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1.  Effects of azithromycin on Pseudomonas aeruginosa isolates from catheter-associated urinary tract infection 
Pseudomonas aeruginosa is a common pathogenic bacterium in urinary tract infections (UTIs), particularly catheter-associated UTIs. The aim of this study was to investigate the effect of azithromycin (AZM) on P. aeruginosa isolated from UTIs. Isolates were identified by biochemical assays and the Vitek system. Antimicrobial susceptibility was determined using the disk diffusion assay. Biofilm formation and adhesion were assayed using a crystal violet staining method. The swimming motility was assayed on agar plates. The elastase activity and rhamnolipid production were determined by the elastin-Congo red method and orcinol reaction, respectively. A total of 32 bacterial isolates were collected from 159 urinary catheters and eight of them were P. aeruginosa isolates. The results showed that the P. aeruginosa isolates had stronger biofilm formation capability and the biofilms were thicker than those of P. aeruginosa PAO1. AZM inhibited biofilm formation and adhesion on urinary catheters, and also decreased swimming motility and the production of virulence factors. The results of this study indicated that AZM is potentially a good choice for use in the treatment of UTIs.
PMCID: PMC4280936  PMID: 25574236
Pseudomonas aeruginosa; azithromycin; urinary tract infection; biofilm; swimming; virulence factor
2.  Characterization of Nestin-positive stem Leydig cells as a potential source for the treatment of testicular Leydig cell dysfunction 
Cell Research  2014;24(12):1466-1485.
The ability to identify and isolate lineage-specific stem cells from adult tissues could facilitate cell replacement therapy. Leydig cells (LCs) are the primary source of androgen in the mammalian testis, and the prospective identification of stem Leydig cells (SLCs) may offer new opportunities for treating testosterone deficiency. Here, in a transgenic mouse model expressing GFP driven by the Nestin (Nes) promoter, we observed Nes-GFP+ cells located in the testicular interstitial compartment where SLCs normally reside. We showed that these Nes-GFP+ cells expressed LIFR and PDGFR-α, but not LC lineage markers. We further observed that these cells were capable of clonogenic self-renewal and extensive proliferation in vitro and could differentiate into neural or mesenchymal cell lineages, as well as LCs, with the ability to produce testosterone, under defined conditions. Moreover, when transplanted into the testes of LC-disrupted or aging models, the Nes-GFP+ cells colonized the interstitium and partially increased testosterone production, and then accelerated meiotic and post-meiotic germ cell recovery. In addition, we further demonstrated that CD51 might be a putative cell surface marker for SLCs, similar with Nestin. Taken together, these results suggest that Nes-GFP+ cells from the testis have the characteristics of SLCs, and our study would shed new light on developing stem cell replacement therapy for testosterone deficiency.
PMCID: PMC4260348  PMID: 25418539
stem Leydig cell; Nestin; self-renewal; multipotency; Leydig cell dysfunction
3.  Compliance with severe sepsis bundles and its effect on patient outcomes of severe community-acquired pneumonia in a limited resources country 
Archives of Medical Science : AMS  2014;10(5):970-978.
Validation of compliance with severe sepsis bundles is still needed. The purpose of this study was to determine compliance and its outcomes in severe community-acquired pneumonia (CAP) patients in a limited resources country.
Material and methods
A prospective cohort study of 212 severe CAP patients was carried out. The implementation programme was organized into two continuous phases. The primary outcomes were compliance and hospital mortality.
Compliance with administration of antibiotics and vasopressors as well as plateau pressure on average < 30 cm H2O was high in both groups. In the bundles group, patients received more serum lactate monitoring (62.3% vs. 11.3%), more blood cultures (47.1% vs. 24.5%), more fluid resuscitation (63.2% vs. 26.4%) and volumes infused (1319.8 ±1107.4 ml vs. 461.9 ±799.3 ml), more inotropic dobutamine and/or packed red blood cells (21.7% vs. 10.0%), more low-dose steroids (56.5% vs. 15.0%), and more glucose control (51.9% vs. 6.6%) compared with such patients in the control group. The rates of total compliance with 6-hour, 24-hour, and 6/24-hour bundles in the prospective period were 47.1%, 51.9%, and 42.5%, respectively. Hospital mortality was reduced from 44.3% to 29.2% (p = 0.023) in the bundles group, and the compliant subgroup had a more than twofold decrease in mortality (17.8% vs. 37.7%, p = 0.003). Serum lactate measured, blood cultures, and fluid resuscitation showed independent relationships with decreased mortality.
