 in cerebrum and cerebellum, whereas suppression of Akt phosphorylation at Thr308 was observed only in cerebellum. Selective suppression of eukaryotic translation initiation factor-binding protein (eIF4E-BP1) in cerebrum was induced by high levels of Pi, which induced cap-dependent and cap-independent protein translation in cerebrum and cerebellum, respectively. Phosphorylation of extracellular regulated kinase 1 (ERK1) in comparison with that of ERK2 was significantly reduced in both cerebrum and cerebellum. High levels of Pi reduced protein expressions of proliferating cell nuclear antigen (PCNA) and cyclin D1 in cerebrum and cerebellum. In conclusion, the results indicate that high dietary Pi can perturb normal brain growth, possibly through Akt-ERK signaling in developing mice.</P>