PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (26)
 

Clipboard (0)
None

Select a Filter Below

Year of Publication
1.  Relationships of Urinary VEGF/CR and IL-6/CR with Glomerular Pathological Injury in Asymptomatic Hematuria Patients 
Background
Interleukin-6 (IL-6) and vascular endothelial growth factor (VEGF) have important functions in injury and repair processes of glomerular intrinsic cells. A study was conducted to analyze the urinary VEGF/creatinine (CR) and IL-6/CR levels in simple hematuria patients after excluding the interference of creatinine. We aimed to investigate the function and relationships of the above indices in the glomerular pathological injury process, and to elaborate the values of urinary VEGF and IL-6 changes in the diagnosis of asymptomatic hematuria or hematuria with proteinuria.
Material/Methods
A total of 121 renal hematuria patients diagnosed by clinical and laboratory tests were included as research subjects. The midstream fresh morning urine was collected on the day renal biopsy was performed.
Results
The IL-6/CR value of the group III was significantly greater than in group I (Z=−2.478, P<0.05), with a statistically significant difference between these 2 groups. The VEGF/CR value of group III was significantly greater than in group II (P<0.01). Compared with group I, the VEGF/CR of group III was significantly greater (Z=−4.65, P<0.01), with a statistically significant difference.
Conclusions
The VEGF/CR and IL-6/CR values in simple hematuria patients were positively correlated with glomerular pathological injury scores. VEGF/CR and IL-6/CR might be used as biological diagnostic indicators in determining the extent of simple hematuria glomerular injury.
doi:10.12659/MSM.892085
PMCID: PMC4321409  PMID: 25634015
Cytokine Receptor gp130; Kidney Glomerulus; Vascular Endothelial Growth Factor A; Hematuria
2.  Red Cell Distribution Width Is Associated with Presence, Stage, and Grade in Patients with Renal Cell Carcinoma 
Disease Markers  2014;2014:860419.
It has been reported that red blood cell width (RDW) is a marker associated with the presence and adverse outcomes of various diseases. However, no data are available on the correlation of RDW with presence, stage, and grade in patients with renal cell carcinoma (RCC) yet. By retrospectively analyzing clinical and laboratory data at baseline of histologically confirmed RCC cases and controls, the present study demonstrated that the RDW values were significantly higher in patients with RCC than those in controls, and the baseline RDW value was independently associated with the presence of RCC. Besides, the data revealed a positive association between RCC stage and grade and the level of RDW. These findings may have important clinical implications due to future application using a RDW value in predicting RCC.
doi:10.1155/2014/860419
PMCID: PMC4280806  PMID: 25580051
3.  Minimally invasive surgery treatment for the patients with spontaneous supratentorial intracerebral hemorrhage (MISTICH): protocol of a multi-center randomized controlled trial 
BMC Neurology  2014;14(1):206.
Background
The choice of surgical or conservative treatment for patients with spontaneous intracerebral hemorrhage is controversial. Some minimally invasive treatments have been applied to hematoma evacuation and could improve prognosis to some extent. Up to now, studies on minimally invasive surgery for patients with spontaneous intracerebral hemorrhage are still insufficient.
Design
The MISTICH is a multi-center, prospective, randomized, assessor-blinded, parallel group, controlled clinical trial. 2448 eligible patients will be assigned to neuroendoscopy group, stereotactic aspiration group and craniotomy group randomly. Patients will receive the corresponding surgery based on the result of randomization. Surgeries will be performed by well-trained surgeons and standard medical treatment will be given to all patients. Patients will be followed up at 7 days, 30 days, and 6 months. The primary outcome of this study is unfavorable outcome at 6 months. Secondary outcomes include: mortality at 30 days and 6 months after surgery; neurological functional status of 6 months after surgery; complications including rebleeding, ischemic stroke and intracranial infection; days of hospitalization.
Discussion
The MISTICH trial is a randomized controlled trial designed to determine whether minimally invasive surgeries could improve the prognosis for patients with spontaneous intracerebral hemorrhage compared with craniotomy. (ChiCTR-TRC-12002026. Registered 23 March 2012).
doi:10.1186/s12883-014-0206-z
PMCID: PMC4194378  PMID: 25300611
Intracerebral hemorrhage; Minimally invasive surgical treatment; Craniotomy; Neuroendoscope; Stereotactic aspiration
4.  Thioredoxin Reductase Was Nitrated in the Aging Heart After Myocardial Ischemia/Reperfusion 
Rejuvenation Research  2013;16(5):377-385.
