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1.
Cell ; 158(2): 353-367, 2014 Jul 17.
Article in English | MEDLINE | ID: mdl-25036632

ABSTRACT

Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. Although isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple nonspecific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA.


Subject(s)
DNA Transposable Elements , Houseflies/enzymology , Transposases/chemistry , Animals , Base Sequence , Crystallography, X-Ray , Dimerization , Houseflies/genetics , Insect Proteins/chemistry , Insect Proteins/genetics , Insect Proteins/metabolism , Models, Molecular , Molecular Sequence Data , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Transposases/genetics , Transposases/metabolism
2.
Small ; 20(27): e2308283, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38412406

ABSTRACT

Unsatisfactory performance of ethanol oxidation reaction (EOR) catalysts hinders the application of direct ethanol fuel cells (DEFCs), while traditional alloy catalysts (like PdPt) is cursed by Sabatier principle due to countable active site types. However, bacterial soluble extracellular polymeric substances (s-EPS) owning abundent functional groups may help breacking through it by contrusting different active sites on PdPt and inducing them to play synergy effect, which is called interface engineering. Using s-EPS to engineer catalysts is more green and consumes lower energy compared to chemical reagents. Herein, PdPt alloy nanoparticles (≈2.1 nm) are successfully in situ synthesized by/on s-EPS of Bacillus megaterium, an ex-holotype. Tryptophan residuals are proved as the main reductant. In EOR, PdPt@s-EPS shows higher activity (3.89 mA cm-2) than Pd@s-EPS, Pt@s-EPS, Pt/C and most reported akin catalysts. Its stability and durability are excellent, too. DFT modelling further demonstrates that, interface engineering by s-EPS breaks through Sabatier principle, by the synergy of diverse sites owning different degrees of d-p orbital hybridization. This work not only makes DEFCs closer to practice, but provides a facile and green strategy to design more catalysts.

3.
BMC Pediatr ; 24(1): 107, 2024 Feb 12.
Article in English | MEDLINE | ID: mdl-38347448

ABSTRACT

OBJECTIVE: As the predominant complication in preterm infants, Bronchopulmonary Dysplasia (BPD) necessitates accurate identification of infants at risk and expedited therapeutic interventions for an improved prognosis. This study evaluates the potential of Monosaccharide Composite (MC) enriched with environmental information from circulating glycans as a diagnostic biomarker for early-onset BPD, and, concurrently, appraises BPD risk in premature neonates. MATERIALS AND METHODS: The study incorporated 234 neonates of ≤32 weeks gestational age. Clinical data and serum samples, collected one week post-birth, were meticulously assessed. The quantification of serum-free monosaccharides and their degraded counterparts was accomplished via High-performance Liquid Chromatography (HPLC). Logistic regression analysis facilitated the construction of models for early BPD diagnosis. The diagnostic potential of various monosaccharides for BPD was determined using Receiver Operating Characteristic (ROC) curves, integrating clinical data for enhanced diagnostic precision, and evaluated by the Area Under the Curve (AUC). RESULTS: Among the 234 neonates deemed eligible, BPD development was noted in 68 (29.06%), with 70.59% mild (48/68) and 29.41% moderate-severe (20/68) cases. Multivariate analysis delineated several significant risk factors for BPD, including gestational age, birth weight, duration of both invasive mechanical and non-invasive ventilation, Patent Ductus Arteriosus (PDA), pregnancy-induced hypertension, and concentrations of two free monosaccharides (Glc-F and Man-F) and five degraded monosaccharides (Fuc-D, GalN-D, Glc-D, and Man-D). Notably, the concentrations of Glc-D and Fuc-D in the moderate-to-severe BPD group were significantly diminished relative to the mild BPD group. A potent predictive capability for BPD development was exhibited by the conjunction of gestational age and Fuc-D, with an AUC of 0.96. CONCLUSION: A predictive model harnessing the power of gestational age and Fuc-D demonstrates promising efficacy in foretelling BPD development with high sensitivity (95.0%) and specificity (94.81%), potentially enabling timely intervention and improved neonatal outcomes.


