Protein Interactions in Regulation and Assembly

The objectives of this work include: validation of yeast-based assays, investigation of protein-protein interactions in the regulatory role of an intrinsically disordered protein, Ultrabithorax (Ubx), and exploration of possible application of Ubx self-assemble protein materials for cell culture study. Yeast based assays are useful for detecting DNA-protein and protein-protein interactions. Although yeast-based assays are sensitive, substantial amount of artifacts often hinder the correct interpretation of the results. The first part of the project was focused on the validation of yeast one-hybrid and two- hybrid assay and assessment for the possible source of artifacts. We found that media sources and preparation methods had significant influence on the results to yeast-one-hybrid and yeast-two hybrid assay. Using condition optimized yeast-two hybrid assay to match in vivo experiments, we examined protein interactions formed by Ubx, a protein with intrinsically disordered regions. In the classical protein structure-function paradigm, protein function is determined by particular protein structure. However, some proteins do not have rigid structure, and these proteins extensively interact with proteins with diverse functions. The second part of this dissertation was focused on dissecting the topological features of binding partner of an intrinsically disordered protein, Ubx. We found that the binding partners of Ubx protein were enriched in particular folds and disordered regions on Ubx protein were essential for Ubx-partner protein interactions, which may explain why proteins with multiple binding partners often have disordered regions. Ubx protein not only interacts with other proteins but also with itself. This self-association has been explored for the application for tissue engineering purposes. The cytocompatible and biocompatible characteristics of Ubx self-assemble protein materials could provide an unmet need for 3-dimensional (3D) scaffolds on which to culture cancer cells for carcinogenesis characterization. The third part of this dissertation was focused on determining the compatibility between isogenic human mammary gland cell lines with various degrees of tumorigenesis and characterization of cell behavior on Ubx materials. We found that Ubx materials were not toxic to human mammary gland cells with similar genetic background but different degree of tumorigenesis. In addition, Ubx materials enabled further characterization of cancer cell specific cell behaviors

Media composition influences yeast one- and two-hybrid results

Although yeast two-hybrid experiments are commonly used to identify protein interactions, the frequent occurrence of false negatives and false positives hampers data interpretation. Using both yeast one-hybrid and two-hybrid experiments, we have identified potential sources of these problems: the media preparation protocol and the source of the yeast nitrogen base may not only impact signal range but also effect whether a result appears positive or negative. While altering media preparation may optimize signal differences for individual experiments, media preparation must be reported in detail to replicate studies and accurately compare results from different experiments

Risk factors for complications and graft failure in kidney transplant patients with sepsis

Immunosuppressive therapies decreased the incidence of acute kidney rejection after kidney transplantation, but also increased the risk of infections and sepsis. This study aimed to identify the risk factors associated with complications and/or graft failure in kidney transplant patients with sepsis. A total of 14,658 kidney transplant patients with sepsis, identified in the National Inpatient Sample (NIS) database (data from 2005–2014), were included in the study and classified into three groups: patients without complications or graft failure/dialysis (Group 1), patients with complications only (Group 2), and patients with complications and graft failure/dialysis (Group 3). Multinomial logistic regression analyses were conducted to evaluate factors associated with kidney transplant recipients. Multivariate analysis showed that, compared to Group 1, patients from Group 2 or Group 3 were more likely to be Black and to have cytomegalovirus infection, coagulopathy, and glomerulonephritis (p ≤ 0.041). Also, Group 2 was more likely to have herpes simplex virus infection, and Group 3 was more likely to have hepatitis C infection and peripheral vascular disorders, compared to Group 1 (p ≤ 0.002). In addition, patients from Group 3 were more likely to be Black and to have hepatitis C infection, peripheral vascular disorders, coagulopathy, and hypertension compared to Group 2 (p ≤ 0.039). Age and female gender were associated with lower odds of complications after kidney transplantation regardless of graft rejection/dialysis (p ≤ 0.049). Hyperlipidemia and diabetes decreased the chance of complications and graft failure/dialysis after kidney transplant (p < 0.001). In conclusion, the study highlights that black race, male gender, and specific comorbidities can increase the risk of complications and graft failure in kidney transplant patients with sepsis

