Xanthomonas campestris pv. campestris expresses a chromosomally encoded class A ?-lactamase Blaxc. Basal expression and induction of blaxc require the transcriptional factor AmpRxc and the peptidoglycan-monomers permease AmpGxc. NagZ is a ?-GlcNAcase which cleaves GlcNAc-anhMurNAc peptides (peptidoglycan-monomers) to generate anhMurNAc-peptides. In many bacteria, anhMurNAc-peptides act as activation ligands for AmpR. Nevertheless, the role of NagZ in ?-lactamase induction differs among species. In this paper, we studied the roles of nagZxc in the regulation of blaxc and pathogenicity in X. campestris pv. campestris. Our data showed that cells lacking nagZxc dramatically reduced the basal expression and induction of blaxc, suggesting that anhMurNAc-peptides, products of NagZxc, are required for blaxc expression regardless of the presence or absence of inducers. Expression of blaxc is regulated via an ampG-nagZ-ampR pathway. Pathogenicity assay demonstrated that an ampGxc mutant excited more severe symptoms than the wild-type; on the contrary, the nagZxc mutant became less virulent. To our knowledge, this is the first demonstration of a link between the ampG or nagZ defects and the pathogenicity in a plant pathogen.
Recognizing patients at risk for deterioration and in need of critical care after emergency department (ED) admission may prevent unplanned intensive care unit (ICU) transfers and decrease the number of deaths in the hospital. The objective of this research was to study if the predisposition, insult, response, and organ dysfunction (PIRO) concept of sepsis can be used to predict the risk of unplanned ICU transfer after ED admission.
Several dynamic models of a gene regulatory network of the light-induced floral transition process in Arabidopsis have been developed to capture the behavior of gene transcription and infer predictions based on experimental observations. It has been proven that the models can make accurate and novel predictions, which generate testable hypotheses.Two major issues were addressed in this study. First, construction of dynamic models for gene regulatory networks requires the use of mathematic modeling that comprises equations of a large number of parameters. Second, the binding mechanism of the transcription factor with DNA is another factor that requires detailed modeling. The first issue was tackled by adopting an optimization algorithm, and the second was addressed by comparing the performance of three alternative modeling approaches, namely the S-system, the Michaelis-Menten model and the Mass-action model. The efficiencies of parameter estimation and modeling performance were calculated based on least square error (O(p)), mean relative error (MRE) and Akaike Information Criterion (AIC).
Plants are continuously subjected to infection by pathogens, including bacteria and viruses. Bacteria can inject a variety of effector proteins into the host to reprogram host defense mechanism. It is known that microRNAs participate in plant disease resistance to bacterial pathogens and previous studies have suggested that some bacterial effectors have evolved to disturb the host's microRNA-regulated pathways; and so enabling infection. In this study, the inter-species interaction between an Xanthomonas campestris pv campestris (Xcc) pathogen effector and Arabidopsis thaliana microRNA transcription promoter was investigated using three methods: (1) interolog, (2) alignment based on using transcription factor binding site profile matrix, and (3) the web-based binding site prediction tool, PATSER. Furthermore, we integrated another two data sets from our previous study into the present web-based system. These are (1) microRNA target genes and their downstream effects mediated by protein-protein interaction (PPI), and (2) the Xcc-Arabidopsis PPI information. This present work is probably the first comprehensive study of constructing pathways that comprises effector, microRNA, target genes and PPI for the study of pathogen-host interactions. It is expected that this study may help to elucidate the role of pathogen-host interplay in a plant's immune system. The database is freely accessible at: http://ppi.bioinfo.asia.edu.tw/EDMRP .
The objectives of this study were to compare the risk factors for unplanned intensive care unit (ICU) transfer after emergency department (ED) admission in patients with infections and those without infections and to explore the feasibility of using risk stratification tools for sepsis to derive a prediction system for such unplanned transfer.
Denosumab is a humanized monoclonal antibody to receptor activator of nuclear factor-?B ligand used primarily for postmenopausal osteoporosis and skeletal-related events from metastatic cancer. Its safety in children has not been established.