Total compliance was relatively low, but the implementation of severe sepsis bundles could clearly reduce mortality from severe CAP.
PMCID: PMC4223141  PMID: 25395949
severe sepsis bundles; severe community-acquired pneumonia; severe sepsis; septic shock; compliance; mortality
4.  Construction and management of ARDS/sepsis registry with REDCap 
Journal of Thoracic Disease  2014;6(9):1293-1299.
The study aimed to construct and manage an acute respiratory distress syndrome (ARDS)/sepsis registry that can be used for data warehousing and clinical research.
The workflow methodology and software solution of research electronic data capture (REDCap) was used to construct the ARDS/sepsis registry. Clinical data from ARDS and sepsis patients registered to the intensive care unit (ICU) of our hospital formed the registry. These data were converted to the electronic case report form (eCRF) format used in REDCap by trained medical staff. Data validation, quality control, and database management were conducted to ensure data integrity.
The clinical data of 67 patients registered to the ICU between June 2013 and December 2013 were analyzed. Of the 67 patients, 45 (67.2%) were classified as sepsis, 14 (20.9%) as ARDS, and eight (11.9%) as sepsis-associated ARDS. The patients’ information, comprising demographic characteristics, medical history, clinical interventions, daily assessment, clinical outcome, and follow-up data, was properly managed and safely stored in the ARDS/sepsis registry. Data efficiency was guaranteed by performing data collection and data entry twice weekly and every two weeks, respectively.
The ARDS/sepsis database that we constructed and manage with REDCap in the ICU can provide a solid foundation for translational research on the clinical data of interest, and a model for development of other medical registries in the future.
PMCID: PMC4178117  PMID: 25276372
Acute respiratory distress syndrome (ARDS)/sepsis registry; research electronic data capture (REDCap); data quality; data management
5.  Associations of radiological features in Mycoplasma pneumoniae pneumonia 
Archives of Medical Science : AMS  2014;10(4):725-732.
The associations of radiological features with clinical and laboratory findings in Mycoplasma pneumoniae infection are poorly understood. The purpose of this study was to assess the associations.
Material and methods
A retrospective cohort study of 1230 patients with community-acquired pneumonia was carried out between January 2005 and December 2009. The diagnosis of M. pneumoniae infection was made using the indirect microparticle agglutinin assay and enzyme-linked immunosorbent assay.
Females were more susceptible to M. pneumoniae infection. Ground-glass opacification on radiographs was positively associated with M. pneumoniae-IgM titres (rank correlation coefficient (r s) = 0.141, p = 0.006). The left upper lobe was more susceptible to infection with M. pneumoniae compared with other pathogens. More increases in the risk of multilobar opacities were found among older or male patients with M. pneumoniae pneumonia (odds ratio, 1.065, 3.279; 95% confidence interval, 1.041–1.089, 1.812–5.934; p < 0.001, p < 0.001; respectively). Patients with M. pneumoniae pneumonia showing multilobar opacities or consolidation had a significantly longer hospital length of stay (r s = 0.111, r s = 0.275; p = 0.033, p < 0.001; respectively), incurring significantly higher costs (r s = 0.119, r s = 0.200; p = 0.022, p < 0.001; respectively).
Our study highlighted female susceptibility to M. pneumoniae pneumonia and the association of ground-glass opacification with higher M. pneumoniae-IgM titres. The left upper lobe might be more susceptible to M. pneumoniae infection. Older or male patients with M. pneumoniae pneumonia were more likely to show multilobar opacities. Multilobar opacities and consolidation were positively associated with hospital length of stay and costs.
