Dynamic Multivariate Simplex Splines For Volume Representation And Modeling

Volume representation and modeling of heterogeneous objects acquired from real world are very challenging research tasks and playing fundamental roles in many potential applications, e.g., volume reconstruction, volume simulation and volume registration. In order to accurately and efficiently represent and model the real-world objects, this dissertation proposes an integrated computational framework based on dynamic multivariate simplex splines (DMSS) that can greatly improve the accuracy and efficacy of modeling and simulation of heterogenous objects. The framework can not only reconstruct with high accuracy geometric, material, and other quantities associated with heterogeneous real-world models, but also simulate the complicated dynamics precisely by tightly coupling these physical properties into simulation. The integration of geometric modeling and material modeling is the key to the success of representation and modeling of real-world objects. The proposed framework has been successfully applied to multiple research areas, such as volume reconstruction and visualization, nonrigid volume registration, and physically based modeling and simulation

Identification of dissociation factors in pancreatic Cancer using a mass spectrometry-based proteomic approach

Backgroud Pancreatic cancer is a highly malignant tumor of the digestive system. This secretome of pancreatic cancer is key to its progression and metastasis. But different methods of protein extraction affect the final results. In other words, the real secretion of proteins in cancer cells has been changed. Based on mass spectrometry, we analyze the secretome from the serum-containing and serum-free medium, using different protein pretreatment methods. This study aims to identify dissociation factors in pancreatic cancer. Methods In this study, pancreatic cancer cells were cultured in serum-containing or serum-free medium, and the corresponding supernatants were extracted as samples. Subsequently, the above samples were separated by size exclusion chromatography (SEC), and peptide segments were identified by LC-MS/MS. The final results were identified via the hamster secreted protein database and a public database. Results Although the number of identified proteins in the serum-free medium group was high, the real secretion of proteins in pancreatic cancer cells was changed. There were six significant secreted proteins in the serum-containing medium group. Survival analysis via the TCGA database suggested that patients with higher expression levels of YWHAG showed a worse overall survival rate than those with lower YWHAG expression. Conclusions Our study demonstrated the results in the serum-containing medium group were more similar to the real secretome of pancreatic cancer cells. YWHAG could be used as a prognostic indicator for pancreatic cancer

Differential secretome of pancreatic cancer cells in serum-containing conditioned medium reveals CCT8 as a new biomarker of pancreatic cancer invasion and metastasis

Background Pancreatic cancer is a malignancy with a very poor prognosis. The emergence of liquid biopsy is expected to achieve accurate early diagnosis through detection of tumor-derived secreted proteins in the blood. Early diagnosis and treatment of pancreatic cancer could help to improve prognosis. Methods The pretreatment approach of samples can have a major effect on downstream analysis. In this study, we used a pair of homologous pancreatic cancer cell supernatants with different capacities for invasion and metastasis to examine secreted proteins in the conditioned media without the removal of fetal bovine serum, namely through size exclusion chromatography combined with high-abundance protein affinity chromatography to enrich low-concentration protein, followed by mass spectrometry using triple dimethyl labeling. Identification of proteins was performed using an online public database and western blot. Results Mass spectrometry data revealed 77 proteins with quantitative properties, of which 12 proteins had over a 1.5-fold difference (in the supernatant of the highly invasive pancreatic cancer cell line PC-1.0, the expression of 8 proteins were increased and the expression of 4 proteins were decreased). Bioinformatics analysis results showed that CCT8, CTSL, SAA1, IGF2 are secreted via the exosome pathway. According to the literature, with the exception of CCT8, the other three proteins can be detected in blood samples of pancreatic cancer patients, and they can be used as prognostic markers. Western blot results were used to validate consistency with MS results. Conclusion This study found that CCT8 can be used as a liquid biopsy marker to assess the prognosis of pancreatic cancer patients

Identification of Coxiella burnetii Type IV Secretion Substrates Required for Intracellular Replication and Coxiella-Containing Vacuole Formation

Coxiella burnetii, the etiological agent of acute and chronic Q fever in humans, is a naturally intracellular pathogen that directs the formation of an acidic Coxiella-containing vacuole (CCV) derived from the host lysosomal network. Central to its pathogenesis is a specialized type IVB secretion system (T4SS) that delivers effectors essential for intracellular replication and CCV formation. Using a bioinformatics-guided approach, 234 T4SS candidate substrates were identified. Expression of each candidate as a TEM-1 β-lactamase fusion protein led to the identification of 53 substrates that were translocated in a Dot/Icm-dependent manner. Ectopic expression in HeLa cells revealed that these substrates trafficked to distinct subcellular sites, including the endoplasmic reticulum, mitochondrion, and nucleus. Expression in Saccharomyces cerevisiae identified several substrates that were capable of interfering with yeast growth, suggesting that these substrates target crucial host processes. To determine if any of these T4SS substrates are necessary for intracellular replication, we isolated 20 clonal T4SS substrate mutants using the Himar1 transposon and transposase. Among these, 10 mutants exhibited defects in intracellular growth and CCV formation in HeLa and J774A.1 cells but displayed normal growth in bacteriological medium. Collectively, these results indicate that C. burnetii encodes a large repertoire of T4SS substrates that play integral roles in host cell subversion and CCV formation and suggest less redundancy in effector function than has been found in the comparative Legionella Dot/Icm model

