A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

Jia-Feng Yu,Jing Guo,Qing-Bin Liu,Yue Hou,Ke Xiao,Qing-Li Chen,Ji-Hua Wang,Xiao Sun 한국유전학회 2015 Genes & Genomics Vol.37 No.4

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.

Synthesis and Characterization of pH and Temperature Sensitive Hydrogel Based on Poly(N-isopropylacrylamide), Poly(ε-caprolactone), Methylacrylic Acid, and Methoxyl Poly(ethylene glycol)

Xu Xu,Jia Song,Ke Wang,YingChun Gu,Feng Luo,XiaoHai Tang,Ping Xie,ZhiYong Qian 한국고분자학회 2013 Macromolecular Research Vol.21 No.8

In this paper, a novel biodegradable and pH/thermo-sensitive hydrogel based on poly(ε-caprolactone),methoxyl poly(ethylene glycol), methylacrylic acid and N-isopropylacrylamide was prepared by UV-initiated free radical polymerization. The hydrogels were characterized by Fourier transforms infrared ray. The thermal responsibility was investigated with the help of differential scanning calorimetry. Swelling behavior in aqueous medium with different pH value was studied in detail. When the pH value of the aqueous medium was increased from 1.2 to 7.2,the swelling ratio of the hydrogels increased accordingly. The morphology was observed by scanning electron microscopy, and the hydrolytic degradation behavior in different aqueous media (pH 1.2 and pH 7.2) was also investigated in detail. The prepared biodegradable pH/thermo-sensitive hydrogel based on poly(ε-caprolactone), methoxyl poly(ethylene glycol), methylacrylic acid and N-isopropylacrylamide hold great promise in the development of a smart drug delivery system.

First Principles Study of Structural and Electronic Properties of Pentagonal and Hexagonal Noble Metal Nanowires

Zhijian Fu,Li-Jun Jia,JIHONG XIA,Hai-Bo Ruan,Ke Tang,Yong Pu,Zhao-Yi Zeng,Dian-Yong Tang,Bo Kong,Qi-Feng Chen 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2016 NANO Vol.11 No.6

The equilibrium structure and electronic properties of four ultrathin free-standing pentagonal and hexagonal noble metal nanowires, that is, copper nanowires (CuNWs), silver nanowires (AgNWs), gold nanowires (AuNWs) and platinum nanowires (PtNWs), have been studied comprehensively by adopting a first-principles simulation based on the density-functional theory. The staggered topologies are more stable than the eclipsed ones by analyzing the bonding energy. The staggered ones with a linear atom chain in the center of the pentagonal or hexagons topologies are the preferred structures for CuNWs and AgNWs, but the staggered ones without a linear atom chain in the center of the pentagon or hexagon are the preferred structures for AuNWs and PtNWs due to the increasing core–core repulsions. The calculated electronic band structures and density of states present that all the noble metal nanowires are metallic. The projected densities of states (PDOS) of dominant d-states and the charge density show that the narrower d-state moved to the Fermi energy and metallic bonding character for all the noble metal nanowires.

Isoindolin-1-ones from the stems of Nicotiana tabacum and their antiviral activities

Guang-Yu Yang,Jia-Meng Dai,Zhen-Jie Li,Jin Wang,Feng-Xian Yang,Xin Liu,Jing Li,Qian Gao,Xue-Mei Li,Yin-Ke Li,Wei-Guang Wang,Min Zhou,Qiu-Fen Hu 대한약학회 2022 Archives of Pharmacal Research Vol.45 No.8

In previous studies, several isoindolin-1-oneanalogs that exhibited signifi cant anti-tobacco mosaic virus(anti-TMV) activities were isolated from Nicotiana tabacum . Since gene-editing mutants provide a new sample for thediscovery of active metabolites, we focused on the stems ofYN-18–23 (a mutant N. tabacum for gene editing with thealkaloid metabolic pathway cultivated by Yunnan TobaccoCompany), which led to the isolation of four new ( 1–4 )and four known ( 5–8 ) isoindolin-1-ones. To the best of ourknowledge, nicindole C ( 3 ) is the fi rst subclass of isoindolin-1-one bearing a pentacyclic ketone, while nicindole D ( 4 )is the fi rst example of isoindolin-1-one bearing a methylpyridin-2-(1 H )-one moiety. Compounds 1–4 were testedfor their anti-TMV activities, and the results revealed thatcompounds 1 , 3 , and 4 exhibited high anti-TMV activities atconcentrations of 20 μM with inhibition rates of 48.6, 42.8,and 71.5%, respectively. These rates are higher than the inhibitionrate of the positive control (33.2%). The mechanisticstudy of compound 4 , which had the highest anti-TMV activityrevealed that increased potentiation of defense-related enzyme activities and downregulation of expression of theNtHsp70 protein may induce resistance in tobacco againstthe viral pathogen TMV. Molecular docking studies alsorevealed that the isoindolin-1-one substructure is fundamentalfor anti-TMV activity. The methyl-pyridin-2-(1 H )-onemoiety in compound 4 and the 2-oxopropyl groups in compounds1 and 3 at the N -2 position may increase inhibitoryactivities. This study of the structure–activity relationshipis helpful for fi nding new anti-TMV activity inhibitors. Tostudy whether the isoindolin-1-ones have broader antiviralactivities, compounds 1–4 were also tested for their antirotavirusactivities. Compound 4 exhibited high anti-rotavirusactivity with a therapeutic index (TI) value of 20.7. This TI value is close to that of the positive control (20.2).