PMCID: PMC4175773  PMID: 25276157
community-acquired pneumonia; Mycoplasma pneumoniae; radiological features; association
6.  The High-Throughput Protein Sample Production Platform of the Northeast Structural Genomics Consortium 
Journal of structural biology  2010;172(1):21-33.
We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (> 97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as > 26,000 constructs. Over the past nine years, more than 16,000 of these expressed protein, and more than 4,400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last five years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities.
PMCID: PMC4110633  PMID: 20688167
Structural Genomics; High throughput protein production; Construct optimization; Disorder prediction; Ligation independent cloning; Multiple Displacement Amplification; Laboratory Information Management System; Protein Structure Initiative; NMR; X-ray crystallography; T7 Escherichia Coli expression system; Wheat Germ Cell Free; NMR microprobe screening; Parallel protein purification; 6X-His tag; HDX-MS
7.  Seroprevalence and evolutionary dynamics of genotype 4 hepatitis E virus in Shandong Province, China 
AIM: To investigate the seroprevalence and evolutionary dynamics of hepatitis E virus (HEV) and assess the ancestor of HEVs in China’s Shandong Province.
METHODS: A total of 2028 serum, 60 fecal and 82 bile samples were collected from the general human population, patients and swine, respectively. This seroepidemiological study was conducted using an immunnosorbent assay and HEV RNA was detected by the reverse transcription-nested polymerase chain reaction (RT-nPCR) method. Complete genome sequences of the prevalent strains (CH-YT-HEV01, CH-YT-HEV02 and CH-YT-sHEV01) were determined, and the sequences were analyzed phylogenetically. In addition, the evolutionary dynamics of three HEV isolates were determined using the framework of coalescent analysis in the program package BEAST, and the time of the most recent common ancestors (TMRCAs) of China-indigenous genotype 4 HEV isolates was calculated.
RESULTS: The overall viral burden in the general human population was 0.1%, and the positive rates of anti-HEV IgG and IgM in the serum specimens were 25.1% (509/2028) and 2.3% (51/2028), respectively. In addition, IgG positivity increased with age. The phylogenetic analysis based on the full-length nucleotide sequences showed that the strain CH-YT-HEV02 was directly related to CH-YT-sHEV01 with a 94% identity, suggesting that they were involved in cross-species transmission. The isolate CH-YT-HEV01 was close to HB-3 and CHN-SD-sHEV with a bootstrap value of 100%, sharing a 96.1%-96.4% identity with each other. Surprisingly, the HB-3 strain was a representative strain prevalent in swine in Hubei, and the isolate CHN-SD-sHEV was obtained from swine in Shandong in a previous report. TMRCA for the clade of CH-YT-HEV01 and HB-3 was 2003, which was consistent with the TMRCA for the clade of CHN-SD-sHEV and HB-3, and they were both earlier than the TMRCA for the clade of CH-YT-HEV01 and CHN-SD-sHEV (2004).
CONCLUSION: The strains CH-YT-HEV01, CHN-SD-sHEV and HB-3 are involved in trans-regional transmission, and the ancestors of HEVs in Shandong come from Hubei Province.
PMCID: PMC4069323  PMID: 24976732
Hepatitis E virus; Zoonotic; Cross-species transmission; Trans-regional transmission; Evolutionary dynamics
8.  The Prevalence of Nonalcoholic Fatty Liver Disease and Relationship with Serum Uric Acid Level in Uyghur Population 
The Scientific World Journal  2014;2014:393628.