Abstract
The age-related loss of anti-oxidant defense reduces recovery from myocardial ischemia/reperfusion injury (MI/R) in aged people. Our previous data showed that inactivation of thioredoxin (Trx) was involved in enhanced aging MI/R injury. Thioredoxin reductase (TrxR), the enzyme known to regulate Trx, is less efficient with age. The aim of the current study was to determine why TrxR activity was reduced and whether reduced TrxR activity contributed to enhanced aging MI/R injury. Both Trx and TrxR activity were decreased in the aging heart, and this difference was further amplified after MI/R. However, MI/R injury did not change TrxR expression between young and aging rats. Increased nitrogen oxide (NOx) but decreased nitric oxide (NO) bioavailability (decreased phosphorylated vasodilator-stimulated phosphoprotein) was observed in aging hearts. Peroxynitrite (ONOO−) was increased in aging hearts and was further amplified after MI/R. TrxR nitration in young and aging hearts was detected by immunoprecipitation (anti-nitrotyrosine) followed by immunoblotting (anti-TrxR). Compared with young hearts, TrxR nitration was increased in the aging hearts, and this was further intensified after MI/R. The ONOO− decomposition catalyst (FeTMPyp) reduced TrxR nitration and increased TrxR and Trx activity. More importantly, FeTMPyp attenuated the MI/R injury in aging hearts as evidenced by decreased caspase-3 and malondialdehyde (MDA) concentration and increased cardiac function. Increased ONOO− nitrated TrxR in the aging heart as a post-translational modification, which may be related to the enhanced MI/R injury of aging rats. Interventions that inhibit nitration and restore TrxR activity might be a therapy for attenuating enhanced MI/R injury in aging heart.
doi:10.1089/rej.2013.1437
PMCID: PMC3804317  PMID: 23802942
5.  Common intermediates and kinetics, but different energetics, in the assembly of SNARE proteins 
eLife  2014;3:e03348.
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are evolutionarily conserved machines that couple their folding/assembly to membrane fusion. However, it is unclear how these processes are regulated and function. To determine these mechanisms, we characterized the folding energy and kinetics of four representative SNARE complexes at a single-molecule level using high-resolution optical tweezers. We found that all SNARE complexes assemble by the same step-wise zippering mechanism: slow N-terminal domain (NTD) association, a pause in a force-dependent half-zippered intermediate, and fast C-terminal domain (CTD) zippering. The energy release from CTD zippering differs for yeast (13 kBT) and neuronal SNARE complexes (27 kBT), and is concentrated at the C-terminal part of CTD zippering. Thus, SNARE complexes share a conserved zippering pathway and polarized energy release to efficiently drive membrane fusion, but generate different amounts of zippering energy to regulate fusion kinetics.
DOI: http://dx.doi.org/10.7554/eLife.03348.001
eLife digest
Many processes in living things need molecules to be transported within, or between, cells. For example, damaged or waste molecules are transported within a cell to structures that can break the molecules down, while nerve impulses are transmitted from one neuron to the next via the release of signaling molecules.
Cells—and the compartments within cells—are surrounded by membranes that act as barriers to certain molecules. Vesicles are small, membrane-enclosed packages that are used to transport molecules between different membranes; and in order to release its cargo, a vesicle must fuse with its target membrane. To fuse like this, the forces that act to push membranes away from one another need to be overcome. Proteins called SNARES, which are embedded in both membranes, are the molecular engines that power the fusion process. Once the SNARE proteins from the vesicle and the target membrane bind, they assemble into a more compact complex that pulls the two membranes close together and allows fusion to take place.
The final shape of an assembled SNARE complex is essentially the same for all SNARE complexes; however, it is not known whether all of these complexes fold using the same method. Now Zorman et al. have used optical tweezers—an instrument that uses a highly focused laser beam to hold and manipulate microscopic objects—to observe the folding and unfolding of four different types of SNARE complex. All four SNARE complexes followed the same step-by-step process: the leading ends of the SNARE proteins slowly bound to each other; the process paused; then the rest of the proteins rapidly ‘zippered’ together.
Zorman et al. revealed that, although the steps in the processes were the same, the energy released in the last step was different when different complexes assembled. This suggests that the energy released by the ‘zippering’ of different SNARE proteins is optimized to match the required speed of different membrane fusion events. Furthermore, Zorman et al. propose that the reason why the majority of energy is released in the later stages of complex assembly is because this is when the repulsion between the two membranes is strongest.
The discoveries of Zorman et al. will now aid future efforts aimed at understanding better how the numerous other proteins that interact with SNARE proteins regulate the process of membrane fusion.
DOI: http://dx.doi.org/10.7554/eLife.03348.002
doi:10.7554/eLife.03348
PMCID: PMC4166003  PMID: 25180101
SNAREs; optical tweezers; protein folding; membrane fusion; SNARE assembly; energy landscape; E. coli
6.  Anti-Peroxynitrite Treatment Ameliorated Vasorelaxation of Resistance Arteries in Aging Rats: Involvement with NO-sGC-cGKs Pathway 
PLoS ONE  2014;9(8):e104788.