Subject(s)
Bronchopulmonary Dysplasia , Infant, Premature , Infant , Male , Female , Pregnancy , Infant, Newborn , Humans , Gestational Age , Bronchopulmonary Dysplasia/complications , Fucose , Monosaccharides
4.
Epidemiol Infect ; 151: e107, 2023 06 14.
Article in English | MEDLINE | ID: mdl-37311733

ABSTRACT

We describe an outbreak of echovirus 18 infection involving 10 patients in our neonatal intensive care unit (an attack rate of 33%). The mean age at the onset of illness was 26.8 days. Eighty percent were preterm infants. All were discharged home without sequelae. There were no differences in gestation age, birth weight, delivery mode, use of antibiotics, and parenteral nutrition between the enterovirus (EV) group and non-EV group, but the rate of breastfeeding was significantly higher in the EV group. Separation care and reinforcement of hand-washing seemed to be effective in preventing further spread of the virus. Visiting policy, hygiene practice, and handling of expressed breastmilk should be reinforced.


Subject(s)
Cross Infection , Echovirus Infections , Enterovirus Infections , Meningitis, Aseptic , Humans , Infant , Infant, Newborn , Cross Infection/epidemiology , Disease Outbreaks , Echovirus Infections/epidemiology , Enterovirus B, Human , Enterovirus Infections/epidemiology , Infant, Premature , Meningitis, Aseptic/epidemiology , Meningitis, Aseptic/virology
5.
Acta Biochim Biophys Sin (Shanghai) ; 55(11): 1833-1839, 2023 11 25.
Article in English | MEDLINE | ID: mdl-37705347

ABSTRACT

Esterases/lipases from the GDSL family have potential applications in the hydrolysis and synthesis of important esters of pharmaceutical, food, and biotechnical interests. However, the structural and functional understanding of GDSL enzymes is still limited. Here, we report the crystal structure of the GDSL family esterase EstL5 complexed with PMSF at 2.34 Šresolution. Intriguingly, the PMSF binding site is not located at the active site pocket but is situated in a surface cavity. At the active site, we note that there is a trapped crystallization solvent 1,6-hexanediol, which mimics the bound ester chain, allowing for further definition of the active site pocket of EstL5. The most striking structural feature of EstL5 is the presence of a unique channel, which extends approximately 18.9 Å, with a bottleneck radius of 6.8 Å, connecting the active-site pocket and the surface cavity. Replacement of Ser205 with the bulk aromatic residue Trp or Phe could partially block the channel at one end and perturb its access. Reduced enzymatic activity is found in the EstL5 S205W and EstL5 S205F mutants, suggesting the functional relevance of the channel to enzyme catalysis. Our study provides valuable information regarding the properties of the GDSL-family enzymes for designing more efficient and robust biocatalysts.


Subject(s)
Esterases , Lipase , Esterases/genetics , Esterases/chemistry , Esterases/metabolism , Catalytic Domain , Lipase/metabolism , Binding Sites
6.
Sensors (Basel) ; 23(6)2023 Mar 17.
Article in English | MEDLINE | ID: mdl-36991916

ABSTRACT

This paper proposes an encoding-decoding network with a pyramidal representation module, which will be referred to as EDPNet, and is designed for efficient semantic image segmentation. On the one hand, during the encoding process of the proposed EDPNet, the enhancement of the Xception network, i.e., Xception+ is employed as a backbone to learn the discriminative feature maps. The obtained discriminative features are then fed into the pyramidal representation module, from which the context-augmented features are learned and optimized by leveraging a multi-level feature representation and aggregation process. On the other hand, during the image restoration decoding process, the encoded semantic-rich features are progressively recovered with the assistance of a simplified skip connection mechanism, which performs channel concatenation between high-level encoded features with rich semantic information and low-level features with spatial detail information. The proposed hybrid representation employing the proposed encoding-decoding and pyramidal structures has a global-aware perception and captures fine-grained contours of various geographical objects very well with high computational efficiency. The performance of the proposed EDPNet has been compared against PSPNet, DeepLabv3, and U-Net, employing four benchmark datasets, namely eTRIMS, Cityscapes, PASCAL VOC2012, and CamVid. EDPNet acquired the highest accuracy of 83.6% and 73.8% mIoUs on eTRIMS and PASCAL VOC2012 datasets, while its accuracy on the other two datasets was comparable to that of PSPNet, DeepLabv3, and U-Net models. EDPNet achieved the highest efficiency among the compared models on all datasets.