Objective. To investigate the prevalence of nonalcoholic fatty liver disease (NAFLD) and the association of serum uric acid level with NAFLD in Uygur people, Xinjiang. Methods. A total of 2241 Uyghur persons (1214 males and 1027 females) were interviewed for physical checkups from 2011 to 2012. The clinical data of questionnaire survey, body mass index (BMI), abdominal circumference, blood pressure, blood sugar, blood lipid, and serum uric acid level were collected for analysis. Results. The prevalence rates of NAFLD determined by abdominal ultrasound examination and hyperuricemia were 43.9% and 8.4%, respectively. The persons with NAFLD had significantly higher serum uric acid levels than those without NAFLD (320 ± 88 versus 254 ± 80 μmol/L; P < 0.001). The prevalence rate of NAFLD was significantly higher in subjects with hyperuricemia than that in those without hyperuricemia (78.19% versus 40.83%; P < 0.001), and the prevalence rate increased with progressively higher serum uric acid levels (P < 0.001). Multiple regression analysis showed that hyperuricemia was associated with an increased risk of NAFLD (odds ratio (OR): 2.628, 95% confidence interval (CI): 1.608–4.294, and P < 0.001). Conclusion. Serum uric acid level was significantly associated with NAFLD, and the prevalence rate of NAFLD increased with progressively higher serum uric acid levels.
PMCID: PMC3910275  PMID: 24516367
9.  Solution NMR Structure of Dsy0195 Homodimer from Desulfitobacterium hafniense: First Structure Representative of the YabP Domain Family of Proteins Involved in Spore Coat Assembly 
Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions used for structure determination using NMR spectroscopy. The structure of the Dsy0195 homodimer contains two identical 62-residue monomeric subunits, each consisting of five anti-parallel beta strands (β1, 23-29; β2, 31-38; β3, 41-46; β4, 49-59; β5, 69-80). The tertiary structure of the Dsy0195 monomer adopts a cylindrical fold composed of two beta sheets. The two monomer subunits fold into a homodimer about a single C2 symmetry axis, with the interface composed of two anti-parallel beta strands, β1-β1’ and β5b-β5b’, where β5b refers to the C-terminal half of the bent β5 strand, without any domain swapping. Potential functional regions of the Dsy0195 structure were predicted based on conserved sequence analysis. The Dsy0195 structure reported here is the first representative structure from the YabP family.
PMCID: PMC3697068  PMID: 21904870
PF07873; YabP; Dsy0195; Sporulation Protein; Structural Genomics; NMR
10.  Severe Fever with Thrombocytopenia Syndrome Virus among Domesticated Animals, China 
Emerging Infectious Diseases  2013;19(5):756-763.
To investigate the infections of severe fever with thrombocytopenia syndrome virus (SFTSV) in domesticated animals, we sampled a total of 3,039 animals in 2 counties in Shandong Province, People’s Republic of China, from April to November 2011. SFTSV-specific antibodies were detected in 328 (69.5%) of 472 sheep, 509 (60.5%) of 842 cattle, 136 (37.9%) of 359 dogs, 26 (3.1%) of 839 pigs, and 250 (47.4%) of 527 chickens. SFTSV RNA was detected in all sampled animal species, but the prevalence was low, ranging from 1.7% to 5.3%. A cohort study in 38 sheep was conducted to determine when seroconversion to SFTSV occured. SFTSVs were isolated from sheep, cattle, and dogs and shared >95% sequence homology with human isolates from the same disease-endemic regions. These findings demonstrate that natural infections of SFTSV occur in several domesticated animal hosts in disease-endemic areas and that the virus has a wide host range.
PMCID: PMC3647489  PMID: 23648209
severe fever with thrombocytopenia syndrome virus; SFTSV; infection; domesticated animals; host; China; Phlebovirus; family Bunyaviridae; pathogenic disease; transmission; viruses; zoonoses; prevalence
11.  Chemistry and Tumor Cell Growth Inhibitory Activity of 11,20-Epoxy-3Z,5(6)E-diene Briaranes from the South China Sea Gorgonian Dichotella gemmacea 
Marine Drugs  2013;11(5):1565-1582.