Declined vasorelaxation function in aging resistance arteries is responsible for aging-related multiple organ dysfunctions. The aim of the present study is to explore the role of peroxynitrite (ONOO-) in aging resistance arterial vasorelaxation dysfunction and the possible mechanism. In the present study, young (3–4 months olds) and aging (20 months olds) male SD rats were randomized to receive vehicle (Saline) or FeTMPyP (ONOO- scavenger) for 2 weeks. The vasorelaxation of resistance arteries was determined in vitro; NOx level was tested by a colorimetric assay; the expression of nitrotyrosine (NT), soluble Guanylate Cyclase (sGC), vasodilator-stimulated phosphoprotein (VASP), phosphorylated VASP (P-VASP) and cGMP in resistance arteries were detected by immunohistochemical staining. In the present study, endothelium-dependent dilation in aging resistance arteries was lower than in those from young rats (young vs. aging: 68.0%±4.5% vs. 50.4%±2.9%, P<0.01). And the endothelium-independent dilation remained constant. Compared with young rats, aging increased nitrative stress in resistance arteries, evidenced by elevated NOx production in serum (5.3±1.0 nmol/ml vs. 3.3±1.4 nmol/ml, P<0.05) and increased NT expression (P<0.05). ONOO- was responsible for the vasorelaxation dysfunction, evidenced by normalized vasorelaxation after inhibit ONOO- or its sources (P<0.05) and suppressed NT expression after FeTMPyP treatment (P<0.05). The expression of sGC was not significantly different between young and aging resistance arteries, but the cGMP level and P-VASP/VASP ratio (biochemical marker of NO-sGC-cGKs signaling) decreased, which was reversed by FeTMPyP treatment in vivo (P<0.05). The present study suggested that ONOO- mediated the decline of endothelium-dependent vasorelaxation of aging resistance arteries by induction of the NO-sGC-cGKs pathway dysfunction.
doi:10.1371/journal.pone.0104788
PMCID: PMC4130589  PMID: 25117910
7.  Neuropilin-1 Promotes Epithelial-to-Mesenchymal Transition by Stimulating Nuclear Factor-Kappa B and Is Associated with Poor Prognosis in Human Oral Squamous Cell Carcinoma 
PLoS ONE  2014;9(7):e101931.
Background
The epithelial-to-mesenchymal transition (EMT) is a key process in carcinogenesis, invasion, and metastasis of oral squamous cell carcinoma (OSCC). In our previous studies, we found that neuropilin-1 (NRP1) is overexpressed in tongue squamous cell carcinoma and that this overexpression is associated with cell migration and invasion. Nuclear factor-kappa B (NF-κB) plays an essential role both in the induction and the maintenance of EMT and tumor metastasis. Therefore, we hypothesized that NRP1 induces EMT, and that NRP1-induced migration and invasion may be an important mechanism for promoting invasion and metastasis of OSCC through NF-κB activation.
Methods/Results
The variations in gene and protein expression and the changes in the biological behavior of OSCC cell lines transfected with a vector encoding NRP1, or the corresponding vector control, were evaluated. NRP1 overexpression promoted EMT and was associated with enhanced invasive and metastatic properties. Furthermore, the induction of EMT promoted the acquisition of some cancer stem cell (CSC)-like characteristics in OSCC cells. We addressed whether selective inhibition of NF-κB suppresses the NRP1-mediated EMT by treating cells with pyrrolidinedithiocarbamate ammonium (PDTC), an inhibitor of NF-κB. Immunohistochemical analysis of NRP1 in OSCC tissue samples further supported a key mediator role for NRP1 in tumor progression, lymph node metastasis, and indicated that NRP1 is a predictor for poor prognosis in OSCC patients.
Conclusion
Our results indicate that NRP1 may regulate the EMT process in OSCC cell lines through NF-κB activation, and that higher NRP1 expression levels are associated with lymph node metastasis and poor prognosis in OSCC patients. Further investigation of the role of NRP1 in tumorigenesis may help identify novel targets for the prevention and therapy of oral cancers.
doi:10.1371/journal.pone.0101931
PMCID: PMC4084996  PMID: 24999732
8.  Insight into Resolution Enhancement in Generalized Two-Dimensional Correlation Spectroscopy 
Applied spectroscopy  2013;67(3):283-290.
Generalized two-dimensional correlation spectroscopy (2D COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) are not completely understood. In the work here we studied the 2D COS of simulated spectra in order to develop new insights into the dependence of the 2D COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We find that the features in the 2D COS maps that derive from overlapping bands are determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identify the conditions required to resolve overlapping bands. In particular, 2D COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands.
doi:10.1366/11-06541
PMCID: PMC3976562  PMID: 23452492
Two dimensional correlation spectroscopy; resolution enhancement; overlapping bands; normalized half-intensity
9.  Alleviation of Plasma Homocysteine Level by Phytoestrogen α-Zearalanol Might Be Related to the Reduction of Cystathionine β-Synthase Nitration 
BioMed Research International  2014;2014:143192.
Hyperhomocysteinemia is strongly associated with cardiovascular diseases. Previous studies have shown that phytoestrogen α-zearalanol can protect cardiovascular system from hyperhomocysteinemia and ameliorate the level of plasma total homocysteine; however, the underlying mechanisms remain to be clarified. The aim of this research is to investigate the possible molecular mechanisms involved in ameliorating the level of plasma homocysteine by α-zearalanol. By the successfully established diet-induced hyperhomocysteinemia rat models, we found that, after α-zearalanol treatment, the activity of cystathionine β-synthase, the key enzyme in homocysteine metabolism, was significantly elevated and level of nitrative stress in liver was significantly reduced. In correlation with this, results also showed a decreased nitration level of cystathionine β-synthase in liver. Together data implied that alleviation of plasma homocysteine level by phytoestrogen α-zearalanol might be related to the reduction of cystathionine β-synthase nitration.
doi:10.1155/2014/143192
PMCID: PMC3982276  PMID: 24783194
10.  Driving-Simulator-Based Test on the Effectiveness of Auditory Red-Light Running Vehicle Warning System Based on Time-To-Collision Sensor 
Sensors (Basel, Switzerland)  2014;14(2):3631-3651.