MicroRNAs are small, endogenous RNAs found in many different species and are known to have an influence on diverse biological phenomena. They also play crucial roles in plant biological processes, such as metabolism, leaf sidedness and flower development. However, the functional roles of most microRNAs are still unknown. The identification of closely related microRNAs and target genes can be an essential first step towards the discovery of their combinatorial effects on different cellular states. A lot of research has tried to discover microRNAs and target gene interactions by implementing machine learning classifiers with target prediction algorithms. However, high rates of false positives have been reported as a result of undetermined factors which will affect recognition. Therefore, integrating diverse techniques could improve the prediction. In this paper we propose identifying microRNAs target of Arabidopsis thaliana by integrating prediction scores from PITA, miRanda and RNAHybrid algorithms used as a feature vector of microRNA-target interactions, and then implementing SVM, random forest tree and neural network machine learning algorithms to make final predictions by majority voting. Furthermore, microRNA target genes are linked with their protein-protein interaction (PPI) partners. We focus on plant resistance genes and transcription factor information to provide new insights into plant pathogen interaction networks. Downstream pathways are characterized by the Jaccard coefficient, which is implemented based on Gene Ontology. The database is freely accessible at http://ppi.bioinfo.asia.edu.tw/At_miRNA/.
The chromosomal ampR(Xc) -bla(Xc) module is essential for the ?-lactam resistance of Xanthomonas campestris pv. campestris. Bla(Xc) ?-lactamase is expressed at a high basal level in the absence of an inducer and its expression can be further induced by ?-lactam. In enterobacteria, ampG encodes an inner membrane facilitator involved in the recycling of murein degradation compounds. An isogenic ampG mutant (XcampG) of X. campestris pv. campestris str. 17 (Xc17) was constructed to investigate the link between murein recycling and bla(Xc) expression. Our data demonstrate that (1) XcampG is susceptible to ?-lactam antibiotics; (2) AmpG(Xc) is essential for expression of bla(Xc) ; (3) AmpGs of Xc17, Stenotrophomonas maltophilia KJ (SmKJ) and Escherichia coli DH5? can complement the defect of XcampG; (4) overexpression of AmpG(X) (c) significantly increased bla(Xc) expression; and (5) AmpG(Xc) from Xc17 is able to restore ?-lactamase induction of the ampN(Xc) -ampG(Xc) double mutant of SmKJ. In Xc17, ampG(Xc) can be expressed from the promoter residing in the intergenic region of ampN(Xc) -ampG(Xc) and the expression is independent of ?-lactam induction. AmpN, which is required for ?-lactamases induction in SmKJ, is not required for the ?-lactam antibiotic resistance of Xc17.
Deregulated cell cycle can contribute to the unscheduled proliferation in cancer cells. Overexpression of cell cycle regulators CDK4 and Cyclin D1 has been reported in many cancers. The aim of this study is to determine the clinical implications of CDK4 and Cyclin D1 in hepatocellular carcinoma (HCC). The levels of mRNA and protein were analyzed by quantitative real-time RT-PCR and immunohistochemistry, respectively, in 59 paired HCC and the neighboring noncancer tissues. The relationship between CDK4 and Cyclin D1 expression, clinicopathological parameters, and prognosis was investigated. Our data demonstrated that the mRNA level of CDK4 was up-regulated (p = 0.019), while that of Cyclin D1 was down-regulated (p = 0.002), in HCC. Immunohistochemical data confirmed that CDK4 protein was increased in 73 % and Cyclin D1 protein was decreased in 66 % of HCC samples. Overexpression of CDK4 was correlated with HBV (p = 0.054, borderline significant), tumor size (p = 0.014), and stage (p = 0.010). The Kaplan-Meier survival curves showed that high CDK4 was correlated with a poor survival rate (I vs. II, p < 0.001; I vs. III, p < 0.001). Univariate analysis showed that tumor size (p = 0.002), stage (p = 0.021), and high CDK4 score (I vs. II-III, p < 0.001) were significant prognostic factors. Multivariate analysis showed that tumor size (p = 0.007) and high CDK4 score (I vs. II-III, p < 0.001) were independent factors for overall survival of HCC. The expression of Cyclin D1 was not correlated with CDK4 expression, tumor grades, survival rate, and any clinicopathological parameters. CDK4 could provide a clinical prognostic marker for HCC progression.
