Molecular and cellular functions of the alternatively spliced isoforms of GDNF receptor complex in neuronal differentiation

Ph.DDOCTOR OF PHILOSOPH

Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells

<p>Abstract</p> <p>Background</p> <p>Gene regulation at transcript level can provide a good indication of the complex signaling mechanisms underlying physiological and pathological processes. Transcriptomic methods such as microarray and quantitative real-time PCR require stable reference genes for accurate normalization of gene expression. Some but not all studies have shown that housekeeping genes (HGKs), β-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which are routinely used for normalization, may vary significantly depending on the cell/tissue type and experimental conditions. It is currently unclear if these genes are stably expressed in cells undergoing drastic morphological changes during neuronal differentiation. Recent meta-analysis of microarray datasets showed that some but not all of the ribosomal protein genes are stably expressed. To test the hypothesis that some ribosomal protein genes can serve as reference genes for neuronal differentiation, a genome-wide analysis was performed and putative reference genes were identified based on stability of expressions. The stabilities of these potential reference genes were then analyzed by reverse transcription quantitative real-time PCR in six differentiation conditions.</p> <p>Results</p> <p>Twenty stably expressed genes, including thirteen ribosomal protein genes, were selected from microarray analysis of the gene expression profiles of GDNF and NGF induced differentiation of PC12 cells. The expression levels of these candidate genes as well as ACTB and GAPDH were further analyzed by reverse transcription quantitative real-time PCR in PC12 cells differentiated with a variety of stimuli including NGF, GDNF, Forskolin, KCl and ROCK inhibitor, Y27632. The performances of these candidate genes as stable reference genes were evaluated with two independent statistical approaches, geNorm and NormFinder.</p> <p>Conclusions</p> <p>The ribosomal protein genes, RPL19 and RPL29, were identified as suitable reference genes during neuronal differentiation of PC12 cells, regardless of the type of differentiation conditions. The combination of these two novel reference genes, but not the commonly used HKG, GAPDH, allows robust and accurate normalization of differentially expressed genes during PC12 differentiation.</p

Photo-Attachment of Biomolecules for Miniaturization on Wicking Si-Nanowire Platform

We demonstrated the surface functionalization of a highly three-dimensional, superhydrophilic wicking substrate using light to immobilize functional biomolecules for sensor or microarray applications. We showed here that the three-dimensional substrate was compatible with photo-attachment and the performance of functionalization was greatly improved due to both increased surface capacity and reduced substrate reflectivity. In addition, photo-attachment circumvents the problems induced by wicking effect that was typically encountered on superhydrophilic three-dimensional substrates, thus reducing the difficulty of producing miniaturized sites on such substrate. We have investigated various aspects of photo-attachment process on the nanowire substrate, including the role of different buffers, the effect of wavelength as well as how changing probe structure may affect the functionalization process. We demonstrated that substrate fabrication and functionalization can be achieved with processes compatible with microelectronics processes, hence reducing the cost of array fabrication. Such functionalization method coupled with the high capacity surface makes the substrate an ideal candidate for sensor or microarray for sensitive detection of target analytes.National University of Singapore (Graduate School for Integrative Sciences and Engineering scholarship)GLOBALFOUNDRIES Singapore Pte. Ltd.Singapore-MIT Allianc

Emergently Alteration of Procedural Strategy During Transcatheter Aortic Valve Replacement to Prevent Coronary Occlusion: A Case Report

BackgroundCoronary occlusion is an uncommon but fatal complication of transcatheter aortic valve replacement (TAVR) with a poor prognosis.Case PresentationA patient with symptomatic severe bicuspid aortic valve stenosis was admitted to a high-volume center specializing in transfemoral TAVR with self-expanding valves. No anatomical risk factors of coronary occlusion were identified on pre-procedural computed tomography analysis. The patient was scheduled for a transfemoral TAVR with a self-expanding valve. Balloon pre-dilatation prior to prosthesis implantation was routinely used for assessing the supra-annular structure and assessing the risk of coronary occlusion. Immediately after the tubular balloon inflation, fluoroscopy revealed that the right coronary artery was not visible, and the flow in the left coronary artery was reduced. The patient would be at high-risk of coronary occlusion if a long stent self-expanding valve was implanted. Therefore, our heart team decided to suspend the ongoing procedure. A transapical TAVR with a 23 mm J-valve was performed 3 days later. The prosthesis was deployed at a proper position without blocking the coronary ostia and the final fluoroscopy showed normal flow in bilateral coronary arteries with the same filling as preoperatively.DiscussionOur successful case highlights the importance of a comprehensive assessment of coronary risk and a thorough understanding of the TAVR procedure for the heart team. A short-stent prosthesis is feasible for patients at high risk of coronary occlusion. Most importantly TAVR should be called off even if the catheter has been introduced when an extremely high risk of coronary obstruction is identified during the procedure and no solution can be found