Silencing of long noncoding RNA PVT1 inhibits podocyte damage and apoptosis in diabetic nephropathy by upregulating FOXA1

Dong-Wei Liu,Jia-Hui Zhang,Feng-Xun Liu,Xu-Tong Wang,Shao-Kang Pan,Deng-Ke Jiang,Zi-Hao Zhao,Zhang-Suo Liu 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

The number of patients with diabetic nephropathy (DN) is still on the rise worldwide, and this requires the development of new therapeutic strategies. Recent reports have highlighted genetic factors in the treatment of DN. Herein, we aimed to study the roles of long noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) and histone 3 lysine 27 trimethylation (H3K27me3) in DN. A model of DN was established by inducing diabetes in mice with streptozotocin. Mouse podocyte clone 5 (MPC5) podocytes and primary podocytes were cultured in normal and high glucose media to observe cell morphology and to quantify PVT1 expression. The roles of PVT1 and enhancer of zeste homolog 2 (EZH2) were validated via loss-of-function and gain-of-function in vitro experiments to identify the interactions among PVT1, EZH2, and forkhead box A1 (FOXA1). The podocyte damage and apoptosis due to PVT1 and FOXA1 were verified with in vivo experiments. PVT1 was highly expressed in MPC5 and primary podocytes in DN patients and in cultures grown in high glucose medium. A large number of CpG (C-phosphate-G) island sites were predicted at the FOXA1 promoter region, where PVT1 recruited EZH2 to promote the recruitment of H3K27me3. The silencing of PVT1 or the overexpression of FOXA1 relieved the damage and inhibited the apoptosis of podocytes in DN, as was evidenced by the upregulated expression of synaptopodin and podocin, higher expression of Bcl-2, and lower expression of Bax and cleaved caspase-3. The key findings of this study collectively indicate that the suppression of lncRNA PVT1 exerts inhibitory effects on podocyte damage and apoptosis via FOXA1 in DN, which is of clinical significance.

Nonsingular Fixed-time Consensus Tracking for Heterogeneous Multi-agent Systems With External Disturbances and Actuator Faults

Pu Yang,Yu Ding,Ke-Jia Feng,Zi-Wei Shen 제어·로봇·시스템학회 2024 International Journal of Control, Automation, and Vol.22 No.3

This paper studies the leader-follower consensus tracking for a group of heterogeneous multi-agent systems with nonlinear hybrid order dynamics, external disturbances and actuator faults. First, a novel finite-timeobserver is designed based on a combination of high-order sliding mode and dual layers adaptive rules to realizefast estimation and compensation of disturbances and faults. Then the fixed-time consensus protocols are achievedwith the aid of a novel sliding mode surface. Additionally, the proposed protocols solve the singularity by introducing a continuous sinusoid function. The distributed control protocols are designed for all followers with first-orderor second-order dynamics to achieve synchronization with the leader. Finally, the effectiveness of the algorithm isverified by simulation.

Upregulation of PITX2 Promotes Letrozole Resistance Via Transcriptional Activation of IFITM1 Signaling in Breast Cancer Cells

Ying-ying Xu,Hai-ru Yu,Jia-yi Sun,Zhao Zhao,Shuang Li,Xin-feng Zhang,Zhi-xuan Liao,Ming-ke Cui,Juan Li,Chan Li,Qiang Zhang 대한암학회 2019 Cancer Research and Treatment Vol.51 No.2