Eighteen new 11,20-epoxy-3Z,5E-dien briaranes, gemmacolides AA–AR (1–18), were isolated together with three known analogs, dichotellides F (19) and I (20), and juncenolide C (21), from the South China Sea gorgonian Dichotella gemmacea. The structures of the compounds were elucidated by detailed spectroscopic analysis and comparison with reported data. The absolute configuration was determined based on the ECD experiment. In the in vitro bioassay, compounds 1–3, 5, 6, 8–12, and 14–19 exhibited different levels of growth inhibition activity against A549 and MG63 cell lines. Preliminary structure-activity analysis suggests that 12-O-isovalerate may increase the activity whereas 13- or 14-O-isovalerate may decrease the activity. Contribution of substitutions at C-2 and C-16 remains uncertain.
PMCID: PMC3707162  PMID: 23697947
structure activity relationship; briarane diterpenoids; biological activity; Dichotella gemmacea; gorgonian
12.  Downregulation of Cyclophilin A by siRNA diminishes non-small cell lung cancer cell growth and metastasis via the regulation of matrix metallopeptidase 9 
BMC Cancer  2012;12:442.
Cyclophilin A (CypA) is a cytosolic protein possessing peptidyl-prolyl isomerase activity that was recently reported to be overexpressed in several cancers. Here, we explored the biology and molecular mechanism of CypA in non-small cell lung cancer (NSCLC).
The expression of CypA in human NSCLC cell lines was detected by real-time reverse transcription PCR. The RNA interference-mediated knockdown of CypA was established in two NSCLC cell lines (95C and A549). 239836 CypA inhibitor was also used to suppress CypA activity. Tumorigenesis was assessed based on cellular proliferation, colony formation assays, and anchorage-independent growth assays; metastasis was assessed based on wound healing and transwell assays.
Suppression of CypA expression inhibited the cell growth and colony formation of A549 and 95C cells. CypA knockdown resulted in the inhibition of cell motility and invasion. Significantly, we show for the first time that CypA increased NSCLC cell invasion by regulating the activity of secreted matrix metallopeptidase 9 (MMP9). Likewise, suppression of CypA with 239836 CypA inhibitor decreased cell proliferation and MMP9 activity.
The suppression of CypA expression was correlated with decreased NSCLC cell tumorigenesis and metastasis.
PMCID: PMC3518206  PMID: 23031673
Cyclophilin A; Non-small cell lung cancer; Proliferation; Metastasis; Matrix metallopeptidase 9
13.  MicroRNAs as potential therapeutics for treating spinal cord injury 
Neural Regeneration Research  2012;7(17):1352-1359.
MicroRNAs are a class of recently discovered, small non-coding RNAs that have been shown to play essential roles in a vast majority of biological processes. Very little is known about the role of microRNAs during spinal cord injury. This review summarizes the changes in expression levels of microRNAs after spinal cord injury. These aberrant changes suggest that microRNAs play an important role in inflammation, oxidative stress, apoptosis, glial scar formation and axonal regeneration. Given their small size and specificity of action, microRNAs could be potential therapeutics for treating spinal cord injury in the future. There are rapidly developing techniques for manipulating microRNA levels in animals; we review different chemical modification and delivery strategies. These may provide platforms for designing efficient microRNA delivery protocols for use in the clinic.
PMCID: PMC4308808
microRNAs; spinal cord injury; reactive astrogliosis; axonal regeneration; antagomir; anti-miR; neural regeneration; reviews
14.  Differences in iNOS and Arginase Expression and Activity in the Macrophages of Rats Are Responsible for the Resistance against T. gondii Infection 
PLoS ONE  2012;7(4):e35834.
Toxoplasma gondii infects humans and warm blooded animals causing devastating disease worldwide. It has long been a mystery as to why the peritoneal macrophages of rats are naturally resistant to T. gondii infection while those of mice are not. Here, we report that high expression levels and activity of inducible nitric oxide synthase (iNOS) and low levels of arginase-1 (Arg 1) activity in the peritoneal macrophages of rats are responsible for their resistance against T. gondii infection, due to high nitric oxide and low polyamines within these cells. The opposite situation was observed in the peritoneal macrophages of mice. This discovery of the opposing functions of iNOS and Arg 1 in rodent peritoneal macrophages may lead to a better understanding of the resistance mechanisms of mammals, particularly humans and livestock, against T. gondii and other intracellular pathogens.