Xanthomonas campestris pv. campestris (Xcc) constitutively expresses penicillinase activity in the absence of an inducer. An ampR-bla module is required for the antibiotic resistance phenotype. In this study, we demonstrate that AmpR negatively autoregulates its own expression in a ?-lactam-independent manner. In the absence of inducer, bla is expressed at a high basal level. Expression of bla is inducible by ?-lactam, however, with a period. AmpR protein and the LysR-motif located upstream of bla promoter are essential for basal expression and induction of bla. Most ?-lactamase activity is present in the culture medium, suggesting that Bla protein can be secreted by Xcc into the environment.
The origin of neural hyperexcitability underlying idiopathic generalized epilepsy (IGE) is not known. The objective of this study is to identify evidence of hyperexcitability in precisely measured visual evoked responses and to understand the nature of changes in excitation and inhibition that lead to altered responses in human patients with IGE.
Listening to Korotkoff sounds (K-sounds) to determine systolic and diastolic blood pressure (BP) has been the standard for noninvasive BP measurement in medical practices for nearly 100 years. It is the essential tool used for evaluation and assessment of patients with hypertension and risks of cardiovascular diseases (CVD) by physicians and nurses despite limited understanding of the nature of K-sounds. Analyzing cuff oscillometric signals to obtain BP has been the foundation of most digital BP monitors available today. DynaPulse is an oscillometric digital BP monitor that records and analyzes subtle changes of pulse waveforms during the course of a BP measurement while cuff pressure slowly decreases from above systolic to below diastolic. This study compares systolic and diastolic readings obtained by K-sound method following the Bogalusa Heart Study protocol and BP measured by DynaPulse (DP2000A) monitor, in order to better understand the nature and difference between K-sound and oscillometric methods. Analysis of means and differences is applied to BP data collected from 803 subjects examined in the Bogalusa Heart Study. The results indicated: 1) DynaPulse systolic was 9 mm Hg higher (P < .0001) than Phase 1 (K1) systolic, 2) DynaPulse diastolic was 5 mm Hg lower (P < .0001) than Phase 4 (K4), and 3) is less than 1 mm Hg higher than Phase 5 (K5) diastolic (P < .0001), when compared with K-sound auscultatory measurement. Understanding the methods and differences of DynaPulse oscillometric and K-sound BP measurements is important for clinic BP screening and self-BP monitoring, as well as future research to improve hypertension and CVD managements.
Acute neurotoxic effects of high-dose methylmercury (MeHg) in humans have been well documented in the scientific literature. However, low-dose effects are less well described. This study was designed to evaluate the effects of low-dose MeHg (<100 nM) on human brain cells in a tissue culture model. Neuroblastoma (NB) cells (SH-SY5Y) were used in the cell culture model to study low-dose effects of MeHg on cell growth, cell survival, reactive oxygen species (ROS), and the phosphorylation of tau protein, as a measure of potential markers of cellular events associated with tauopathies. When cells were incubated in culture with MeHg (50 and 100 nM), there were significant decreases in cell viability as well as significant increase in ROS generation as determined by fluorescent dye analysis (H(2)DCFDA). Furthermore, a concomitant decrease in glutathione levels to 25% of control was observed at both 50 and 100 nM MeHg. In addition, the level of phosphorylated tau was significantly increased after treatment at both 50 and 100 nM MeHg, compared with controls. Pretreatment of NB cells with the antioxidant, N-acetylcysteine (1.25 mM) and the calpain inhibitor, MDL-28170 (10 ?M), significantly attenuated the effects of MeHg (50 and 100 nM) on cell viability as well as on tau phosphorylation. These results indicate that low-dose MeHg toxicity may be related to an induction of tau phosphorylation through an oxidative stress-dependent mechanism and that blockade of this pathway may attenuate the toxic effects of MeHg.
