Chien-Sheng Chen

Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.

Evidence suggesting that eukaryotes and archaea use reversible N ε-lysine (N ε-Lys) acetylation to modulate gene expression has been reported, but evidence for bacterial use of N ε-Lys acetylation for this purpose is lacking. Here, we report data in support of the notion that bacteria can control gene expression by modulating the acetylation state of transcription factors (TFs). We screened the E. coli proteome for substrates of the bacterial Gcn5-like protein acetyltransferase (Pat). Pat acetylated four TFs, including the RcsB global regulatory protein, which controls cell division, and capsule and flagellum biosynthesis in many bacteria. Pat acetylated residue Lys180 of RcsB, and the NAD+-dependent Sir2 (sirtuin)-like protein deacetylase (CobB) deacetylated acetylated RcsB (RcsBAc), demonstrating that N ε-Lys acetylation of RcsB is reversible. Analysis of RcsBAc and variant RcsB proteins carrying substitutions at Lys180 provided biochemical and physiological evidence implicating Lys180 as a critical residue for RcsB DNA-binding activity. These findings further the likelihood that reversible N ε-Lys acetylation of transcription factors is a mode of regulation of gene expression used by all cells.

Applications of Protein Microarray Technology

Protein microarrays, an emerging class of proteomic technologies, are quickly becoming essential tools for large-scale and high throughput biochemistry and molecular biology. Recent progress has been made in all the key steps of protein microarray fabrication and application, such as the large-scale cloning of expression-ready prokaryotic and eukaryotic ORFs, high throughput protein purification, surface chemistry, protein delivery systems, and detection methods. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. In the case of analytical protein microarrays, well-characterized molecules with specific activity, such as antibodies, peptide-MHC complexes, or lectins, are used as immobilized probes. These arrays have become one of the most powerful multiplexed detection platforms. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including drug target identification/validation and studies of protein interaction, biochemical activity, and immune responses. Great progress has been achieved in both classes of protein microarrays in terms of sensitivity and specificity, and new protein microarray technologies are continuing to emerge. Finally, protein microarrays have found novel applications in both scientific research and clinical diagnostics.

Overview of protein microarrays

Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high‐throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse‐phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post‐translational modifications, the analysis of host‐microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases. Curr. Protoc. Protein Sci. 72:27.1.1‐27.1.16.

Studies of the binding mechanism between aptamers and thrombin by circular dichroism, surface plasmon resonance and isothermal titration calorimetry.

Thrombin, a multifunctional serine protease, has both procoagulant and anticoagulant functions in human blood. Thrombin has two electropositive exosites. One is the fibrinogen-binding site and the other is the heparin-binding site. Over the past decade, two thrombin-binding aptamers (15-mer and 29-mer) were reported by SELEX technique. Recently, many studies examined the interactions between the 15-mer aptamer and thrombin extensively, but the data on the difference of these two aptamers binding to thrombin are still lacking and worth investigating for fundamental understanding. In the present study, we combined conformational data from circular dichroism (CD), kinetics and thermodynamics information from surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to compare the binding mechanism between the two aptamers with thrombin. Special attentions were paid to the formation of G-quadruplex and the effects of ions on the aptamer conformation on the binding and the kinetics discrimination between specific and nonspecific interactions of the binding. The results indicated reasonably that the 15-mer aptamer bound to fibrinogen-binding site of thrombin using a G-quadruplex structure and was dominated by electrostatic interactions, while the 29-mer aptamer bound to heparin-binding site thrombin using a duplex structure and was driven mainly by hydrophobic effects.