PMCID: PMC3338469  PMID: 22558235
15.  Cigarette Smoking and p16INK4α Gene Promoter Hypermethylation in Non-Small Cell Lung Carcinoma Patients: A Meta-Analysis 
PLoS ONE  2011;6(12):e28882.
Aberrant methylation of promoter DNA and transcriptional repression of specific tumor suppressor genes play an important role in carcinogenesis. Recently, many studies have investigated the association between cigarette smoking and p16INK4α gene hypermethylation in lung cancer, but could not reach a unanimous conclusion.
Methods and Findings
Nineteen cross-sectional studies on the association between cigarette smoking and p16INK4α methylation in surgically resected tumor tissues from non-small cell lung carcinoma (NSCLC) patients were identified in PubMed database until June 2011. For each study, a 2×2 cross-table was extracted. In total, 2,037 smoker and 765 nonsmoker patients were pooled with a fixed-effects model weighting for the inverse of the variance. Overall, the frequency of p16INK4α hypermethylation was higher in NSCLC patients with smoking habits than that in non-smoking patients (OR = 2.25, 95% CI = 1.81–2.80). The positive association between cigarette smoking and p16INK4α hypermethylation was similar in adenocarcinoma and squamous-cell carcinoma. In the stratified analyses, the association was stronger in Asian patients and in the studies with larger sample sizes.
Cigarette smoking is positively correlated to p16INK4α gene hypermethylation in NSCLC patients.
PMCID: PMC3236763  PMID: 22174919
16.  Combining NMR and EPR Methods For Homo-Dimer Protein Structure Determination 
Journal of the American Chemical Society  2010;132(34):11910-11913.
There is a general need to develop more powerful and more robust methods for structural characterization of homo-dimers, homo-oligomers and multi-protein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multi-protein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and EPR-based techniques such as Double Electron Electron Resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70Å. In this communication, we describe integration of PRE and DEER data with conventional solution-state NMR methods for structure determination of Dsy0195, a homo-dimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of inter-chain NOE constraints that can be used to accurately define both the homo-dimer interface and global homo-dimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is only limited by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.
PMCID: PMC3057626  PMID: 20698532
17.  catena-Poly[[tetra­aqua­manganese(II)]-μ-5-carboxyl­ato-1-carboxyl­atomethyl-2-oxidopyridinium-κ2 O 5:O 1] 
In the title coordination polymer, [Mn(C8H5NO5)(H2O)4]n, the MnII atom is coordinated by two carboxyl­ate O atoms from two 5-carboxyl­ato-1-carboxyl­atomethyl-2-oxidopyridinium (L 2−) ligands and by four water mol­ecules in a distorted octa­hedral geometry. The L 2− ligands bridge the Mn atoms into an infinite chain motif along [100]; the chains are further inter­linked by O—H⋯O hydrogen bonds into a three-dimensional supra­molecular net.
PMCID: PMC3212127  PMID: 22090829
18.  Construct Optimization for Protein NMR Structure Analysis Using Amide Hydrogen / Deuterium Exchange Mass Spectrometry 
Proteins  2009;76(4):882-894.
Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three-dimensional structure determination of the ordered regions of proteins by NMR methods. In this paper, we demonstrate the application of 1H/2H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N- and C-terminal tails were evaluated using 1H-15N HSQC and 1H-15N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS-based truncated construct for a 77-residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination.