Proteomic profiling reveals α1-antitrypsin, α1-microglobulin, and clusterin as preeclampsia-related serum proteins in pregnant women

AbstractObjectivePreeclampsia is a major cause of mortality in pregnant women but the underlying mechanism remains unclear to date. In this study, we attempted to identify candidate proteins that might be associated with preeclampsia in pregnant women by means of proteomics tools.Materials and methodsDifferentially expressed proteins in serum samples obtained from pregnant women with severe preeclampsia (n = 8) and control participants (n = 8) were identified using two-dimensional gel electrophoresis (2-DE) followed by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Additional serum samples from 50 normal and 41 pregnant women with severe preeclampsia were analyzed by immunoassay for validation.ResultsTen protein spots were found to be upregulated significantly in women with severe preeclampsia. These protein spots had the peptide mass fingerprints matched to α1-antitrypsin, α1-microglobulin, clusterin, and haptoglobin. Immunoassays in an independent series of serum samples showed that serum α1-antitrypsin, α1-microglobulin, and clusterin levels of severe preeclampsia patients (n = 41) were significantly higher than those in the normal participants (n = 50; α1-antitrypsin 295.95 ± 50.94 mg/dL vs. 259.31 ± 33.90 mg/dL, p = 0.02; α1-microglobulin 0.029 ± 0.004 mg/mL vs. 0.020 ± 0.004 mg/mL, p < 0.0001; clusterin 77.6 ± 16.15 μg/dL vs. 67.6 ± 15.87 μg/dL, p < 0.05).ConclusionIdentification of these proteins by proteomics analysis enables further understanding of the pathophysiology of preeclampsia. Further studies are warranted to investigate the role of these biomarkers in prediction of this disease

Clinical Study of Uric Acid Urolithiasis

Uric acid urolithiasis develops from various causes. To investigate the clinical and biochemical presentation of patients with uric acid urolithiasis, a retrospective study was designed. A total of 46 cases were enrolled between January 2004 and December 2005. The compositions of the stones were analyzed by infrared spectrophotometry. There were 39 males (84.8%) and seven females (15.2%), with a mean age of 61.5 ± 10.6 years and mean body mass index (BMI) of 26.7 ± 3.1 kg/m2. The stone location was kidney in 10 (21.7%), ureter in 22 (41.8%), and bladder in 14 (30.5%). Multiple stones were diagnosed in 36 patients (78.3%). Pre-existing comorbidities included diabetes mellitus in 11 patients (23.9%), hypertension in 23 (50%), gout in 13 (28.2%), and benign prostatic hyperplasia in 14 (30.4%). Mean serum creatinine and uric acid was 1.6 ± 0.6 mg/dL and 7.6 ± 1.8 mg/dL, respectively. There were 27 patients (58%) with creatinine > 1.4 mg/dL. The mean urinary pH was 5.42 ± 0.46. Patients with uric acid urolithiasis were predominantly male, older, with higher BMI, multiple stone presentation, with lower urinary pH, and hyperuricemia. Exacerbation of the renal function should also be of concern because of the high proportion of patients with renal insufficiency diagnosed in this study

Identified single-nucleotide polymorphisms and haplotypes at 16q22.1 increase diabetic nephropathy risk in Han Chinese population