Identification of Novel Serological Biomarkers for Inflammatory Bowel Disease Using Escherichia coli Proteome Chip

Specific antimicrobial antibodies present in the sera of patients with inflammatory bowel disease (IBD) have been proven to be valuable serological biomarkers for diagnosis/prognosis of the disease. Herein we describe the use of a whole Escherichia coli proteome microarray as a novel high throughput proteomics approach to screen and identify new serological biomarkers for IBD. Each protein array, which contains 4,256 E. coli K12 proteins, was screened using individual serum from healthy controls (n = 39) and clinically well characterized patients with IBD (66 Crohn disease (CD) and 29 ulcerative colitis (UC)). Proteins that could be recognized by serum antibodies were visualized and quantified using Cy3-labeled goat anti-human antibodies. Surprisingly significance analysis of microarrays identified a total of 417 E. coli proteins that were differentially recognized by serum antibodies between healthy controls and CD or UC. Among those, 169 proteins were identified as highly immunogenic in healthy controls, 186 proteins were identified as highly immunogenic in CD, and only 19 were identified as highly immunogenic in UC. Using a supervised learning algorithm (k-top scoring pairs), we identified two sets of serum antibodies that were novel biomarkers for specifically distinguishing CD from healthy controls (accuracy, 86 ± 4%; p < 0.01) and CD from UC (accuracy, 80 ± 2%; p < 0.01), respectively. The Set 1 antibodies recognized three pairs of E. coli proteins: Era versus YbaN, YhgN versus FocA, and GabT versus YcdG, and the Set 2 antibodies recognized YidX versus FrvX. The specificity and sensitivity of Set 1 antibodies were 81 ± 5 and 89 ± 3%, respectively, whereas those of Set 2 antibodies were 84 ± 1 and 70 ± 6%, respectively. Serum antibodies identified for distinguishing healthy controls versus UC were only marginal because their accuracy, specificity, and sensitivity were 66 ± 5, 69 ± 5, and 61 ± 7%, respectively (p < 0.04). Taken together, we identified novel sets of serological biomarkers for diagnosis of CD versus healthy control and CD versus UC.

Simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes with an array-based immunosorbent assay using universal protein G-liposomal nanovesicles

A novel universal reagent for immunoassays, protein G-liposomal nanovesicles has been developed and successfully used in an immunomagnetic bead sandwich assay for the detection of Escherichia coli O157:H7 [C.-S. Chen, A.J. Baeumner, R.A. Durst, Talanta 67 (2005) 205]. To demonstrate the universal capability of protein G-liposomal nanovesicles, this reagent was used to develop an array-based immunosorbent assay for the simultaneous detection of E. coli O157:H7, Salmonella, and Listeria monocytogenes. Both direct and competitive immunoassay formats were used to demonstrate the feasibility of detecting multiple analytes in a single test by using universal protein G-liposomal nanovesicles. Both pure and mixed cultures were examined in the direct immunoassay format. Results indicate that the limits of detection (LODs) of the direct assay for E. coli O157:H7, Salmonella enterica serovar Typhimurium and L. monocytogenes in pure cultures were approximately 100, 500 and 1.5 x 10(4)CFU/ml, respectively. In mixed cultures, the LODs were approximately 3.1 x 10(3), 7.8 x 10(4), and 7.9 x 10(5)CFU/ml. In the competitive assay format, the LODs for E. coli O157:H7, S. enterica serovar Typhimurium, and L. monocytogenes were approximately 1.5 x 10(4), 5 x 10(4), and 1.2 x 10(5)CFU/ml for the pure cultures. These results showed that protein G-liposomal nanovesicles can be successfully used in a simultaneous immunoassay for several food-borne pathogens, thereby demonstrating that they are effective universal reagents for use in immunoassays.

Nonsteroidal Anti-Inflammatory Drugs for Wounds: Pain Relief or Excessive Scar Formation?

The inflammatory process has direct effects on normal and abnormal wound healing. Hypertrophic scar formation is an aberrant form of wound healing and is an indication of an exaggerated function of fibroblasts and excess accumulation of extracellular matrix during wound healing. Two cytokines—transforming growth factor-β (TGF-β) and prostaglandin E2 (PGE2)—are lipid mediators of inflammation involving wound healing. Overproduction of TGF-β and suppression of PGE2 are found in excessive wound scarring compared with normal wound healing. Nonsteroidal anti-inflammatory drugs (NSAIDs) or their selective cyclooxygenase-2 (COX-2) inhibitors are frequently used as a pain-killer. However, both NSAIDs and COX-2 inhibitors inhibit PGE2 production, which might exacerbate excessive scar formation, especially when used during the later proliferative phase. Therefore, a balance between cytokines and medication in the pathogenesis of wound healing is needed. This report is a literature review pertaining to wound healing and is focused on TGF-β and PGE2.