The collision avoidance warning system is an emerging technology designed to assist drivers in avoiding red-light running (RLR) collisions at intersections. The aim of this paper is to evaluate the effect of auditory warning information on collision avoidance behaviors in the RLR pre-crash scenarios and further to examine the casual relationships among the relevant factors. A driving-simulator-based experiment was designed and conducted with 50 participants. The data from the experiments were analyzed by approaches of ANOVA and structural equation modeling (SEM). The collisions avoidance related variables were measured in terms of brake reaction time (BRT), maximum deceleration and lane deviation in this study. It was found that the collision avoidance warning system can result in smaller collision rates compared to the without-warning condition and lead to shorter reaction times, larger maximum deceleration and less lane deviation. Furthermore, the SEM analysis illustrate that the audio warning information in fact has both direct and indirect effect on occurrence of collisions, and the indirect effect plays a more important role on collision avoidance than the direct effect. Essentially, the auditory warning information can assist drivers in detecting the RLR vehicles in a timely manner, thus providing drivers more adequate time and space to decelerate to avoid collisions with the conflicting vehicles.
doi:10.3390/s140203631
PMCID: PMC3958215  PMID: 24566631
red-light running; audio warning information; driving simulator; driving behavior; structural equation modeling
11.  High-Resolution Optical Tweezers for Single-Molecule Manipulation 
Forces hold everything together and determine its structure and dynamics. In particular, tiny forces of 1-100 piconewtons govern the structures and dynamics of biomacromolecules. These forces enable folding, assembly, conformational fluctuations, or directional movements of biomacromolecules over sub-nanometer to micron distances. Optical tweezers have become a revolutionary tool to probe the forces, structures, and dynamics associated with biomacromolecules at a single-molecule level with unprecedented resolution. In this review, we introduce the basic principles of optical tweezers and their latest applications in studies of protein folding and molecular motors. We describe the folding dynamics of two strong coiled coil proteins, the GCN4-derived protein pIL and the SNARE complex. Both complexes show multiple folding intermediates and pathways. ATP-dependent chromatin remodeling complexes translocate DNA to remodel chromatin structures. The detailed DNA translocation properties of such molecular motors have recently been characterized by optical tweezers, which are reviewed here. Finally, several future developments and applications of optical tweezers are discussed. These past and future applications demonstrate the unique advantages of high-resolution optical tweezers in quantitatively characterizing complex multi-scale dynamics of biomacromolecules.
PMCID: PMC3767221  PMID: 24058311
optical tweezers; single-molecule manipulation; protein folding; molecular motors; DNA translocation; SNARE proteins
12.  Timing of operation for poor-grade aneurysmal subarachnoid hemorrhage: study protocol for a randomized controlled trial 
BMC Neurology  2013;13:108.
Background
Subarachnoid hemorrhage is a common and dangerous disease with an unfavorable prognosis. Patients with poor-grade subarachnoid hemorrhage (Hunt & Hess Grades 4–5) are unconscious on admission. Because of the high mortality and disability rate associated with poor-grade subarachnoid hemorrhage, it is often treated conservatively. Timing of surgery for poor-grade aneurysmal subarachnoid hemorrhage is still controversial, therefore this study aims to identify the optimal time to operate on patients admitted in poor clinical condition.
Methods/design
Ninety-nine patients meeting the inclusion criteria were randomly assigned into three treatment groups. The early surgery group received operation within 3 days after onset of subarachnoid hemorrhage (day of SAH = day 1); the intermediate surgery group received operation from days 4 to 7, and surgery was performed on the late surgery group after day 7. Follow-up was performed 1, 3, and 6 months after aneurysm clipping. Primary indicators of outcome included the Extended Glasgow Outcome Scale and the Modified Rankin Scale, while secondary indicators of outcome were assessed using the Barthel Index and mortality.
Discussion
This is the first prospective, single-center, observer-blinded, randomized controlled trial to elucidate optimal timing for surgery in poor-grade subarachnoid hemorrhage patients. The results of this study will be used to direct decisions of surgical intervention in poor-grade subarachnoid hemorrhage, thus improving clinical outcomes for patients.
Trial registration
Chinese Clinical Trial Registry: ChiCTR-TRC-12002917
doi:10.1186/1471-2377-13-108
PMCID: PMC3751917  PMID: 23957458
Timing of surgery; Poor-grade; Subarachnoid hemorrhage; ICP; Prognosis
13.  Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages 
Science (New York, N.Y.)  2012;337(6100):1340-1343.
