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1.  Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions 
A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.
The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.
PMCID: PMC4304694  PMID: 25615868
model building; refinement;  electron cryo-microscopy reconstructions; LIBG
2.  Genome-Wide Identification and Expression Profile Analysis of Citrus Sucrose Synthase Genes: Investigation of Possible Roles in the Regulation of Sugar Accumulation 
PLoS ONE  2014;9(11):e113623.
Sucrose synthase (Sus) (EC is a key enzyme for the sugar accumulation that is critical to form fruit quality. In this study, extensive data-mining and PCR amplification confirmed that there are at least six Sus genes (CitSus1-6) in the citrus genome. Gene structure and phylogeny analysis showed an evolutionary consistency with other plant species. The six Sus genes contain 12–15 exons and 11–14 introns and were evenly distributed into the three plant Sus groups (CitSus1 and CitSus2 in the Sus I group, CitSus3 and CitSus6 in the Sus II group, and CitSus4 and CitSus5 in the Sus III group). Transcripts of these six CitSus genes were subsequently examined. For tissues and organs, CitSus1 and 2 were predominantly expressed in fruit juice sacs (JS) whereas CitSus3 and 4 were predominantly expressed in early leaves (immature leaves), and CitSus5 and 6 were predominantly expressed in fruit JS and in mature leaves. During fruit development, CitSus5 transcript increased significantly and CitSus6 transcript decreased significantly in fruit JS. In the fruit segment membrane (SM), the transcript levels of CitSus2 and 5 were markedly higher and the abundant levels of CitSus3 and 6 gradually decreased. Moreover, transcript levels of CitSus1-4 examined were higher and the CitSus5 transcript level was lower in the fruit SM than in fruit JS, while CitSus6 had a similar transcript level in fruit JS and SM. In addition, transcripts of CitSus1-6 responded differently to dehydration in mature leaves or to mild drought stress in fruit JS and SM. Finally, the possible roles of Sus genes in the regulation of sugar accumulation are discussed; however, further study is required.
PMCID: PMC4242728  PMID: 25420091
3.  Modification of a single-molecule AFM probe with highly defined surface functionality 
Single-molecule force spectroscopy with an atomic force microscope has been widely used to study inter- and intramolecular interactions. To obtain data consistent with single molecular events, a well-defined method is critical to limit the number of molecules at the apex of an AFM probe to one or to a few. In this paper, we demonstrate an easy method for single-molecule probe modification by using the Cu-catalyzed alkyne–azide cycloaddition reaction. Excess terminal alkynes were covalently attached to the probe, and a bi-functional molecule containing an azide at one end and a carboxylic acid at the other was dissolved in the reaction solution. By simply contacting the probe and the Cu substrate, controlled carboxylation on the probe apex could be achieved, since the ‘click’ reaction requires the co-exist of alkyne, azide and Cu(I). The finite contact area would result in a highly defined surface functionality of the probe down to single molecule level with high reproducibility.
PMCID: PMC4273215  PMID: 25551040
atomic force microscopy; click reaction; force spectroscopy; single molecule modification
4.  Facile electrochemical synthesis of antimicrobial TiO2 nanotube arrays 
Infection-related complications have been a critical issue for the application of titanium orthopedic implants. The use of Ag nanoparticles offers a potential approach to incorporate antimicrobial properties into the titanium implants. In this work, a novel and simple method was developed for synthesis of Ag (II) oxide deposited TiO2 nanotubes (TiNTs) using electrochemical anodization followed by Ag electroplating processes in the same electrolyte. The quantities of AgO nanoparticles deposited in TiNT were controlled by selecting different electroplating times and voltages. It was shown that AgO nanoparticles were crystalline and distributed throughout the length of the nanotubes. Inductively coupled plasma mass spectrometry tests showed that the quantities of released Ag were less than 7 mg/L after 30 days at 37°C. Antimicrobial assay results show that the AgO-deposited TiNTs can effectively kill the Escherichia coli bacteria. Although the AgO-deposited TiNTs showed some cytotoxicity, it should be controllable by optimization of the electroplating parameters and incorporation of cell growth factor. The results of this study indicated that antimicrobial properties could be added to nanotextured medical implants through a simple and cost effective method.