PMCID: PMC2739808  PMID: 19306341
DXMS; hydrogen-deuterium exchange; mass spectrometry; NMR; partially disordered proteins; protein construct optimization; structural genomics
19.  Bis(μ-5-carboxyl­ato-1-carboxyl­ato­methyl-2-oxidopyridinium)-κ2 O 5:O 1;κ2 O 1:O 5-[diaqua­(phenan­throline-κ2 N,N′)manganese(II)] dihydrate 
The centrosymmetric binuclear title complex, [Mn2(C8H5NO5)2(C12H8N2)2(H2O)4]·2H2O, was obtained by the reaction of manganese chloride with 5-carb­oxy-1-carboxy­methyl-2-oxidopyridinium and 1,10-phenanthroline. The MnII atom is coordinated by two N atoms from the 1,10-phenanthroline ligand, two O atoms from two 5-carboxyl­ato-1-carboxyl­atomethyl-2-oxidopyridinium ligands and two water mol­ecules, leading to a distorted octahedral MnN2O4 environment. Inter­molecular O—H⋯O hydrogen bonds link neighbouring mol­ecules into a layer structure parallel to (001).
PMCID: PMC2969745  PMID: 21583018
20.  Interaction of methylenetetrahydrofolate reductase C677T, cytochrome P4502E1 polymorphism and environment factors in esophageal cancer in Kazakh population 
AIM: To evaluate the association and interaction of genetic polymorphisms in methylenetetrahydrofolate reductase (MTHER) and cytochrome P4502E1 (CYP4502E1), environment risk factors with esophageal cancer (EC) in Kazakh, a high EC incidence area of Xinjiang Uygur Autonomous Region, China.
METHODS: A 1:2 matched case-control study was conducted with 120 cases of EC and 240 population- or hospital-based controls. The controls were matched for sex, nationality, area of residence and age within a 5-year difference. MTHER and CYP4502E1 genotypes were identified by PCR-based restriction fragment length polymorphism (RFLP). A conditional logistic regression model was established to identify risk factors. The strata method was adopted in interaction analysis.
RESULTS: Low consumption of green vegetables and fresh fruits, alcohol drinking, and unsafe water (shallow well, or river) were found to be the risk factors for EC. Individuals with the MTHFR677 (C/T + T/T) genotype had a 2.62-fold (95% CI: 1.61-4.28) risk of developing EC compared with those who carried the C/C genotype. Individuals with the CYP4502E1C1/C1 genotype had a 3.00-fold (95% CI: 1.82-4.96) risk compared with those who carried the CYP4502E1 (C1/C2 + C2/C2) genotype. Gene-environment interaction analysis showed that MTHFR677 gene polymorphism was correlated with consumption of green vegetables and fresh fruit, while CYP4502E1 C1/C1 was correlated with alcohol drinking and unsafe drinking water. MTHFR and CYP4502E1 analysis of gene-gene interaction showed that individuals with the MTHFR677 (C/T + T/T) and CYP4502E1C1/C1 genotypes had a 7.41-fold (95% CI: 3.60-15.25) risk of developing EC compared with those who carried the MTHFR677C/C and CYP4502E1 RsaI C1/C2 + C2/C2 genes, and the interaction rate was higher than that of the two factors alone.
CONCLUSION: Low consumption of green vegetables and fresh fruits, alcohol drinking, and unsafe water (shallow well, or river) and polymorphisms in MTHFR and CYP4502E1 genes are important risk factors for EC. There is a synergistic interaction among polymorphisms in MTHFR and CYP4502E1 genes and environment factors. MTHFR and CYP4502E1 genes can be used as biomarkers for prevention of EC in Kazakh, Xinjiang Uygur Autonomous Region, China.
PMCID: PMC2773864  PMID: 19058336
Kazakh; Esophageal Cancer; Methylenetetrahydrofolate reductase C677T; Cytochrome P4502E1; Genetic polymorphism; Environment risk factors; Interaction; Case control study
21.  Tetra­aqua­bis(5-hydroxy­nicotinato-κN)cadmium(II) 
The title compound, [Cd(C6H4NO3)2(H2O)4], was obtained by the reaction of cadmium chloride with 5-hydroxy­nicotinic acid. The CdII atom is located on an inversion centre and is coordinated by two N atoms from two 5-hydroxy­nicotinic acid ligands and four water mol­ecules in a distorted octa­hedral geometry. The structure is stabilized by inter­molecular O—H⋯O hydrogen bonds, forming a three-dimensional network.
PMCID: PMC2960042  PMID: 21581135

Results 1-21 (21)