7.
Int J Mol Sci ; 24(13)2023 Jun 27.
Article in English | MEDLINE | ID: mdl-37445879

ABSTRACT

Radiation injury- and radiation combined with skin injury-induced inflammatory responses in the mouse brain were evaluated in this study. Female B6D2F1/J mice were subjected to a sham, a skin wound (SW), 9.5 Gy 60Co total-body gamma irradiation (RI), or 9.5 Gy RI combined with a skin puncture wound (RCI). Survival, body weight, and wound healing were tracked for 30 days, and mouse brain samples were collected on day 30 after SW, RI, RCI, and the sham control. Our results showed that RCI caused more severe animal death and body weight loss compared with RI, and skin wound healing was significantly delayed by RCI compared to SW. RCI and RI increased the chemokines Eotaxin, IP-10, MIG, 6Ckine/Exodus2, MCP-5, and TIMP-1 in the brain compared to SW and the sham control mice, and the Western blot results showed that IP-10 and p21 were significantly upregulated in brain cells post-RI or -RCI. RI and RCI activated both astrocytes and endothelial cells in the mouse brain, subsequently inducing blood-brain barrier (BBB) leakage, as shown by the increased ICAM1 and GFAP proteins in the brain and GFAP in the serum. The Doublecortin (DCX) protein, the "gold standard" for measuring neurogenesis, was significantly downregulated by RI and RCI compared with the sham group. Furthermore, RI and RCI decreased the expression of the neural stem cell marker E-cadherin, the intermediate progenitor marker MASH1, the immature neuron cell marker NeuroD1, and the mature neuron cell marker NeuN, indicating neural cell damage in all development stages after RI and RCI. Immunohistochemistry (IHC) staining further confirmed the significant loss of neural cells in RCI. Our data demonstrated that RI and RCI induced brain injury through inflammatory pathways, and RCI exacerbated neural cell damage more than RI.


Subject(s)
Brain Injuries , Radiation Injuries , Mice , Female , Animals , Chemokine CXCL10 , Endothelial Cells , Radiation Injuries/etiology , Disease Models, Animal , Brain , Brain Injuries/etiology , Skin/radiation effects
8.
Angew Chem Int Ed Engl ; 62(34): e202301901, 2023 Aug 21.
Article in English | MEDLINE | ID: mdl-37395563

ABSTRACT

Construction of a "net-zero-emission" system through CO2 hydrogenation to methanol with solar energy is an eco-friendly way to mitigate the greenhouse effect. Traditional CO2 hydrogenation demands centralized mass production for cost reduction with mass water electrolysis for hydrogen supply. To achieve continuous reaction with intermittent and fluctuating flow of H2 on a small-scale for distributed application scenarios, modulating the catalyst interface environment and chemical adsorption capacity to adapt fluctuating reaction conditions is highly desired. This paper describes a distributed clean CO2 utilization system in which the surface structure of catalysts is carefully regulated. The Ni catalyst with unsaturated electrons loaded on In2 O3 can reduce the dissociation energy of H2 to overcome the slow response of intermittent H2 supply, exhibiting a faster response (12 min) than bare oxide catalysts (42 min). Moreover, the introduction of Ni enhances the sensitivity of the catalyst to hydrogen, yielding a Ni/In2 O3 catalyst with a good performance at lower H2 concentrations with a 15 times adaptability for wider hydrogen fluctuation range than In2 O3 , greatly reducing the negative impact of unstable H2 supplies derived from renewable energies.