Abstract Background Diabetic nephropathy (DN) has become one of the most common causes of end-stage renal disease (ESRD) in many countries, such as 44.5% in Taiwan. Previous studies have shown that there is a genetic component to ESRD. Studies attempting to determine which genetic variants are related to DN in Han Chinese are limited. A case–control study was conducted to identify DN susceptibility variants in Han Chinese patients with type 2 diabetes. Results We included 574 unrelated type 2 diabetes patients (217 DN cases and 357 controls), who were genotyped using Illumina HumanHap550-Duo BeadChip. In single-SNP association tests, the SNPs rs11647932, rs11645214, and rs6499323 located at 16q22.1 under the additive-effect disease model were significantly associated with an approximately 2-fold increased risk of DN. In haplotype association tests, identified haplotypes located in the chromosome 16q22.1 region (containing ST3GAL2, COG4, SF3B3, and IL34 genes) raised DN risk. The strongest association was found with haplotype rs2288491-rs4985534-rs11645214 (C-C-G) (adjusted odds ratio [AOR] 1.93, 95% confidence interval [CI] 1.83-2.03, p = 6.25 × 10−7), followed by haplotype rs8052125-rs2288491-rs4985534-rs11645214 (G-C-C-G) (AOR 1.92, 95% CI 1.82-2.02, p = 6.56 × 10−7), and haplotype rs2303792-rs8052125-rs2288491-rs4985534-rs11645214 (A-G-C-C-G) (AOR 1.91, 95% CI 1.81-2.01, p = 1.15 × 10−6). Conclusions Our results demonstrate that the novel SNPs and haplotypes located at the 16q22.1 region may involve in the biological pathways of DN in Han Chinese patients with type 2 diabetes. This study can provide new insights into the etiology of DN.http://deepblue.lib.umich.edu/bitstream/2027.42/109508/1/12863_2014_Article_113.pd

Impairment of IgG Fc functions promotes tumor progression and suppresses NK cell antitumor actions

Natural killer (NK) cells mediate antibody dependent cytotoxic killing of cancer cells via cross-linking FcγR on NK cells with IgG-Fc. Studies have shown that the single-hinge cleaved IgGs (scIgGs) have dysfunctional Fc and failed engagement with FcγRs on immune cells. However, little is known about how scIgGs impact on antitumor immunity in the tumor microenvironment. In this study, we revealed a significant association of tumor scIgGs with tumor progression and poor outcomes of breast cancer patients (n = 547). Using multiple mouse tumor models, we demonstrated that tumor scIgGs reduced NK cell cytotoxic activities and resulted in aggressive tumor progression. We further showed that an anti-hinge specific monoclonal antibody (AHA) rescued the dysfunctional Fc in scIgGs by providing a functional Fc and restored NK cell cytotoxic activity. These findings point to a novel immunotherapeutic strategy to enhance Fc engagement with FcγRs for activation of anticancer immunity

Look, the World is Watching How We Treat Migrants! The Making of the Anti-Trafficking Legislation during the Ma Administration

Employing the spiral model, this research analyses how anti-human trafficking legislation was promulgated during the Ma Ying-jeou (Ma Yingjiu) presidency. This research found that the gov- ernment of Taiwan was just as accountable for the violation of mi- grants’ human rights as the exploitive placement agencies and abusive employers. This research argues that, given its reliance on the United States for political and security support, Taiwan has made great ef- forts to improve its human rights records and meet US standards for protecting human rights. The reform was a result of multilevel inputs, including US pressure and collaboration between transnational and domestic advocacy groups. A major contribution of this research is to challenge the belief that human rights protection is intrinsic to dem- ocracy. In the same light, this research also cautions against Taiwan’s subscription to US norms since the reform was achieved at the cost of stereotyping trafficking victimhood, legitimising state surveillance, and further marginalising sex workers

An all-statistics, high-speed algorithm for the analysis of copy number variation in genomes

Detection of copy number variation (CNV) in DNA has recently become an important method for understanding the pathogenesis of cancer. While existing algorithms for extracting CNV from microarray data have worked reasonably well, the trend towards ever larger sample sizes and higher resolution microarrays has vastly increased the challenges they face. Here, we present Segmentation analysis of DNA (SAD), a clustering algorithm constructed with a strategy in which all operational decisions are based on simple and rigorous applications of statistical principles, measurement theory and precise mathematical relations. Compared with existing packages, SAD is simpler in formulation, more user friendly, much faster and less thirsty for memory, offers higher accuracy and supplies quantitative statistics for its predictions. Unique among such algorithms, SAD's running time scales linearly with array size; on a typical modern notebook, it completes high-quality CNV analyses for a 250 thousand-probe array in ∼1 s and a 1.8 million-probe array in ∼8 s