PMCID: PMC4243507  PMID: 25429214
TiO2 nanotube arrays; anodization; AgO nanoparticles; antimicrobial; cytotoxicity
5.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit 
Science (New York, N.Y.)  2014;343(6178):1485-1489.
Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle electron cryo-microscopy. The resolution of 3.2 Ångstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site and a putative membrane docking site.
PMCID: PMC4046073  PMID: 24675956
6.  Application of piezoelectric nanogenerator in medicine: bio-experiment and theoretical exploration 
Journal of Thoracic Disease  2014;6(9):1300-1306.
A large number of wearable and implantable electronic medical devices are widely used in clinic and playing an increasingly important role in diagnosis and treatment, but the limited battery capacity restricts their service life and function expansion. Piezoelectric nanogenerators can convert mechanical energy into electrical energy. Our experiment tries to find out if the piezoelectric nanogenerator fixed to the surface of the heart can convert the natural contractions and relaxations of the heart into stable electric energy for electronic medical devices such as pacemakers.
We used Chinese miniature pig and prepared with standard open chest procedure. Then we fixed two opposite edges of the rectangular nanogenerator at the following three positions of the heart respectively to detect the electric voltage output: Position A, right ventricular surface, near the atrioventricular groove, parallel to the long axis of the heart; Position B, right ventricular surface, parallel to the atrioventricular groove; and Position C, left ventricular surface, near cardiac apex, parallel to the left anterior descending branch. Then we selected the place which has the highest voltage output to fix both ends of the nanogenerator and closed the chest of pig. We recorded the voltage output of nanogenerator under closed chest condition (natural condition) and compared the result with open chest condition. Finally we used Dopamine (positive inotropic agents) and Esmolol (negative inotropic agents) respectively to detect the relation between voltage output of nanogenerator and myocardial contractility.
With its both ends fixed on the surface of the heart, the piezoelectric nanogenerator produced stable voltage output from the mechanical contractions of the heart. Piezoelectric nanogenerator which was fixed at Position A produced the highest voltage output (3.1 V), compared with those fixed at Position B or Position C. The voltage is enough for the pacemaker’s operation. The voltage output of piezoelectric nanogenerator at the natural condition (closed chest) was the same as the open chest condition and made a light emitting diode (LED) light continue to shine, which further confirmed its clinical application value. The voltage output of piezoelectric nanogenerator is positively correlated with the myocardial contractile force. The voltage output increased after we used positive inotropic agents and decreased after we used negative inotropic agents.
Piezoelectric nanogenerators can convert the kinetic energy of the heart during the contractions and relaxations of the muscles to electric energy. The output voltage was stable in three positions on the surface of the heart. The highest voltage appeared on the surface of right ventricle, near atrioventricular groove, parallel to the long axis direction of the heart, which can be the potential new energy source for pacemakers. Piezoelectric nanogenerator can be used as cardiac function monitor in the future for its voltage output is positively correlated with myocardial contractile force.
PMCID: PMC4178096  PMID: 25276373
Implantable medical electronic device; wearable medical electronic device; piezoelectric nanogenerator; body mechanical energy; biomechanical energy harvester; new power source
7.  Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients 
AIM: To screen lymph nodes metastasis associated long noncoding RNAs (lncRNAs) in colorectal cancer through microarray analysis.
METHODS: Metastatic lymph node (MLN), normal lymph node (NLN) and tumor tissues of 3 colorectal cancer (CRC) patients were collected during the operation and validated by pathological examinations. RNAs were extracted from MLN, NLN, and cancer tissues separately. RNA quantity and quality were measured with a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by standard denaturing agarose electrophoresis. Agilent Feature Extraction Software (Version was used to analyze acquired array images. Four differently expressed lncRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) in 26 subsets of MLN, NLN, and tumor tissues.
RESULTS: Of 33045 lncRNAs, 1133 were differentially expressed in MLN compared with NLN, of which 260 were up-regulated and 873 down-regulated (≥ 2 fold-change). Five hundred and forty-five lncRNAs were differentially expressed in MLN compared with tumor tissues, of which 460 were up-regulated and 85 down-regulated (≥ 2 fold-change). Compared with NLN and cancer tissues, 14 lncRNAs were specifically up-regulated and 5 specifically down-regulated in MLN. AK307796, ENST00000425785, and AK021444 were confirmed to be specifically up-regulated in MLN and ENST00000465846 specifically down-regulated in MLN by qRT-PCR in 26 CRC patients.