9.
Chin J Cancer Res ; 35(5): 536-549, 2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37969960

ABSTRACT

Objective: To explore the application of genetic abnormalities in the diagnosis of angioimmunoblastic T-cell lymphoma (AITL) and the reliable pathological prognostic factors. Methods: This study included 53 AITL cases, which were reviewed for morphological patterns, immunophenotypes, presence of Hodgkin and Reed-Sternberg (HRS)-like cells, and co-occurrence of B cell proliferation. The Epstein-Barr virus (EBV)-positive cells in tissues were counted, and cases were classified into "EBV encoded RNA (EBER) high-density" group if >50/HPF. Targeted exome sequencing was performed. Results: Mutation data can assist AITL diagnosis: 1) with considerable HRS-like cells (20 cases): RHOA mutated in 14 cases (IDH2 co-mutated in 3 cases, 4 cases with rare RHOA mutation), TET2 was mutated in 5 cases (1 case co-mutated with DNMT3A), and DNMT3A mutated in 1 case; 2) accompanied with B cell lymphoma (7 cases): RHOA mutated in 4 cases (1 case had IDH2 mutation), TET2 mutated in 2 cases and DNMT3A mutated in 1 case; 3) mimic peripheral T cell lymphoma, not otherwise specified (5 cases): RHOA mutated in 2 cases (IDH2 co-mutated in 1 case), TET2 mutated in 3 cases, and DNMT3A mutated in 1 case; 4) pattern 1 (1 case), RHOA and TET2 co-mutated. Besides RHOAG17V (30/35), rare variant included RHOAK18N, RHOAR68H, RHOAC83Y, RHOAD120G and RHOAG17del, IDH2R172 co-mutated with IDH2M397V in one case. There were recurrent mutations of FAT3, PCLO and PIEZO1 and genes of epigenetic remodeling, T-cell activation, APC and PI3K/AKT pathway. EBER high-density independently indicated adverse overall survival and progression-free survival (P=0.046 and P=0.008, Kaplan-Meier/log-rank). Conclusions: Over half AITL cases might be confused in diagnosis for certain conditions without mutation data. Targeted exome sequencing with a comprehensive panel is crucial to detect both hot-spot and rare mutation variants for RHOA and IDH2 and other recurrent mutated genes in addition to TET2 and DNMT3A. EBER high-density independently indicated adverse survival.

10.
J Transl Med ; 20(1): 75, 2022 02 05.
Article in English | MEDLINE | ID: mdl-35123494

ABSTRACT

Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the metastasis and recurrence of hepatocellular carcinoma (HCC). A kinds of lncRNAs were found to be involved in regulating epithelial-mesenchymal transition (EMT) or stem-like traits in human cancers, however, the molecular mechanism and signaling pathways targeting EMT and stemness remains largely unknown. Previously, we found that linc00261 was down-regulated in HCC and associated with multiple worse clinical pathological parameters and poor prognosis. Here, we show that linc00261 was down-regulated in TGF-ß1 stimulated cells, and forced expression of linc00261 attenuated EMT and stem-like traits in HCC. Linc00261 also inhibited the tumor sphere forming in vitro and decreased the tumorigenicity in vivo. Furthermore, we revealed that linc00261 suppressed the expression and phosphorylation of SMAD3 (p-SMAD3), which could be core transcriptional modulator in TGF-ß1 signaling mediated EMT and the acquisition of stemness traits. A negative correlation between linc00261 and p-SMAD3 was determined in HCC samples. Conclusion: Our study revealed that linc00261 suppressed EMT and stem-like traits in HCC cells by inhibiting TGF-ß1/SMAD3 signaling.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cell Movement/genetics , Epithelial-Mesenchymal Transition/genetics , Humans , Liver Neoplasms/pathology , RNA, Long Noncoding , Smad3 Protein/metabolism , Transforming Growth Factor beta1/metabolism
11.
Inorg Chem ; 61(24): 8997-9011, 2022 Jun 20.
Article in English | MEDLINE | ID: mdl-35657382