SNARE proteins drive membrane fusion by assembling into a four-helix bundle in a zippering process. Here we used optical tweezers to observe in real time a long-sought SNARE assembly intermediate in which only the membrane-distal N-terminal half of the bundle is assembled. Our finding supports the zippering hypothesis, but suggests that zippering proceeds through three sequential binary switches, not continuously, in the N- and C-terminal halves of the bundle and the linker domain. The half-zippered intermediate was stabilized by externally applied force which mimicked the repulsion between apposed membranes being forced to fuse. This intermediate then rapidly and forcefully zippered, delivering free energy of 36 kBT to mediate fusion.
doi:10.1126/science.1224492
PMCID: PMC3677750  PMID: 22903523
14.  Clinical values of urinary IL-6 in asymptomatic renal hematuria and renal hematuria with proteins 
Renal hematuria is caused by glomerular disease. Under pathological conditions, the distribution of interleukin-6 (IL-6) in kidney tissue is abnormal and urinary IL-6 levels are increased. Abnormal IL-6 secretion promotes the hyperplasia of mesangial cells and matrix and, thus, affects the permeability of the glomerular filtration membrane. Therefore, the detection of urinary IL-6 levels in patients with renal hematuria is beneficial for disease evaluation. A total of 82 patients with primary renal hematuria were divided into group 1 (UPr/24 h < 150 mg; pure hematuria group), group 2 (150 mg ≤ UPr/24 h ≤ 1,000 mg) and group 3 (UPr/24 h > 1,000 mg). A total of 30 normal individuals were selected as the controls. The urinary IL-6 levels were detected by the enzyme-linked immunosorbent assay (ELISA) method and a renal biopsy was conducted. The urinary IL-6 levels and renal pathological damage scores in groups 1 and 2 were significantly reduced compared with those in group 3, (P<0.001 and 0.01, respectively), with no significant difference between groups 1 and 2 (P>0.05). The correlation coefficient (r) of urinary IL-6 with 24 h urinary protein (UPr/24 h) in groups 1, 2 and 3 was 0.017, 0.045 and 0.747, respectively, and that of urinary IL-6 with renal pathological damage score was 0.627, 0.199 and 0.119, respectively. The UPr/24 h was significantly correlated with IL-6 level (r=0.7320, P<0.000). In group 1, the urinary IL-6 levels were correlated with the degree of renal pathological damage. A positive correlation was observed between urinary IL-6 levels and UPr/24 h.
doi:10.3892/etm.2013.1124
PMCID: PMC3786858  PMID: 24137196
interleukin-6; renal hematuria; 24 h urinary protein
15.  Conformation of poly-L-glutamate is independent of ionic strength 
Biophysical Chemistry  2011;162:1-5.
CD and UV resonance Raman measurements surprisingly find that the charge screening of even 2 M concentrations of NaCl and KCl do not alter the unfolded PPII and 2.51-helix conformations of poly-L-glutamate. These salts appear to be excluded from the region between the side chain charges and the peptide backbone. Furthermore, no direct ion pairing occurs between these salts and the side chain carboxylates.
doi:10.1016/j.bpc.2011.11.002
PMCID: PMC3288237  PMID: 22236769
poly-L-glutamate; PPII; 2.51-helix; salt exclusion; UV resonance Raman
16.  UV resonance Raman studies of the NaClO4 dependence of poly-L-lysine conformation and hydrogen exchange kinetics 
The Journal of Physical Chemistry. B  2012;116(3):1134-1142.
We used 204 nm excitation UV Resonance Raman (UVRR) spectroscopy to examine the effects of NaClO4 on the conformation of poly–L–lysine (PLL). The presence of NaClO4 induces the formation of α–helix, π–helix/bulge and turn conformations. The dependence of the AmIII3 frequency on the peptide Ψ Ramachandran angle allows us to experimentally determine the conformational population distributions and the energy landscape of PLL along the Ramachandran Ψ angle. We also used UVRR to measure the NaClO4 concentration dependence of PLL amide hydrogen exchange kinetics. Exchange rates were determined by fitting the D2O exchanging PLL UVRR AmII′ band time evolution. Hydrogen exchange is slowed at high NaClO4 concentrations. The PLL AmII′ band exchange kinetics at 0.0, 0.2 and 0.35 M NaClO4 can be fit by single exponentials, but the AmII′ band kinetics of PLL at 0.8 M NaClO4 requires a double exponential fit. The exchange rates for the extended conformations were monitored by measuring the Cα–H band kinetics. These kinetics are identical to those of the AmII′ band until 0.8 M NaClO4 whereupon the extended conformation exchange becomes clearly faster than that of the α–helix–like conformations. Our results indicate that ClO4− binds to the PLL backbone to protect it from OH− exchange catalysis. In addition, ClO4− binding also slows the conformational exchange between the extended and α–helix–like conformations, probably by increasing the activation barriers for conformational interchanges.
doi:10.1021/jp208918n
PMCID: PMC3266997  PMID: 22117822
Conformational distribution; Energy landscape; Conformational dynamics; Salt binding
17.  Endothelin-receptor antagonists for aneurysmal subarachnoid hemorrhage: an updated meta-analysis of randomized controlled trials 
Critical Care  2012;16(5):R198.