CONCLUSION: The specifically expressed lncRNAs in MLN may exert a partial or key role in the progress of lymph nodes metastasis of CRC.
PMCID: PMC4081685  PMID: 25009386
Long noncoding RNAs; Colorectal cancer; Lymph nodes metastasis; Quantitative real-time polymerase chain reaction; MicroRNA
8.  The PDB_REDO server for macromolecular structure model optimization 
IUCrJ  2014;1(Pt 4):213-220.
The PDB_REDO pipeline aims to improve macromolecular structures by optimizing the crystallographic refinement parameters and performing partial model building. Here, algorithms are presented that allowed a web-server implementation of PDB_REDO, and the first user results are discussed.
The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive validation’, aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo­graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.
PMCID: PMC4107921  PMID: 25075342
PDB_REDO; validation; model optimization
9.  Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200 
Genome Announcements  2014;2(2):e00096-14.
Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantially varied lifestyles, including free-living, commensal, pathogenic, symbiotic, and piezophilic. Here, we present the genome sequence of a luminous, piezophilic Photobacterium phosphoreum strain, ANT-2200, isolated from a water column at 2,200 m depth in the Mediterranean Sea. It is the first genomic sequence of the P. phosphoreum group. An analysis of the sequence provides insight into the adaptation of bacteria to the deep-sea habitat.
PMCID: PMC3990738  PMID: 24744322
10.  Premature Graying as a Consequence of Compromised Antioxidant Activity in Hair Bulb Melanocytes and Their Precursors 
PLoS ONE  2014;9(4):e93589.
Intricate coordinated mechanisms that govern the synchrony of hair growth and melanin synthesis remain largely unclear. These two events can be uncoupled in prematurely gray hair, probably due to oxidative insults that lead to the death of oxidative stress-sensitive melanocytes. In this study, we examined the gene expression profiles of middle (bulge) and lower (hair bulb) segments that had been micro-dissected from unpigmented and from normally pigmented hair follicles from the same donors using quantitative real-time RT-PCR (qPCR) arrays. We found a significant down-regulation of melanogenesis-related genes (TYR, TYRP1, MITF, PAX3, POMC) in unpigmented hair bulbs and of marker genes typical for melanocyte precursor cells (PAX3, SOX10, DCT) in unpigmented mid-segments compared with their pigmented analogues. qPCR, western blotting and spin trapping assays revealed that catalase protein expression and hydroxyl radical scavenging activities are strongly repressed in unpigmented hair follicles. These data provide the first clear evidence that compromised antioxidant activity in gray hair follicles simultaneously affects mature hair bulb melanocytes and their immature precursor cells in the bulge region.
PMCID: PMC3973559  PMID: 24695442
11.  Double-bundle anatomical versus single-bundle isometric medial patellofemoral ligament reconstruction for patellar dislocation 
International Orthopaedics  2013;37(4):617-624.
The purpose of this study was to evaluate reconstruction of the medial patellofemoral ligament (MPFL) using the double-bundle anatomical or single-bundle isometric procedure with respect to the patients’ clinical outcomes.
In this retrospective study, we evaluated the clinical outcome of double-bundle anatomical versus single-bundle isometric reconstruction of the MPFL for patellar dislocation patients. Sixty-three patients were included in this study from August 2004 to January 2008. From August 2004 to September 2006, MPFL reconstruction using a single-bundle isometric technique was performed in 21 patients (26 knees). Since October 2006, the double-bundle anatomical reconstruction of the MPFL has been used as the routine surgical procedure. It was performed in 37 patients (44 knees). Fifty-eight patients (70 knees) could be followed up. According to the different techniques, we divided the patients into two groups: group D with double-bundle anatomical reconstruction (37 patients) and group S with single-bundle isometric reconstruction (21 patients). Clinical evaluation consisted of the number with a patellar re-dislocation, patellar apprehension sign, Kujala score, subjective questionnaire score, the patella lateral shift rate and patellar tilt angle measured by cross-sectional CT scan.