ABSTRACT

A novel family of ruthenium nitrosyl complexes [Ru(bpy)(C∧N)(MeCN)NO](PF6)2 (2a-2e, bpy = 2,2'-bipyridine, HC∧N = 2-phenylpyridine and its derivatives) has been prepared by reacting cyclometalated ruthenium complexes [Ru(bpy)2(C∧N)][PF6] (1a-1e) with NO+, which were comprehensively characterized by mass, IR, NMR, and UV-vis spectra as well as the single-crystal X-ray structure determinations. Herein, the coordination geometry of Ru atoms in 2a-2e is a distorted octahedron and {RuII-NO+}6 is present in these complexes. Theoretical calculations suggest that the reactions involving dissociation of one bipyridine and coordination with NO+ proceed spontaneously (ΔG < 0) and the transformation from 1a-1e to the intermediates is dominated by substituents (ΔGRI varies from -1.19 to -1.53 eV), which influence the binding energy between Ru(II) and NO+ in complexes 2a-2e (-89.42 to -101.17 kcal/mol) and thus control the photorelease of NO on a certain scale. The weak absorption bands in the visible region could be attributed to the contribution of dπ(RuII) → π*(NO+), which were enhanced greatly under light, indicating the possible release of NO. The photoinduced NO, as well as singlet oxygen (1O2), was then confirmed by EPR spectra, and the amount of NO released from 2a-2e was estimated via Griess reagent assay. The cytotoxicity of these complexes with or without visible light irradiation was also investigated using an MTT assay.


Subject(s)
Heterocyclic Compounds , Ruthenium , 2,2'-Dipyridyl/chemistry , Light , Ruthenium/chemistry , Singlet Oxygen
12.
Xenobiotica ; 51(3): 345-354, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33332226

ABSTRACT

Abstracts Zhenwu Tang (ZWT) is a traditional Chinese medicine that is primarily composed of Radix Aconiti Lateralis Praeparata (FZ) and diterpenoid alkaloids are believed to be the pharmacologically active compounds of ZWT. In this study, the pharmacokinetic profiles of hypaconitine, mesaconitine, aconitine, benzoylmesaconitine, benzoylaconitine, and benzoylhypacoitine were assessed in rats following intragastric ZWT administration. Furthermore, differences in the pharmacokinetic profiles of these six alkaloids were assessed as a function of rat sex and the administration of ZWT or FZ extracts to these animals. Plasma levels of these alkaloids were quantified via HPLC-MS/MS. Significant differences in key pharmacokinetic parameters were observed when comparing rats administered FZ or ZWT. Relative to FZ extract treatment, ZWT administration was associated with Cmax and AUC0-∞ values of benzoylmesaconitine that were about 3.5 and 5.5 times higher. Considerable variations in hypaconitine pharmacokinetic parameters were also revealed between female and male rats. The Cmax and AUC0-∞ of hypaconitine were about 2.5- and 2.7-fold elevated in female rats in comparison with male rats. These results suggested that the other compounds within ZWT can enhance the absorption of benzoylmesaconitine, while hypaconitine exhibits higher bioavailability in female rats, as compared with male rats.


Subject(s)
Aconitum/chemistry , Alkaloids/pharmacokinetics , Diterpenes/pharmacokinetics , Drugs, Chinese Herbal/pharmacokinetics , Animals , Chromatography, High Pressure Liquid , Female , Male , Rats , Tandem Mass Spectrometry
13.
Sensors (Basel) ; 21(23)2021 Nov 29.
Article in English | MEDLINE | ID: mdl-34883983