Intestinal fungi contribute to development of alcoholic liver disease

Chronic liver disease with cirrhosis is the 12th leading cause of death in the United States, and alcoholic liver disease accounts for approximately half of all cirrhosis deaths. Chronic alcohol consumption is associated with intestinal bacterial dysbiosis, yet we understand little about the contribution of intestinal fungi, or mycobiota, to alcoholic liver disease. Here we have demonstrated that chronic alcohol administration increases mycobiota populations and translocation of fungal &bgr;-glucan into systemic circulation in mice. Treating mice with antifungal agents reduced intestinal fungal overgrowth, decreased &bgr;-glucan translocation, and ameliorated ethanol-induced liver disease. Using bone marrow chimeric mice, we found that &bgr;-glucan induces liver inflammation via the C-type lectin–like receptor CLEC7A on Kupffer cells and possibly other bone marrow–derived cells. Subsequent increases in IL-1&bgr; expression and secretion contributed to hepatocyte damage and promoted development of ethanol-induced liver disease. We observed that alcohol-dependent patients displayed reduced intestinal fungal diversity and Candida overgrowth. Compared with healthy individuals and patients with non–alcohol-related cirrhosis, alcoholic cirrhosis patients had increased systemic exposure and immune response to mycobiota. Moreover, the levels of extraintestinal exposure and immune response correlated with mortality. Thus, chronic alcohol consumption is associated with an altered mycobiota and translocation of fungal products. Manipulating the intestinal mycobiome might be an effective strategy for attenuating alcohol-related liver disease.

Protein G-liposomal nanovesicles as universal reagents for immunoassays

To improve the antigen-binding activity of liposome-coupled antibodies and to develop universal liposomal nanovesicles for immunoassays, protein G was conjugated to dye-loaded liposomal nanovesicles for the preparation of immunoliposomes. Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (sulfo-SMCC), a heterobifunctional cross-linker, was used to modify protein G for conjugation to the liposomal nanovesicles. Liposome immunosorbent assays were used to evaluate the binding ability of protein G after sulfo-SMCC modification, to optimize the protein G density on the liposome surface and to determine the amount of IgG binding to the protein G-liposomal nanovesicles. Test strips coated with a narrow zone of antibodies were used to show the successful conjugation. Immunomagnetic beads were used to demonstrate the feasibility of protein G-tagged universal liposomal nanovesicles for immunoassays. Results indicate that the Fc-binding capacity of protein G decreased by only 5.3% after sulfo-SMCC modification. Antibodies were easily conjugated to universal protein G-liposomal nanovesicles in 30min. The conjugates (protein G-immunoliposomes) were successfully used in immunomagnetic bead assays for the detection of Escherichia coli O157:H7 with a detection limit of approximately 100CFU/ml. This work demonstrated that protein G-liposomal nanovesicles are a successful universal reagent for easily coupling antibodies in an active orientation on the liposome surface for use in immunoassays.

Review of myomectomy

Uterine fibroids (also called leiomyomas or myomas) are the most common disorder among women of reproductive age, with an incidence of between 20% and 80%; they are often detected incidentally in routine healthy examinations, through bimanual pelvic and/or ultrasound examination, because uterine fibroids are rarely associated with symptoms. Sometimes, uterine fibroids may be complicated by a variety of symptoms, including menstrual disturbance (e.g., menorrhagia, dysmenorrhea, intermenstrual bleeding), pressure symptoms, bloated sensation, increased urinary frequency, bowel disturbance, or pelvic pain; therefore definite treatment is requested. Hysterectomy may be the first choice for women who have completed their child-birth; however, many women may prefer to keep the uterus if the uterine fibroids-related symptoms can be appropriately controlled. Among these conservative therapies, myomectomy may be one of the most popular methods for the woman who would like to preserve her future fertility, as the majority of symptoms can be relieved by myomectomy; this contributes to the value of this review. This review addresses the use of myomectomy in the management of symptomatic uterine fibroids.