According to the Kujala score and the subjective questionnaire score, the outcome of the double-bundle group was better than the outcome of the single-bundle group especially in the long-term. Patellar re-dislocation occurred in three patients in the group S, while no re-dislocation occurred in the group D. In total, 26.9 % of group S was considered to have patellar instability, compared to 4.54 % of the group D. After operation, the patellar tilt angle (PTA) and the patella lateral shift rate (PLSR) were restored to the normal range, with statistical significance (P < 0.05) compared to the preoperative state.
Single- and double-bundle reconstruction of the MPFL can both effectively restore patella stability and improve knee function. However, outcomes in the follow-up period showed that the double-bundle surgery procedure was much better than in single-bundle surgery.
PMCID: PMC3609965  PMID: 23371425
12.  (2-Chloro­pyrimidin-4-yl)ferrocene 
In the title compound, [Fe(C5H5)(C9H6ClN2)], the two cyclo­penta­dienyl rings are almost parallel, subtending a dihedral angle of 3.01 (5)°. The dihedral angle between the substituted cyclo­penta­dienyl ring and the pyrimidinyl ring is 12.02 (1)°. The conformation of the two cyclopentadienyl rings in the ferrocenyl moiety is eclipsed.
PMCID: PMC3998571  PMID: 24826094
13.  Colonization and plant growth promoting characterization of endophytic Pseudomonas chlororaphis strain Zong1 isolated from Sophora alopecuroides root nodules 
Brazilian Journal of Microbiology  2013;44(2):623-631.
The endophytic strain Zong1 isolated from root nodules of the legume Sophora alopecuroides was characterized by conducting physiological and biochemical tests employing gfp-marking, observing their plant growth promoting characteristics (PGPC) and detecting plant growth parameters of inoculation assays under greenhouse conditions. Results showed that strain Zong1 had an effective growth at 28 ºC after placed at 4–60 ºC for 15 min, had a wide range pH tolerance of 6.0–11.0 and salt tolerance up to 5% of NaCl. Zong1 was resistant to the following antibiotics (μg/mL): Phosphonomycin (100), Penicillin (100) and Ampicillin (100). It could grow in the medium supplemented with 1.2 mmol/L Cu, 0.1% (w/v) methylene blue and 0.1–0.2% (w/v) methyl red, respectively. Zong1 is closely related to Pseudomonas chlororaphis based on analysis the sequence of 16S rRNA gene. Its expression of the gfp gene indicated that strain Zong1 may colonize in root or root nodules and verified by microscopic observation. Furthermore, co-inoculation with Zong1 and SQ1 (Mesorhizobium sp.) showed significant effects compared to single inoculation for the following PGPC parameters: siderophore production, phosphate solubilization, organic acid production, IAA production and antifungal activity in vitro. These results suggest strains P. chlororaphi Zong1 and Mesorhizobium sp. SQ1 have better synergistic or addictive effect. It was noteworthy that each growth index of co-inoculated Zong1+SQ1 in growth assays under greenhouse conditions is higher than those of single inoculation, and showed a significant difference (p < 0.05) when compared to a negative control. Therefore, as an endophyte P. chlororaphis Zong1 may play important roles as a potential plant-growth promoting agent.
PMCID: PMC3833168  PMID: 24294262
PGPC; endophyte; the gpf-marker; colonization; co-inoculation
14.  Novel Rod-Shaped Magnetotactic Bacteria Belonging to the Class Alphaproteobacteria 
Novel large, rod-shaped magnetotactic bacteria (MTB) were discovered in intertidal sediments of the Yellow Sea, China. They biomineralized more than 300 rectangular magnetite magnetosomes per cell. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that they are affiliated with the Alphaproteobacteria and may represent a new genus of MTB.
PMCID: PMC3623124  PMID: 23455351
15.  Valproic acid increases white matter repair and neurogenesis after stroke 
Neuroscience  2012;220:313-321.