ABSTRACT

The number of deaths due to cardiovascular and respiratory diseases is increasing annually. Cardiovascular diseases with high mortality rates, such as strokes, are frequently caused by atrial fibrillation without subjective symptoms. Chronic obstructive pulmonary disease is another condition in which early detection is difficult owing to the slow progression of the disease. Hence, a device that enables the early diagnosis of both diseases is necessary. In our previous study, a sensor for monitoring biological sounds such as vascular and respiratory sounds was developed and a noise reduction method based on semi-supervised convolutive non-negative matrix factorization (SCNMF) was proposed for the noisy environments of users. However, SCNMF attenuated part of the biological sound in addition to the noise. Therefore, this paper proposes a novel noise reduction method that achieves less distortion by imposing orthogonality constraints on the SCNMF. The effectiveness of the proposed method was verified experimentally using the biological sounds of 21 subjects. The experimental results showed an average improvement of 1.4 dB in the signal-to-noise ratio and 2.1 dB in the signal-to-distortion ratio over the conventional method. These results demonstrate the capability of the proposed approach to measure biological sounds even in noisy environments.


Subject(s)
Noise , Pulmonary Disease, Chronic Obstructive , Algorithms , Humans , Pulmonary Disease, Chronic Obstructive/diagnosis , Respiratory Sounds , Sound
14.
Cancer Sci ; 111(11): 4102-4117, 2020 Nov.
Article in English | MEDLINE | ID: mdl-32808348

ABSTRACT

Hepatocellular carcinoma (HCC) is a common disease worldwide. Accumulating reports have evidenced the internal connection between epithelial-mesenchymal transition (EMT) and cancer stem cells (CSCs), as well as their significance in metastasis and post-operative recurrence. In this study, we investigated an interesting ubiquitin-proteasome pathway associated pseudogene of AOC4, also known as UPAT, and showed that it was downregulated in 39.78% (37/93) of patients with hepatitis B virus (HBV)-related HCC. Downregulation of UPAT was associated with multiple worse clinicopathological parameters, as well as decreased recurrence-free survival (RFS). In vitro and in vivo assays found that overexpression of UPAT significantly suppressed cellular migration, invasion, EMT processes, and CSC properties. Mechanistic studies showed that UPAT promoted ZEB1 degradation via a ubiquitin-proteasome pathway and, in contrast, ZEB1 transcriptionally suppressed UPAT by binding to multiple E-box (CACCTG) elements in the promoter region. Moreover, UPAT was negatively correlated with ZEB1 protein in HCC tissues, their combined expression discriminated RFS outcomes for patients with HBV-related HCC. These data on the UPAT-ZEB1 circuit-mediated pathway will further knowledge on EMT and CSCs, and may help to develop novel therapeutic approaches for the prevention of HCC metastasis.


Subject(s)
Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/pathology , Gene Deletion , Liver Neoplasms/genetics , Liver Neoplasms/pathology , RNA, Long Noncoding/genetics , Zinc Finger E-box-Binding Homeobox 1/genetics , Aged , Animals , Biomarkers , Biomarkers, Tumor , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/mortality , Cell Line, Tumor , Cell Movement , Disease Progression , Female , Gene Expression Regulation, Neoplastic , Humans , Immunohistochemistry , Liver Neoplasms/metabolism , Liver Neoplasms/mortality , Male , Mice , Middle Aged , Prognosis , Pseudogenes , Zinc Finger E-box-Binding Homeobox 1/metabolism
15.
Nucleic Acids Res ; 46(19): 10286-10301, 2018 11 02.
Article in English | MEDLINE | ID: mdl-30239795

ABSTRACT

Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the -2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the -2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.


Subject(s)
DNA Breaks, Double-Stranded , DNA Cleavage , Eukaryota/enzymology , Transposases/physiology , Animals , Binding Sites , Catalysis , Catalytic Domain , DNA Transposable Elements , Eukaryota/genetics , Eukaryota/metabolism , Eukaryotic Cells/enzymology , Eukaryotic Cells/metabolism , Humans , Multigene Family , Protein Conformation , Transposases/chemistry , Transposases/genetics
16.
Nucleic Acids Res ; 46(5): 2660-2677, 2018 03 16.
Article in English | MEDLINE | ID: mdl-29385532

ABSTRACT

The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.