Plasma Protein and MicroRNA Biomarkers of Insulin Resistance: A Network-Based Integrative -Omics Analysis

Although insulin resistance (IR) is a key pathophysiologic condition underlying various metabolic disorders, impaired cellular glucose uptake is one of many manifestations of metabolic derangements in the human body. To study the systems-wide molecular changes associated with obesity-dependent IR, we integrated information on plasma proteins and microRNAs in eight obese insulin-resistant (OIR, HOMA-IR &gt; 2.5) and nine lean insulin-sensitive (LIS, HOMA-IR &lt; 1.0) normoglycemic males. Of 374 circulating miRNAs we profiled, 65 species increased and 73 species decreased in the OIR compared to the LIS subjects, suggesting that the overall balance of the miRNA secretome is shifted in the OIR subjects. We also observed that 40 plasma proteins increased and 4 plasma proteins decreased in the OIR subjects compared to the LIS subjects, and most proteins are involved in metabolic and endocytic functions. We used an integrative -omics analysis framework called iOmicsPASS to link differentially regulated miRNAs with their target genes on the TargetScan map and the human protein interactome. Combined with tissue of origin information, the integrative analysis allowed us to nominate obesity-dependent and obesity-independent protein markers, along with potential sites of post-transcriptional regulation by some of the miRNAs. We also observed the changes in each -omics platform that are not linked by the TargetScan map, suggesting that proteins and microRNAs provide orthogonal information for the progression of OIR. In summary, our integrative analysis provides a network of elevated plasma markers of OIR and a global shift of microRNA secretome composition in the blood plasma

Mitochondrial Localized STAT3 Is Involved in NGF Induced Neurite Outgrowth

Background: Signal transducer and activator of transcription 3 (STAT3) plays critical roles in neural development and is increasingly recognized as a major mediator of injury response in the nervous system. Cytokines and growth factors are known to phosphorylate STAT3 at tyrosine 705 with or without the concomitant phosphorylation at serine 727, resulting in the nuclear localization of STAT3 and subsequent transcriptional activation of genes. Recent evidence suggests that STAT3 may control cell function via alternative mechanisms independent of its transcriptional activity. Currently, the involvement of STAT3 mono-phosphorylated at residue serine 727 (P-Ser-STAT3) in neurite outgrowth and the underlying mechanism is largely unknown. Principal Findings: In this study, we investigated the role of nerve growth factor (NGF) induced P-Ser-STAT3 in mediating neurite outgrowth. NGF induced the phosphorylation of residue serine 727 but not tyrosine 705 of STAT3 in PC12 and primary cortical neuronal cells. In PC12 cells, serine but not tyrosine dominant negative mutant of STAT3 was found to impair NGF induced neurite outgrowth. Unexpectedly, NGF induced P-Ser-STAT3 was localized to the mitochondria but not in the nucleus. Mitochondrial STAT3 was further found to be intimately involved in NGF induced neurite outgrowth and the production of reactive oxygen species (ROS). Conclusion: Taken together, the findings herein demonstrated a hitherto unrecognized novel transcription independen

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Machine Users Detection on Sina Weibo Platform

In recent years, the rapid development of Sina Weibo has made it the representative of many Weibo platforms in China. Sina Weibo has attracted large numbers of users in China because of its fast speed of information dissemination, simple use and many star users. More and more Chinese people get news and share information through Sina Weibo. In addition to the normal users, Sina Weibo also appeared on some machine users, these users are generated in order to create false sentiment, which seriously affected the good order of the Sina Weibo platform. By studying normal users and machine users, this paper extracts eight features, they are the number of followings, the number of followers, the number of Weibos, the number of years using Sina Weibo, Sunshine credit, the number of Weibos you like, the proportion of following others by recommending and the ratio of followings and followers. Naive Bayes classification approach, KNN classification approach and SVC classification approach are used for experiment. The experimental results show that the recall rate of the machine users detection is above 96% and the accuracy rate is above 98%, which validates the validity of the features extracted in this paper

Machine Users Detection on Sina Weibo Platform

In recent years, the rapid development of Sina Weibo has made it the representative of many Weibo platforms in China. Sina Weibo has attracted large numbers of users in China because of its fast speed of information dissemination, simple use and many star users. More and more Chinese people get news and share information through Sina Weibo. In addition to the normal users, Sina Weibo also appeared on some machine users, these users are generated in order to create false sentiment, which seriously affected the good order of the Sina Weibo platform. By studying normal users and machine users, this paper extracts eight features, they are the number of followings, the number of followers, the number of Weibos, the number of years using Sina Weibo, Sunshine credit, the number of Weibos you like, the proportion of following others by recommending and the ratio of followings and followers. Naive Bayes classification approach, KNN classification approach and SVC classification approach are used for experiment. The experimental results show that the recall rate of the machine users detection is above 96% and the accuracy rate is above 98%, which validates the validity of the features extracted in this paper