Acute treatment of stroke with HDAC inhibitors has been shown to reduce ischemic cell damage; however, it is unclear whether delayed treatment with HDAC inhibitors will contribute to the brain repair and plasticity. In the present study, we investigated the effects of delayed treatment of stroke with a pan HDAC inhibitor, valproic acid (VPA), on white matter injury and neurogenesis during stroke recovery. Administration of VPA at a dose of 100 mg/kg for 7 days starting 24 hours after middle cerebral artery occlusion (MCAo) in rats significantly improved neurological outcome measured 7 to 28 days post-MCAo. In addition, the VPA treatment significantly increased oligodendrocyte survival and newly generated oligodendrocytes, which was associated with elevation of myelinated axonal density in the ischemic boundary 28 days after MCAo. VPA treatment also increased the expression of glutamate transporter 1 (GLT1) in the ischemic boundary after stroke, and increased acetylated histone H4 expression in neuroblasts and the number of new neurons in striatal ischemic boundary region. This study provides new evidence that the delayed VPA treatment enhances white matter repair and neurogenesis in ischemic brain, which may contribute to improved functional outcome.
PMCID: PMC3412884  PMID: 22704966
Valproic acid; oligodendrocyte; axon; neural progenitor cells; subventricular zone (SVZ); stroke
16.  A Potential Relationship among Beta-Defensins Haplotype, SOX7 Duplication and Cardiac Defects 
PLoS ONE  2013;8(8):e72515.
To determine the pathogenesis of a patient born with congenital heart defects, who had appeared normal in prenatal screening.
In routine prenatal screening, G-banding was performed to analyse the karyotypes of the family and fluorescence in situ hybridization was used to investigate the 22q11.2 deletion in the fetus. After birth, the child was found to be suffering from heart defects by transthoracic echocardiography. In the following study, sequencing was used to search for potential mutations in pivotal genes. SNP-array was employed for fine mapping of the aberrant region and quantitative real-time PCR was used to confirm the results. Furthermore, other patients with a similar phenotype were screened for the same genetic variations. To compare with a control, these variations were also assessed in the general population.
The child and his mother each had a region that was deleted in the beta-defensin repeats, which are usually duplicated in the general population. Besides, the child carried a SOX7-gene duplication. While this duplication was not detected in his mother, it was found in two other patients with cardiac defects who also had the similar deletion in the beta-defensin repeats.
The congenital heart defects of the child were probably caused by a SOX7-gene duplication, which may be a consequence of the partial haplotype of beta-defensin regions at 8p23.1. To our knowledge, this is the first congenital heart defect case found to have the haplotype of beta-defensin and the duplication of SOX7.
PMCID: PMC3757027  PMID: 24009689
17.  An O Island 172 Encoded RNA Helicase Regulates the Motility of Escherichia coli O157:H7 
PLoS ONE  2013;8(6):e64211.
Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is a major cause of zoonotic food- and water-borne intestinal infections worldwide with clinical consequences ranging from mild diarrhoea to hemolytic uraemic syndrome. The genome of EHEC O157:H7 contains many regions of unique DNA that are referred to as O islands including the Shiga toxin prophages and pathogenicity islands encoding key virulence factors. However many of these O islands are of unknown function. In this study, genetic analysis was conducted on OI-172 which is a 44,434 bp genomic island with 27 open reading frames. Comparative genome analysis showed that O1-72 is a composite island with progressive gain of genes since O157:H7 evolved from its ancestral O55:H7. A partial OI-172 island was also found in 2 unrelated E. coli strains and 2 Salmonella strains. OI-172 encodes several putative helicases, one of which (Z5898) is a putative DEAH box RNA helicase. To investigate the function of Z5898, a deletion mutant (EDL933ΔZ5898) was constructed in the O157:H7 strain EDL933. Comparative proteomic analysis of the mutant with the wild-type EDL933 found that flagellin was down-regulated in the Z5898 mutant. Motility assay showed that EDL933ΔZ5898 migrated slower than the wild-type EDL933 and electron microscopy found no surface flagella. Quantitative reverse transcription PCR revealed that the fliC expression of EDL933ΔZ5898 was significantly lower while the expression of its upstream regulator gene, fliA, was not affected. Using a fliA and a fliC promoter – green fluorescent protein fusion contruct, Z5898 was found to affect only the fliC promoter activity. Therefore, Z5898 regulates the flagella based motility by exerting its effect on fliC. We conclude that OI-172 is a motility associated O island and hereby name it the MAO island.