Thy1/CD90 is an important marker of many types of stem cells. It functions as a tumor suppressor in ovarian cancer and in nasopharyngeal carcinoma. In this study, the expression status of Thy1 in clinical hepatocellular carcinoma (HCC) tissue samples was investigated. Relationships of Thy1 expression with clinical parameters and patient survival rate were analyzed. The quantities of Thy1 mRNA were statistically higher in tumor tissues than those in the adjacent non-tumor tissues (p<0.001). Immunohistochemical data confirmed that Thy1 protein was increased in 73% of HCC samples. Thy1 expression was not influenced by chronic alcohol exposure or cirrhosis. Overexpression in Thy1 was correlated with age (p=0.006), hepatitis B virus (HBV) infection (p=0.044), and histological grade (p=0.014). Patients with the highest level of Thy1 expression showed the poorest prognosis (p=0.040). In conclusion, overexpression of Thy1 may not suppress the development of HCC. Thy1 could provide a clinical prognostic marker for HCC.
HMG CoA reductase inhibitors (statins) are a proven modality to reduce serum cholesterol and have been shown to reduce morbidity and mortality in cardiovascular patients. Statins have also demonstrated improvements in postoperative outcomes among patients taking them in the perioperative period. Many of the studies are limited to select patient populations and/or select surgeries. This review will give an overview of the pharmacology of statins, summarize the mechanisms of the beneficial effects of statins, and provide an overview of evidence in the use of statins in the perioperative period.
An ideal emergency department (ED) triage system accurately prioritises patients on the basis of the urgency of interventions required to avoid under- or over-triage. The objective of this study was to develop and validate a five-level Taiwan triage and acuity scale (TTAS) with an electronic decision support tool.
The aims of this study are to investigate the relationship between p39 expression and clinicopathological parameters of hepatocellular carcinoma (HCC) and to evaluate the prognostic value of p39 for HCC patients. Real-time quantitative PCR and immunohistochemistry was used to measure p39 expression in tumor and adjacent nontumor samples. Relationships of p39 expression with clinical parameters and patient survival were analyzed. Real-time quantitative RT-PCR showed that the quantity of p39 mRNA in cancerous tissue was significantly lower than that in nontumor tissue (P < 0.001). Immunohistochemistry data confirmed that p39 protein was reduced in 64% of HCC. p39 expression was not influenced by chronic alcohol exposure or cirrhosis. Reduction in p39 was correlated with the HBV (P = 0.039), HCV (P = 0.011), and histological grade (P < 0.001). HCC patients with lower p39 expression had poorer overall survival rate than that with high expression (HR, 2.868; 95% CI, 1.451-5.670; P = 0.002). Together with other results, these results reveal that p39 expression was reduced in HCC tissue. p39 could be a useful clinical prognostic marker for hepatocellular carcinoma patients.
We investigated the factors associated with emergency department (ED) use among patients with non-urgent medical problems, with a focus on convenience and preference to use the ED instead of primary care clinics.
Severe acute respiratory syndrome (SARS) was the first major novel infectious disease to hit the international community in the 21st century. While SARS was sweeping over almost 30 countries, most hospitals in Taiwan instituted mandatory quarantine measures, one of the most effective public health strategies for preventing disease transmission. We explored the anti-SARS quarantine experience of patients in a hospital-based fever screening station.
The lateral superior olive (LSO) is one of the earliest sites in the auditory pathway involved in processing acoustical cues to sound location. LSO neurons encode the interaural level difference (ILD) cue to azimuthal location. Here we investigated the effect of variations in the overall stimulus levels of sounds at the two ears on the sensitivity of LSO neurons to small differences in ILDs of pure tones. The neuronal firing rate versus ILD functions were found to depend greatly on the overall stimulus level, typically shifting along the ILD axis toward the excitatory ear and attaining greater maximal firing rates as stimulus level increased. Seventy-five percent of neurons showed significant shifts with changes in overall sound level. The range of ILDs corresponding to best neural acuity for ILDs shifted accordingly. In a simulation using the empirical data, when the overall stimulus level was randomly changed from one trial to the next, the neural discrimination thresholds for ILD, or ILD acuities, were worsened by 50-60% across the population of neurons relative to fixed stimulus levels whether ILD acuity was measured at the azimuthal midline or the ILD pedestal producing the best acuity. The impairment in ILD discrimination was attributed to the increased neural response variance imparted by varying the stimulus level. These results contrast to those observed in psychophysical studies where ILD discrimination thresholds under similar experimental conditions are invariant to overall changes in stimulus level. A simple computational model that incorporated the antagonistic inputs of bilateral LSO nuclei as well as the dorsal nuclei of the lateral lemniscus to the inferior colliculus produced a more robust encoding of ILD even in the setting of roving stimulus level. Testable predictions of this model and comparison to other computational models addressing stimulus invariance were considered.