Comprehensive Identification of Protein Substrates of the Dot/Icm Type IV Transporter of Legionella pneumophila

A large number of proteins transferred by the Legionella pneumophila Dot/Icm system have been identified by various strategies. With no exceptions, these strategies are based on one or more characteristics associated with the tested proteins. Given the high level of diversity exhibited by the identified proteins, it is possible that some substrates have been missed in these screenings. In this study, we took a systematic method to survey the L. pneumophila genome by testing hypothetical orfs larger than 300 base pairs for Dot/Icm-dependent translocation. 798 of the 832 analyzed orfs were successfully fused to the carboxyl end of β-lactamase. The transfer of the fusions into mammalian cells was determined using the β-lactamase reporter substrate CCF4-AM. These efforts led to the identification of 164 proteins positive in translocation. Among these, 70 proteins are novel substrates of the Dot/Icm system. These results brought the total number of experimentally confirmed Dot/Icm substrates to 275. Sequence analysis of the C-termini of these identified proteins revealed that Lpg2844, which contains few features known to be important for Dot/Icm-dependent protein transfer can be translocated at a high efficiency. Thus, our efforts have identified a large number of novel substrates of the Dot/Icm system and have revealed the diverse features recognizable by this protein transporter

Modulation of the host small GTPase Rab1 function by Legionella pneumophila effectors

The vacuolar pathogen Legionella pneumophila utilizes the Dot/Icm apparatus to deliver numerous effectors into the host cytosol where they function to establish a niche permissive for bacterial replication by subverting the host membrane trafficking. Since membrane trafficking events are highly conserved between mammalian cells and the budding yeast Saccharomyces cerevisiae, we performed a yeast-based screen to identify L. pneumophila effectors that modulate the host secretory pathways. This led to the identification of AnkX, which is toxic to yeast and disrupts the host membrane trafficking. Taking advantage of its yeast lethal phenotype, we have identified the N-terminal Fic domain is essential to the function of AnkX. Exemplified by Ypt1, the yeast homologue of the mammalian small GTPase Rab1, several yeast genes involved in vesicle transport could suppress the AnkX mediated yeast toxicity. Mass spectrometry analysis of Rab1 co-expressed with AnkX in yeast revealed that this small GTPase is covalently modified with the phosphorylcholine (PC) moiety at Ser76. In vitro biochemical assay verified that AnkX is a PC transferase that uses CDP-choline as a substrate to target Rab1 in a Fic dependent manner. Phosphorylcholination (PCylation) of Rab1 renders it less accessible to both guanine nucleotide exchange factor (GEF) and GTPase activation protein (GAP). While another bacterial effector Lem3 antagonizes the activity of AnkX by catalyzing the dephosphorylcholination (dePCylation) reaction to remove the PC moiety from Rab1 thereby restoring the normal function of this small GTPase. Together, our results imply that reversible PCylation is a novel virulence strategy used by L. pneumophila to modulate Rab1function. One hallmark during the biogenesis of the Legionella containing vacuole (LCV) is the recruitment of the host small GTPase Rab1 by the coordinated action of several effector proteins. Multifunctional effector SidM activates Rab1 and locks it into an active state with its guanine nucleotide exchange factor (GEF) and AMPylation activities. LepB is a bacterial GTPase activation protein (GAP) which participates in the Rab1 removal process by antagonizing the GEF activity of SidM. However, the inaccessibility of AMPylated Rab1 to LepB indicates the existence of an unknown factor functioning upstream of LepB to deAMPylate Rab1. Here we reported that SidD could suppress the yeast toxicity mediated by SidM. In vitro biochemical analysis and infection data revealed that SidD is a deAMPylase that removes the AMP moiety from Rab1 to facilitate its release from the LCV. Our results suggest that AMPylation is a reversible process controlling by dedicated enzymes. Overall, by studying L. pneumophila effectors targeting the host small GTPase Rab1, my thesis research led to the discovery of three novel post-translational modifications employed by the bacterium to modulate the function of this small GTPase, namely, PCylation, dePCylation and deAMPylation. These findings not only increase our understanding of L. pneumophila pathogenesis but also provide important insight into general host cell biology in that PCylation and AMPylation have been observed in eukaryotic cells under physiological condition. I therefore expect future studies on effector functions in the field of host and pathogen interaction would lead to more and more exciting discoveries with regards to the virulence strategies used by pathogens and the regulatory mechanisms in the eukaryotic cell biology.

VoIP Aggregation in Wireless Backhaul Networks

The newly emerging wireless backhaul network has fundamental difficulties in supporting Voice over IP (VoIP) applications due to the MAC overheads introduced by huge amounts of small packets. Packet aggregation is a promising approach to mitigate these overheads. However, previous approaches to such problems are often stringent, not adaptive to the change of channel conditions. They are operated by each TAP (Transit Access Point) separately without any coordination in the use of shared channels. As a result, they fail to ensure the VoIP quality in terms of delay and loss. The major contribution of this paper is the proposal of a coordinated aggregation algorithm, which is adaptive and distributed. By coordinating with neighboring TAPs, the proposed algorithm is able to assign an appropriate aggregation rate to each TAP, aiming at better channel utilization and lower packet loss and delay. We evaluate this design by comprehensive analysis and simulations. The simulation results show that our algorithm significantly improves the VoIP capacity in wireless backhaul networks and outperforms existing aggregation algorithms