PMCID: PMC3681947  PMID: 23785398
18.  Digital Gene Expression Analysis of Corky Split Vein Caused by Boron Deficiency in ‘Newhall’ Navel Orange (Citrus sinensis Osbeck) for Selecting Differentially Expressed Genes Related to Vascular Hypertrophy 
PLoS ONE  2013;8(6):e65737.
Corky split vein caused by boron (B) deficiency in ‘Newhall’ Navel Orange was studied in the present research. The boron-deficient citrus exhibited a symptom of corky split vein in mature leaves. Morphologic and anatomical surveys at four representative phases of corky split veins showed that the symptom was the result of vascular hypertrophy. Digital gene expression (DGE) analysis was performed based on the Illumina HiSeq™ 2000 platform, which was applied to analyze the gene expression profilings of corky split veins at four morphologic phases. Over 5.3 million clean reads per library were successfully mapped to the reference database and more than 22897 mapped genes per library were simultaneously obtained. Analysis of the differentially expressed genes (DEGs) revealed that the expressions of genes associated with cytokinin signal transduction, cell division, vascular development, lignin biosynthesis and photosynthesis in corky split veins were all affected. The expressions of WOL and ARR12 involved in the cytokinin signal transduction pathway were up-regulated at 1st phase of corky split vein development. Furthermore, the expressions of some cell cycle genes, CYCs and CDKB, and vascular development genes, WOX4 and VND7, were up-regulated at the following 2nd and 3rd phases. These findings indicated that the cytokinin signal transduction pathway may play a role in initiating symptom observed in our study.
PMCID: PMC3673917  PMID: 23755275
19.  Two Genera of Magnetococci with Bean-like Morphology from Intertidal Sediments of the Yellow Sea, China 
Applied and Environmental Microbiology  2012;78(16):5606-5611.
Magnetotactic bacteria have the unique capacity of being able to swim along geomagnetic field lines. They are Gram-negative bacteria with diverse morphologies and variable phylogenetic relatedness. Here, we describe a group of uncultivated marine magnetococci collected from intertidal sediments of Huiquan Bay in the Yellow Sea. They were coccoid-ovoid in morphology, with an average size of 2.8 ± 0.3 μm by 2.0 ± 0.2 μm. Differential interference contrast microscopy, fluorescence microscopy, and transmission electron microscopy revealed that each cell was apparently composed of two hemispheres. The cells synthesized iron oxide-type magnetosomes that clustered on one side of the cell at the interface between the two hemispheres. In some cells two chains of magnetosomes were observed across the interface. Each cell had two bundles of flagella enveloped in a sheath and displayed north-seeking helical motion. Two 16S rRNA gene sequences having 91.8% identity were obtained, and their authenticity was confirmed by fluorescence in situ hybridization. Phylogenetic analysis revealed that the magnetococci are affiliated with the Alphaproteobacteria and are most closely related to two uncultured magnetococci with sequence identities of 92.7% and 92.4%, respectively. Because they display a >7% sequence divergence to all bacteria reported, the bean-like magnetococci may represent two novel genera.
PMCID: PMC3406164  PMID: 22660708
20.  Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17, Which Forms Biofilms on Hydrophobic Organic Compounds 
Journal of Bacteriology  2012;194(13):3539-3540.
Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.