Introduction
The previous meta-analysis on the use of endothelin-receptor antagonists (ETRAs) to treat aneurysmal subarachnoid hemorrhage (SAH) has become outdated due to recently published phase 3 clinical trials. An up-to-date meta-analysis is needed to provide the best available evidence for the efficacy of ETRAs for aneurysmal SAH.
Methods
We performed a systematic review and meta-analysis of published randomized controlled trials that investigate efficacy of ETRAs in patients with aneurysmal SAH. Mortality, unfavorable outcome, delayed ischemic neurological deficit (DIND), delayed cerebral infarction (DCI), angiographic vasospasm and adverse events were analyzed. Meta-analysis was performed in terms of the risk ratio (RR) and 95% confidence interval (CI).
Results
Five eligible studies were reviewed and analyzed, involving 2,595 patients. The pooled RRs of mortality and unfavorable outcome after SAH were 1.03 (95% CI = 0.77 to 1.36) and 1.07 (95% CI = 0.93 to 1.22), respectively. The pooled RRs were 0.87 (95% CI = 0.74 to 1.03) for DCI, 0.77 (95% CI = 0.66 to 0.90) for DIND, and 0.66 (95% CI = 0.57 to 0.77) for angiographic vasospasm. There were significant increases in lung complications (RR = 1.80, 95% CI = 1.55 to 2.09), hypotension (RR = 2.42, 95% CI = 1.78 to 3.29) and anemia (RR = 1.47, 95% CI = 1.19 to 1.83) in patients administered ETRAs.
Conclusion
There is no evidence that ETRAs could benefit clinical outcome in patients with SAH. Owing to the increased adverse events, further clinical trials of ETRAs in SAH patients should be more carefully formulated and designed. The present results also suggest that DCI may be a better outcome measure than vasospasm and DIND in SAH clinical trials and observational studies.
doi:10.1186/cc11686
PMCID: PMC3682300  PMID: 23078672
18.  Is decompressive craniectomy useless in severe traumatic brain injury? 
Critical Care  2011;15(5):193.
Recently, a multicenter randomized controlled trial (RCT) by Cooper and colleagues indicated that decompressive craniectomy (DC) may be associated with a worse functional outcome in patients with diffuse traumatic brain injury (TBI), although DC can immediately and constantly reduce intracranial pressure (ICP). As this trial is well planned and of high quality, the unexpected result is meaningful. However, the evidence of the study is insufficient and the effect of DC in severe TBI is still uncertain. Additional multicenter RCTs are necessary to provide class I evidence on the role of DC in the treatment of refractory raised ICP after severe TBI.
doi:10.1186/cc10358
PMCID: PMC3334735  PMID: 22017925
19.  UV Resonance Raman Study of Side Chain Electrostatic Control of Poly-L-Lysine Conformation 
The journal of physical chemistry. B  2011;115(14):4251-4258.
We used 204 nm excitation UV Resonance Raman (UVRR) spectroscopy to examine the role of side chain electrostatic interactions in determining the conformation of poly-L-lysine (PLL). We examined the pH and ionic strength dependence of the UVRR. The pH dependence of PLL UVRR spectra between pH 7.1 and 11.7 cannot be described by a two-state model, but requires at least one additional state. The AmIII3 region fitting with pH 7.1 and 11.7 basis spectra reveals a small pH induced decrease in the relative fraction of the 2.51-helix conformation compared to the PPII conformation. We performed a 2D general correlation analysis on the PLL pH dependence UVRR spectra. The asynchronous spectrum shows enhanced spectral resolution. The 2D asynchronous spectrum reveals multiple components in the Cα-H b band and the AmII band whose origins are unclear. The cross peaks in the 2D asynchronous spectrum between the AmIII band and the other bands reveals that increasing pH induces three new structures: π-helix, α-helix and some turn structure. We find that 2.5 M NaCl does not change the equilibrium between the PPII and 2.51-helix conformations by screening sidechain electrostatic repulsion. The result indicates that NaCl does not penetrate the region between the sidechain and the peptide backbone. We also compared PLL conformations induced by high pH to that induced by 0.8 M ClO4−. Both conditions induce α-helix-like conformations. 0.8 M ClO4− induces 6% more α-helix-like conformations than at pH 12.4. Higher pH gives rise to longer α-helices and less turn structures.
doi:10.1021/jp2005343
PMCID: PMC3072461  PMID: 21413713
20.  The X Protein of Hepatitis B Virus Inhibits Apoptosis in Hepatoma Cells through Enhancing the Methionine Adenosyltransferase 2A Gene Expression and Reducing S-Adenosylmethionine Production* 
The Journal of Biological Chemistry  2011;286(19):17168-17180.