Subject(s)
DNA-Binding Proteins/chemistry , Transposases/chemistry , Base Sequence , DNA/chemistry , DNA/metabolism , DNA Transposable Elements , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Molecular Docking Simulation , Mutation , Protein Binding , Protein Domains , Transposases/genetics , Transposases/metabolism , Zinc/chemistry , Zinc Fingers
17.
Int J Cancer ; 145(11): 2986-2995, 2019 12 01.
Article in English | MEDLINE | ID: mdl-30977120

ABSTRACT

Primary hepatic neuroendocrine tumors (PHNETs) are extremely rare NETs originating from the liver. These tumors are associated with heterogeneous prognosis, and few treatment targets for PHNETs have been identified. Because the major genetic alterations in PHNET are still largely unknown, we performed whole-exome sequencing of 22 paired tissues from PHNET patients and identified 22 recurring mutations of somatic genes involved in the following activities: epigenetic modification (BPTF, MECP2 and WDR5), cell cycle (TP53, ATM, MED12, DIDO1 and ATAD5) and neural development (UBR4, MEN1, GLUL and GIGYF2). Here, we show that TP53 and the SET domain containing the 1B gene (SETD1B) are the most frequently mutated genes in this set of samples (3/22 subjects, 13.6%). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild-type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates genes including TP53 in the disease. Our findings thus characterize the mutational landscapes of PHNET and implicate novel gene mutations linked to PHNET pathogenesis and potential therapeutic targets.


Subject(s)
Exome Sequencing/methods , Histone-Lysine N-Methyltransferase/genetics , Liver Neoplasms/genetics , Mutation , Neuroendocrine Tumors/genetics , Cell Movement , Cell Proliferation , Female , Genetic Predisposition to Disease , HEK293 Cells , Histone-Lysine N-Methyltransferase/chemistry , Humans , Male , Models, Molecular , Protein Conformation , Tumor Suppressor Protein p53/genetics
18.
Cancer Sci ; 110(4): 1169-1182, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30677195

ABSTRACT

Prior observation has indicated that Frizzled 2 (FZD2)-induced epithelial-mesenchymal transition (EMT) could be a key step in metastasis and early recurrence of hepatocellular carcinoma (HCC). However, the mechanism underlying tumor development and progression due to aberrant FZD2 expression is poorly defined. Here, we provide evidence that FZD2 is a driver for EMT, cancer stem cell properties, and vasculogenic mimicry (VM) in HCC. We found that FZD2 was highly expressed in two cohorts of Chinese hepatitis B virus-related HCC patients, and that high FZD2 expression was associated with poor prognosis. Concerning the mechanism, gain- and loss-of-function experiments showed the oncogenic action of FZD2 in HCC cell proliferation, apoptosis, migration, and invasion. Further investigations in vitro and in vivo suggested that FZD2 promotes the EMT process, enhances stem-like properties, and confers VM capacity to HCC cells. Notably, integrative RNA sequencing analysis of FZD2-knockdown cells indicated the enrichment of Hippo signaling pathway. Taken together, our data suggest for the first time that FZD2 could promote clinically relevant EMT, CD44+ stem-like properties, and the VM phenotype in HCC involving a potential Hippo signaling pathway-dependent mechanism, and should be considered as a promising therapeutic target for the treatment of HCC.


Subject(s)
Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/metabolism , Epithelial-Mesenchymal Transition/genetics , Frizzled Receptors/genetics , Liver Neoplasms/genetics , Liver Neoplasms/metabolism , Neovascularization, Pathologic/genetics , Protein Serine-Threonine Kinases/metabolism , Signal Transduction , Adaptor Proteins, Signal Transducing/metabolism , Adult , Aged , Animals , Carcinoma, Hepatocellular/mortality , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cell Movement/genetics , Cell Survival/genetics , Disease Models, Animal , Disease Progression , Female , Frizzled Receptors/metabolism , Gene Expression Regulation, Neoplastic , Heterografts , Hippo Signaling Pathway , Humans , Liver Neoplasms/pathology , Male , Mice , Middle Aged , Neoplasm Metastasis , Neoplasm Staging , Neoplastic Stem Cells/metabolism , Neovascularization, Pathologic/metabolism , Phosphoproteins/metabolism , Prognosis , Transcription Factors , YAP-Signaling Proteins
19.
BMC Med Genet ; 20(1): 146, 2019 08 27.
Article in English | MEDLINE | ID: mdl-31455269