PMCID: PMC3434751  PMID: 22689231
21.  Expression and purification of 15N- and 13C-isotope labeled 40-residue human Alzheimer’s β-amyloid peptide for NMR-based structural analysis 
Amyloid fibrils of Alzheimer’s β-amyloid peptide (Aβ) are a primary component of amyloid plaques, a hallmark of Alzheimer’s disease (AD). Enormous attention has been given to the structural features and functions of Aβ in amyloid fibrils and other type of aggregates in associated with development of AD. This report describes an efficient protocol to express and purify high-quality 40-residue Aβ(1–40), the most abundant Aβ in brains, for structural studies by NMR spectroscopy. Over-expression of Aβ(1–40) with glutathione S-transferase (GST) tag connected by a Factor Xa recognition site (IEGR▼) in E. Coli resulted in the formation of insoluble inclusion bodies even with the soluble GST tag. This problem was resolved by efficient recovery of the GST-Aβ fusion protein from the inclusion bodies using 0.5% (w/v) sodium lauroyl sarcosinate as solubilizing agent and subsequent purification by affinity chromatography using a glutathione agarose column. The removal of the GST tag by Factor Xa enzymatic cleavage and purification by HPLC yielded as much as ~7 mg and ~1.5 mg of unlabeled Aβ(1–40) and uniformly 15N- and/or 13C-protein Aβ(1–40) from 1 L of the cell culture, respectively. Mass spectroscopy of unlabeled and labeled Aβ and 1H/15N HSQC solution NMR spectrum of the obtained 15N-labeled Aβ in the monomeric form confirmed the expression of native Aβ(1–40). It was also confirmed by electron micrography and solid-state NMR analysis that the purified Aβ(1–40) self-assembles into β-sheet rich amyloid fibrils. To the best of our knowledge, our protocol offers the highest yields among published protocols for production of recombinant Aβ(1–40) samples that are amendable for an NMR-based structural analysis. The protocol may be applied to efficient preparation of other amyloid-forming proteins and peptides that are 13C- and 15N-labeled for NMR experiments.
PMCID: PMC3134129  PMID: 21640828
Amyloid β; GST fusion protein; sodium lauroyl sarcosinate; NMR
22.  Recurrence of inflammatory myofibroblastic tumor in bladder secondary to prostate treated with laparoscopic radical cystectomy 
Inflammatory myofibroblastic tumor (IMT) is a rare borderline tumor. The nomenclature of this disease is confused in the literature.
Case Report
In this report, the case of a 62-year-old man with IMT recurrence of bladder secondary to prostate is presented. The possible etiology of IMT is discussed, along with its clinical manifestation and pathological features. The patient received a laparoscopic bladder radical resection. The pathology finding demonstrated the diagnosis of IMT and no regional lymph node involvement.
IMT is a borderline tumor and unlikely to metastasize to regional lymph nodes. The patient has been observed for 2 years without recurrence.
PMCID: PMC3560699  PMID: 22847204
inflammatory myofibroblastic tumor; bladder; prostate
23.  Papillae alterations around single-implant restorations in the anterior maxillae: thick versus thin mucosa 
To evaluate the papilla alterations around single-implant restorations in the anterior maxillae after crown attachment and to study the influence of soft tissue thickness on the papilla fill alteration. According to the inclusion criteria, 32 patients subjected to implant-supported single-tooth restorations in anterior maxillae were included. The patients were assigned to two groups according to the mucosal thickness: (i) group 1, 1.5 mm≤mucosal thickness≤3 mm; and (ii) group 2, 3 mm
PMCID: PMC3412666  PMID: 22627613
esthetic outcome; papilla fill index; single-implant restoration; soft tissue thickness
Cu2+ binding to Alzheimer’s β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimer’s senile plaque and such association of Aβ with Cu2+ triggers the production of neurotoxic reactive oxygen species (ROS) such as H2O2. However, detailed binding sites and binding structures of Cu2+ to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu2+ binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution 13C SSNMR for full-length 40-residue Aβ(1–40). Selective quenching observed in 13C SSNMR of Cu2+-bound Aβ(1–40) suggested that primary Cu2+ binding sites in Aβ(1–40) fibrils include Nε in His-13 and His-14, and carboxyl groups in Val-40 as well as in Glu side chains (Glu-3, Glu-11, and/or Glu-22). 13C chemical shift analysis demonstrated no major structural changes upon Cu2+ binding in the hydrophobic core regions (residues 18–25 and 30–36). Although the ROS production via oxidization of Met-35 in the presence of Cu2+ has been long suspected, our SSNMR analysis of 13CεH3-S- in M35 showed little changes after Cu2+ binding, excluding the possibility of Met-35 oxidization by Cu2+ alone. Preliminary molecular dynamics (MD) simulations on Cu2+-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu2+-binding modes unique in Aβ fibril, which are realized by both intra- and inter-molecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.
PMCID: PMC3074258  PMID: 21341665
Low-resolution refinement tools implemented in REFMAC5 are described, including the use of external structural restraints, helical restraints and regularized anisotropic map sharpening.
Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.
PMCID: PMC3322599  PMID: 22505260
low-resolution refinement; REFMAC5

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