The X protein (HBx) of hepatitis B virus (HBV) is involved in the development of hepatocellular carcinoma (HCC), and methionine adenosyltransferase 2A (MAT2A) promotes the growth of liver cancer cells through altering S-adenosylmethionine homeostasis. Thus, we speculated that a link between HBx and MAT2A may contribute to HCC development. In this study, the effects of HBx on MAT2A expression and cell apoptosis were investigated, and the molecular mechanism by which HBx and MAT2A regulate tumorigenesis was evaluated. Results from immunohistochemistry analyses of 37 pairs of HBV-associated liver cancer tissues/corresponding peritumor tissues showed that HBx and MAT2A are highly expressed in most liver tumor tissues. Our in vitro results revealed that HBx activates MAT2A expression in a dose-dependent manner in hepatoma cells, and such regulation requires the cis-regulatory elements NF-κB and CREB on the MAT2A gene promoter. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) further demonstrated that HBx facilitates the binding of NF-κB and CREB to MAT2A gene promoter. In addition, overexpression of HBx or MAT2A inhibits cell apoptosis, whereas knockdown of MAT2A expression stimulates apoptosis in hepatoma cells. Furthermore, we demonstrated that HBx reduces MAT1A expression and AdoMet production but enhances MAT2β expression. Thus, we proposed that HBx activates MAT2A expression through NF-κB and CREB signaling pathways to reduce AdoMet production, inhibit hepatoma cell apoptosis, and perhaps enhance HCC development. These findings should provide new insights into our understanding how the molecular mechanisms underline the effects of HBV infection on the production of MAT2A and the development of HCC.
doi:10.1074/jbc.M110.167783
PMCID: PMC3089560  PMID: 21247894
Apoptosis; Cancer Tumor Promoter; Chromatin Immunoprecipitation (ChiP); CREB; DNA-Protein Interaction; DNA Viruses; Gene Regulation; Hepatitis Virus; Oncogene; S-Adenosylmethionine (AdoMet)
21.  Retinal whole genome microarray analysis and early morphological changes in the optic nerves of monkeys after an intraorbital nerve irradiated injury 
Molecular Vision  2011;17:2920-2933.
Purpose
To obtain and analyze early retinal changes at the molecular level 24 h after a radiation injury to the ipsilateral intraorbital nerve using gamma knife surgery (GKS), and to examine the morphological changes in bilateral optic nerves.
Methods
Unilateral intraorbital optic nerves of three rhesus macaques were treated by GKS with irradiated doses of 15 Gy, while contralateral optic nerves and retinas served as the control. Gene expression profiles of the control and affected retinas were analyzed with Affymetrix Rhesus Macaque Genome arrays. To verify the results, a quantitative real-time polymerase chain reaction (qRT–PCR) was performed to test the expression patterns of five function-known genes. Morphological changes in the bilateral optic nerves were examined using a transmission electron microscope (TEM) and light microscopy. The glial cell reaction in bilateral optic nerves was studied using immunohistochemistry.
Results
Of the probe sets, 1,597 (representing 1,081 genes) met the criteria for differential expression, of which 82 genes were significantly up-or down-regulated in treated retinas. There was prominent upregulation of genes associated with glial cell activation in the treated retina. Genes related to an early inflammatory reaction and to cell death were also significantly regulated in response to a radiation injury to the intraorbital optic nerve. In contrast, the messenger ribonucleic acid (mRNA) expression levels of retinal ganglion cell (RGC)-specific genes were low. Morphologically, cytoplasmic processes of astrocytes in treated nerves were shorter than those of the control and were not straight, while also being accompanied by decreased GFAP immunostaining. More oligodendrocytes and inflammatory cells were apparent in treated nerves than in the control. In addition, swollen mitochondria and slight chromation condensation could be seen in the glial cells of treated nerves.
Conclusions
We conclude that the current irradiated dose of 15 Gy was sufficient to lead to a radiation injury of the optic nerve and retina. Several transcripts deregulated in retinas after a radiation injury play a key role in radiation-induced neurogenic visual loss, especially for genes associated with RGC, glial cell, and cell death. Glial cells in optic nerves might be the primary target of a radiation injury in the optic nerve.
PMCID: PMC3224835  PMID: 22128239
22.  Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize 
BMC Plant Biology  2010;10:178.
Background
Modifications of DNA and histones in various combinations are correlated with many cellular processes. In this study, we investigated the possible relationship between histone H4 tetraacetylation, DNA methylation and histone H3 dimethylation at lysine 9 during mitosis in maize root meristems.
Results
Treatment with trichostatin A, which inhibits histone deacetylases, resulted in increased histone H4 acetylation accompanied by the decondensation of interphase chromatin and a decrease in both global H3K9 dimethylation and DNA methylation during mitosis in maize root tip cells. These observations suggest that histone acetylation may affect DNA and histone methylation during mitosis. Treatment with 5-azacytidine, a cytosine analog that reduces DNA methylation, caused chromatin decondensation and mediated an increase in H4 acetylation, in addition to reduced DNA methylation and H3K9 dimethylation during interphase and mitosis. These results suggest that decreased DNA methylation causes a reduction in H3K9 dimethylation and an increase in H4 acetylation.
Conclusions
The interchangeable effects of 5-azacytidine and trichostatin A on H4 acetylation, DNA methylation and H3K9 dimethylation indicate a mutually reinforcing action between histone acetylation, DNA methylation and histone methylation with respect to chromatin modification. Treatment with trichostatin A and 5-azacytidine treatment caused a decrease in the mitotic index, suggesting that H4 deacetylation and DNA and H3K9 methylation may contain the necessary information for triggering mitosis in maize root tips.
doi:10.1186/1471-2229-10-178
PMCID: PMC3095308  PMID: 20718950
23.  Critical Role of the Solvent Environment in Galectin-1 Binding to the Disaccharide Lactose# 
Biochemistry  2009;48(4):786-791.