In Xanthomonas campestris pv. campestris (Xcc), the chromosomally encoded class A ?-lactamase (Bla(xcc)) is expressed at a high basal level in the absence of an inducer and its expression is inducible by ampicillin. Like most of the class A ?-lactamases, Bla(xcc) cannot digest the ?-lactam ring of cefoxitin. However, Xcc exhibits high basal resistance to cefoxitin. A promoter activity assay with P(blaxcc)-lacZ transcriptional fusion from a plasmid and western blotting using anti-Bla(xcc) polyclonal antibodies demonstrated that a sublethal concentration of cefoxitin can induce expression of the bla(xcc) gene. Cefoxitin can be used as an inducer to study bla(xcc) expression in bla(xcc)-deficient mutants such as Xcbla and XcampR. Addition of cefoxitin to the Bla enzyme solution blocks ?-lactamase activity, suggesting that cefoxitin is an inhibitor of Bla(xcc). This explains why there is no ?-lactamase activity in cefoxitin-induced Xcc. A significant synergistic effect was also observed between cefoxitin and other ?-lactam antibiotics. A homology model demonstrated that the methoxy-group in the ?-lactam ring of cefoxitin tends to displace the conserved catalytic water molecule into the active cavity of Bla(xcc), thus leading to formation of a stable but inactive acyl-Bla(xcc) intermediate.
Fluorescent protein (FP) insertions have often been used to localize primary structure elements in mid-resolution 3D cryo electron microscopic (EM) maps of large protein complexes. However, little is known as to the precise spatial relationship between the location of the fused FP and its insertion site within a larger protein. To gain insights into these structural considerations, Förster resonance energy transfer (FRET) measurements were used to localize green fluorescent protein (GFP) insertions within the ryanodine receptor type 1 (RyR1), a large intracellular Ca(2+) release channel that plays a key role in skeletal muscle excitation contraction coupling. A series of full-length His-tagged GFP-RyR1 fusion constructs were created, expressed in human embryonic kidney (HEK)-293T cells and then complexed with Cy3NTA, a His-tag specific FRET acceptor. FRET efficiency values measured from each GFP donor to Cy3NTA bound to each His tag acceptor site were converted into intermolecular distances and the positions of each inserted GFP were then triangulated relative to a previously published X-ray crystal structure of a 559 amino acid RyR1 fragment. We observed that the chromophoric centers of fluorescent proteins inserted into RyR1 can be located as far as 45 Å from their insertion sites and that the fused proteins can also be located in internal cavities within RyR1. These findings should prove useful in interpreting structural results obtained in cryo EM maps using fusions of small fluorescent proteins. More accurate point-to-point distance information may be obtained using complementary orthogonal labeling systems that rely on fluorescent probes that bind directly to amino acid side chains.
Stimulus visibility can be reduced by other stimuli that overlap the same region of visual space, a process known as masking. Here we studied the neural mechanisms of masking in humans using source-imaged steady state visual evoked potentials and frequency-domain analysis over a wide range of relative stimulus strengths of test and mask stimuli. Test and mask stimuli were tagged with distinct temporal frequencies and we quantified spectral response components associated with the individual stimuli (self terms) and responses due to interaction between stimuli (intermodulation terms). In early visual cortex, masking alters the self terms in a manner consistent with a reduction of input contrast. We also identify a novel signature of masking: a robust intermodulation term that peaks when the test and mask stimuli have equal contrast and disappears when they are widely different. We fit all of our data simultaneously with family of a divisive gain control models that differed only in their dynamics. Models with either very short or very long temporal integration constants for the gain pool performed worse than a model with an integration time of ?30 ms. Finally, the absolute magnitudes of the response were controlled by the ratio of the stimulus contrasts, not their absolute values. This contrast-contrast invariance suggests that many neurons in early visual cortex code relative rather than absolute contrast. Together, these results provide a more complete description of masking within the normalization framework of contrast gain control and suggest that contrast normalization accomplishes multiple functional goals.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.