ABSTRACT

BACKGROUND: Although Mitochondrial DNA depletion syndrome (MDS) can be classified into three forms: myopathic, encephalomyopathic and hepatocerebral form, it is difficult to identify its form due to its clinical heterogeneity. Therefore, it is very important to conduct molecular genetic analysis on suspected patients. This study presented a male 38 weeks and 5 days infant with liver cytolysis and leukodystrophy. CASE PRESENTATION: A male infant proband was admitted to the department of NICU for feeding intolerance, irregular rhythm of respiration, hypoglycemia, lactic acidosis, liver cytolysis and neurological abnormalities. He was onset of mild jaundice with leukodystrophy and high lactate and phenylderivatives for urine organic acids on the 7th day. Whole exome sequencing (WES) and Sanger sequencing were performed to screen and confirm the suspicious pathogenic mutations. The results revealed this proband carried two compound heterozygous mutations in TWNK: c.1186 C > T / p.Pro396Ser and c.1844 G > C / p.Gly615Ala inherited by an autosomal recessive form from his parents, of which protein conservative analysis and structural modeling supported the pathogenicity of the two mutations. Unfortunately, the conditions described above were not improved until he was discharged from the hospital on the 23rd day and died at 4 months of age. CONCLUSIONS: In this study, we investigated a Chinese family with the hepatocerebral form of MDS and conducted WES and Sanger sequencing to explore the causative mutations for this proband born from non-consanguineous and healthy parents. We identified two novel TWNK c.1186 C > T/ c.1844 G > C compound heterozygous mutations which were probably the disease-causing mutations of hepatocerebral form of MDS and described the clinical manifestations of the proband, which expanded the phenotypic spectrum of MDS caused by variants in TWNK. This study also emphasized WES technology can provide the genetic diagnosis of Mendelian genetic disease.


Subject(s)
DNA Helicases/genetics , DNA, Mitochondrial/genetics , Exome Sequencing , Heterozygote , Intestinal Pseudo-Obstruction/genetics , Mitochondrial Proteins/genetics , Muscular Dystrophy, Oculopharyngeal/genetics , Mutation , Asian People , Base Sequence , Genetic Predisposition to Disease/genetics , Humans , Infant , Male , Models, Molecular , Ophthalmoplegia/congenital , Pedigree , Sequence Analysis, Protein
20.
Mycopathologia ; 184(5): 597-605, 2019 Oct.
Article in English | MEDLINE | ID: mdl-31376042

ABSTRACT

Foot hyperkeratosis is common. They often coincide with fungal infections, are difficult to cure and relapse rates are high. In this case study, longstanding and intractable plantar hyperkeratotic lesions were investigated for potential causative agents by histological examinations, by using human cell culture medium to grow the infected skin tissue, by sequencing ribosomal DNA and whole genome. Aspergillus sydowii was identified as the pathogen in the hyperkeratotic lesions. A peculiars intracellular infection of the fungus appeared to merge with anucleated epithelial cells of the skin, in which not fungal cells but basophilic nucleus-like bodies and abundant fungal proteins were seen in the cells. The composite fungal-human zombie-like cells were found to grow in the culture and in hyperkeratotic lesions, and some were readily transformed to natural fungus. Such zombie cells might play roles in the pathogenesis and recurrences of plantar hyperkeratotic lesions, resistance to antifungal drugs and relapses of the fungal infections.


Subject(s)
Aspergillus/isolation & purification , Keratinocytes/microbiology , Keratinocytes/pathology , Keratoderma, Palmoplantar/microbiology , Keratoderma, Palmoplantar/pathology , Aspergillus/classification , Aspergillus/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Humans , Male , Middle Aged , Sequence Analysis, DNA , Whole Genome Sequencing
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