Galectin-1, a member of a family of evolutionarily conserved glycan-binding proteins, binds specifically to poly-N-acetyllactosamine-enriched glycoconjugates. Through interactions with these glycoconjugates, this protein modulates inflammatory responses and contributes to tumor progression and immune cell homeostasis. The carbohydrate recognition domain includes the single protein tryptophan (Trp68). UV Resonance Raman spectroscopy and molecular dynamic simulation were used to examine the change in the environment of the Trp on ligand binding. The UV Raman spectra and the calculated water radial distribution functions show that, while no large structural changes in the protein follows lactose binding, substantial solvent reorganization occurs. These new insights into the microscopic role of water molecules on Gal-1 binding to its specific carbohydrate ligands provides a better understanding of the physicochemical properties of Gal-1-saccharide interactions, which will be useful for the design of synthetic inhibitors for therapeutic purposes.
doi:10.1021/bi801855g
PMCID: PMC2633424  PMID: 19128029
24.  45S rDNA Regions Are Chromosome Fragile Sites Expressed as Gaps In Vitro on Metaphase Chromosomes of Root-Tip Meristematic Cells in Lolium spp 
PLoS ONE  2008;3(5):e2167.
Background
In humans, chromosome fragile sites are regions that are especially prone to forming non-staining gaps, constrictions or breaks in one or both of the chromatids on metaphase chromosomes either spontaneously or following partial inhibition of DNA synthesis and have been well identified. So far, no plant chromosome fragile sites similar to those in human chromosomes have been reported.
Methods and Results
During the course of cytological mapping of rDNA on ryegrass chromosomes, we found that the number of chromosomes plus chromosome fragments was often more than the expected 14 in most cells for Lolium perenne L. cv. Player by close cytological examination using a routine chromosome preparation procedure. Further fluorescent in situ hybridization (FISH) using 45S rDNA as a probe indicated that the root-tip cells having more than a 14-chromosome plus chromosome fragment count were a result of chromosome breakage or gap formation in vitro (referred to as chromosome lesions) at 45S rDNA sites, and 86% of the cells exhibited chromosome breaks or gaps and all occurred at the sites of 45S rDNA in Lolium perenne L. cv. Player, as well as in L. multiflorum Lam. cv. Top One. Chromatin depletion or decondensation occurred at various locations within the 45S rDNA regions, suggesting heterogeneity of lesions of 45S rDNA sites with respect to their position within the rDNA region.
Conclusions
The chromosome lesions observed in this study are very similar cytologically to that of fragile sites observed in human chromosomes, and thus we conclude that the high frequency of chromosome lesions in vitro in Lolium species is the result of the expression of 45S rDNA fragile sites. Possible causes for the spontaneous expression of fragile sites and their potential biological significance are discussed.
doi:10.1371/journal.pone.0002167
PMCID: PMC2366065  PMID: 18478113
25.  Trial to evaluate effects of ambient particulate matter on health: A preliminary study using two-dimensional gel electrophoresis 
Objectives
Particulate air pollution is a serious problem all over the world, and the development of a method to evaluate the health effects of ambient particles is necessary. In this study, cells cultured in vitro were exposed to particles sampled at the side of a main road, and their protein expression levels were examined.
Methods
Ambient particles were collected at the side of a main road using a high-volume air sampler. Some of the collected particles (crude particles) were treated with an organic solvent to remove chemical components, and the resulting residues were used as residual particles. Cells from the mouse alveolar epithelial cell line LA-4 were inoculated into tissue-culture dishes at 1.4×104/cm2, exposed to each type of particle or artificial carbon particles (Printex 90) that were dispersed using an ultrasonic homogenizer by mixing in the medium twice at 24 and 48 hours, and incubated for up to 72 hours after the start of inoculation. After exposure, the number of cells and intracellular dehydrogenase activity were measured. Proteins extracted from the cells were subjected to two-dimensional gel electrophoresis with isoelectric focusing at pHs 4–7 using a 10% acrylamide gel, and their expression levels were analyzed after fluorescent staining.
Results
The intracellular dehydrogenase activity of the cells significantly decreased as a result of exposure to the residual (0.70-fold) and crude (0.84-fold) particles compared with that of the control, but it showed no change as a result of exposure to Printex 90. The protein expression levels in the cells exposed to the particles increased or decreased similarly, but different expression levels were also observed. There were differences in the effects observed between the cells exposed to the artificial carbon particles and those exposed to particles collected from ambient air.
Conclusion
This study indicates that protein expression levels in cells change in response to exposure to particles collected from ambient air. To evaluate the effects of particles on health, it is considered necessary to use particles collected from ambient air.
doi:10.1007/BF02898028
PMCID: PMC2723230  PMID: 21432067
particulate matter; air pollution; health effect; biomarker; two-dimensional gel electrophoresis

Results 1-25 (26)