Purpose Although the interferon  (IFN) signaling and the paired-like homeodomain transcription factor 2 (PITX2) have both been implicated in the progression of breast cancer (BCa), it remains obscure whether these two pathways act in a coordinated manner. We therefore aimed to elucidate the expression and function of PITX2 during the pathogenesis of endocrine resistance in BCa. Materials and Methods PITX2 expression was assessed in BCa tissues using quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohistochemistry and in experimentally induced letrozole-resistant BCa cells using RT-qPCR and immunoblotting. Effects of PITX2 deregulation on BCa progression was determined by assessing MTT, apoptosis and xenograft model. Finally, using multiple assays, the transcriptional regulation of interferon-inducible transmembrane protein 1 (IFITM1) by PITX2 was studied at both molecular and functional levels. Results PITX2 expression was induced in letrozole-resistant BCa tissues and cells, and PITX2 induction by IFN signaling powerfully protected BCa cells against letrozole insult and potentiated letrozole-resistance. Mechanistically, PITX2 enhanced IFN-induced AKT activation by transactivating the transcription of IFITM1, thus rendering BCa cells unresponsive to letrozoleelicited cell death. Additionally, ablation of IFITM1 expression using siRNA substantially abolished IFN-elicited AKT phosphorylation, even in the presence of PITX2 overexpression, thus sensitizing BCa cells to letrozole treatment. Conclusion These results demonstrate that constitutive upregulation of PITX2/IFITM1 cascade is an intrinsic adaptive mechanism during the pathogenesis of letrozole-resistance, and modulation of PITX2/IFITM1 level using different genetic and pharmacological means would thus have a novel therapeutic potential against letrozole resistance in BCa.

Prescribed Performance-tangent Barrier Lyapunov Function for Adaptive Neural Backstepping Control of Variable Stiffness Actuator with Input and Output Constraints

Yu Xia,Jun-Yang Li,Yan-Kui Song,Jia-Xu Wang,Yan-Feng Han,Ke Xiao 제어·로봇·시스템학회 2023 International Journal of Control, Automation, and Vol.21 No.3

Due to the complexity of modeling and the strong transmission coupling, the rich background of rigid actuator control has not been transferred to variable stiffness actuator (VSA). Therefore, most model-based control techniques developed for VSA require feedback linearization first. Alternatively, VSA can use non-model-based control techniques such as PD control, but it does not show strong robustness under disturbances. This paper is concerned with designing a novel adaptive neural network backstepping control scheme without using feedback linearization for a special VSA with saturation inputs, output constraints, and disturbances. Firstly, for ensuring the VSA with lower tracking error and higher security, the prescribed performance-tangent barrier Lyapunov function (PP-TBLF) is introduced to handle the prescribed output performance constraints. Subsequently, the Chebyshev neural network and the Nussbaum-type function are exploited to approximate the unknown nonlinearities and unknown gains. Meanwhile, the inverse hyperbolic sine function tracking differentiator is utilized to solve the “explosion of complexity” caused by the differentiation of virtual inputs and also approximate the complex partial derivatives caused by the auxiliary control signals. Finally, the stability of the whole scheme is proved by the Lyapunov criterion. The simulation results illustrate the raised control scheme’s feasibility and show a better closed-loop behavior relative to that obtained using a classic PD controller.

Melatonin Attenuates Mitochondrial Damage in Aristolochic Acid-Induced Acute Kidney Injury

Sun Jian,Pan Jinjin,Liu Qinlong,Cheng Jizhong,Tang Qing,Ji Yuke,Cheng Ke,wang Rui,Liu Liang,Wang Dingyou,Wu Na,Zheng Xu,Li Junxia,Zhang Xueyan,Zhu Zhilong,Ding Yanchun,Zheng Feng,Li Jia,Zhang Ying,Yua 한국응용약물학회 2023 Biomolecules & Therapeutics(구 응용약물학회지) Vol.31 No.1

Aristolochic acid (AA), extracted from Aristolochiaceae plants, plays an essential role in traditional herbal medicines and is used for different diseases. However, AA has been found to be nephrotoxic and is known to cause aristolochic acid nephropathy (AAN). AA-induced acute kidney injury (AKI) is a syndrome in AAN with a high morbidity that manifests mitochondrial damage as a key part of its pathological progression. Melatonin primarily serves as a mitochondria-targeted antioxidant. However, its mitochondrial protective role in AA-induced AKI is barely reported. In this study, mice were administrated 2.5 mg/kg AA to induce AKI. Melatonin reduced the increase in Upro and Scr and attenuated the necrosis and atrophy of renal proximal tubules in mice exposed to AA. Melatonin suppressed ROS generation, MDA levels and iNOS expression and increased SOD activities in vivo and in vitro. Intriguingly, the in vivo study revealed that melatonin decreased mitochondrial fragmentation in renal proximal tubular cells and increased ATP levels in kidney tissues in response to AA. In vitro, melatonin restored the mitochondrial membrane potential (MMP) in NRK-52E and HK-2 cells and led to an elevation in ATP levels. Confocal immunofluorescence data showed that puncta containing Mito-tracker and GFP-LC3A/B were reduced, thereby impeding the mitophagy of tubular epithelial cells. Furthermore, melatonin decreased LC3A/B-II expression and increased p62 expression. The apoptosis of tubular epithelial cells induced by AA was decreased. Therefore, our findings revealed that melatonin could prevent AA-induced AKI by attenuating mitochondrial damage, which may provide a potential therapeutic method for renal AA toxicity.