Doctor of Philosophy

dissertationLysophosphatidic acid (LPA, 1- or 2-radyl-sn-glycerol 3-phosphate) is an important phospholipid, which elicits growth-factor-like effects in a number of cell types through cell surface G protein-coupled receptors (GPCRs). Extracellularly, the sole source of LPA is from the hydrolysis of lysophosphatidylcholine (LPC) by a secreted enzyme Autotaxin (ATX) through its lysophospholipase D activity. Due to exhibition of common features of the phosphodiesterase family, ATX was included as the second member of the nucleotide pyrophosphatase/phosphodiesterase (NPP) family. The emergence of ATX-LPA receptor axis has encouraged researchers to develop novel therapies for the prevention and treatment of cancer and other diseases. In order to study the precise physiological roles of each LPA receptors and ATX, I synthesized a set of LPA and LPC analogues as either ATX inhibitors or LPA receptor agonists/antagonists. Specific modifications in this thesis include optimization of the polar phosphonate head of LPA to phosphorothioate, restriction of glycerol backbone of LPA to phenyl ring and change of phosphonate head to vinyl sulfone in LPC molecule. All these analogues were tested in either in vitro or in vivo assays through external collaborations. One interesting result includes the identification of sn-2 radyl phosphorothioate analogues of LPA (sn-2 OMPT) as the most potent LPA5 receptor agonists. Furthermore, aromatic phosphonate analogues of LPA displayed very potent ATX inhibition. An in vivo study revealed that one of aromatic phosphonate analogues significantly reduced pulmonary fibrosis induced by bleomycin. In addition, fluorophosphonate and vinyl sulfone analogues of LPC were designed as activity-based probe (ABP) for selected enzymes of the NPP family. The study indicated that fluorophosphonate analogues cannot serve as ABP due to its high reactivity. In contrast, vinyl sulfone ABP analogues of LPC showed good inhibition of ATX. Meanwhile, the kinetics and dialysis suggested that vinyl sulfone analogues were irreversible inhibitors of ATX. We are still working on finding further evidence for irreversible inhibition

Six Thallus Surface Types of Coralline Algae with Descriptions of Two New Records of Amphiroa beauvoisii and Neogoniolithon setchellii in Sanya reef, China

Coralline algae are globally distributed calcifying species and play critical ecological roles to marine ecosystems by contributing significantly to their structural complexity and diversity. Thallus surface types of historical samples in Sanya coral reef reserve were studied based on the scanning electron microscope (SEM) method. Our results show six thallus surface types within the study area: Corallina-type, Jania-type, Leptophytum-type, Phymatolithon-type, Pneophyllum-type, and Spongites-type. The Phymatolithon-type is the dominant surface type in Sanya reefs. Two new record species in the region are described: Amphiroa beauvoisii and Neogoniolithon setchellii. Although thallus surface types provide useful diagnostics characters for distinguishing coralline algae at tribe or subfamily level, species identification needs to refer to the reproductive features. This is the first surface study of coralline algae in the South China Sea. This result provides the baseline data needed for the monitoring and management of reef-building organisms of coral reef in China

Responses of soil respiration and its temperature/moisture sensitivity to precipitation in three subtropical forests in southern China

Both long-term observation data and model simulations suggest an increasing chance of serious drought in the dry season and extreme flood in the wet season in southern China, yet little is known about how changes in precipitation pattern will affect soil respiration in the region. We conducted a field experiment to study the responses of soil respiration to precipitation manipulations – precipitation exclusion to mimic drought, double precipitation to simulate flood, and ambient precipitation as control (abbr. EP, DP and AP, respectively) – in three subtropical forests in southern China. The three forest sites include Masson pine forest (PF), coniferous and broad-leaved mixed forest (MF) and monsoon evergreen broad-leaved forest (BF). Our observations showed that altered precipitation strongly influenced soil respiration, not only through the well-known direct effects of soil moisture on plant and microbial activities, but also by modification of both moisture and temperature sensitivity of soil respiration. In the dry season, soil respiration and its temperature sensitivity, as well as fine root and soil microbial biomass, showed rising trends with precipitation increases in the three forest sites. Contrarily, the moisture sensitivity of soil respiration decreased with precipitation increases. In the wet season, different treatments showed different effects in three forest sites. The EP treatment decreased fine root biomass, soil microbial biomass, soil respiration and its temperature sensitivity, but enhanced soil moisture sensitivity in all three forest sites. The DP treatment significantly increased soil respiration, fine root and soil microbial biomass in the PF only, and no significant change was found for the soil temperature sensitivity. However, the DP treatment in the MF and BF reduced soil temperature sensitivity significantly in the wet season. Our results indicated that soil respiration would decrease in the three subtropical forests if soil moisture continues to decrease in the future. More rainfall in the wet season could have limited effect on the response of soil respiration to the rising of temperature in the BF and MF

Adversarial Examples with Unlimited Amount of Additions

Malware detection methods based on gray images and deep learning have the characteristics of high detection accuracy and no need of feature engineering. Unfortunately, adversarial examples (AEs) can deceive such detection methods. However, it is difficult to reduce the detection accuracy of this kind of detection method greatly without destroying the functional integrity of the original file. By analyzing the structure and loading mechanism of portable executable (PE) files, this paper proposes an unrestricted add-amount bytecode attack (BAUAA). BAUAA generates adversarial samples by adding bytecode to a “section additional space” in the PE file that is scattered after each section and is not loaded into memory, and because of the unlimited amount of this space that can be added, the generated adversarial samples can be transformed into grayscale images that vary in size and texture, which can affect the discrimination accuracy of gray images and deep learning-based malware detection methods. The experimental results show that the detection accuracy of the malware detection method based on gray images and deep learning for the AEs generated by BAUAA is significantly lower than that for the non-AEs. To avoid the abuse of BAUAA in reality, it proposes a targeted AE detection method

Establish an allele-specific real-time PCR for Leishmania species identification

Background: Leishmaniasis is a serious neglected tropical disease that may lead to life-threatening outcome, which species are closely related to clinical diagnosis and patient management. The current Leishmania species determination method is not appropriate for clinical application. New Leishmania species identification tool is needed using clinical samples directly without isolation and cultivation of parasites. Methods: A probe-based allele-specific real-time PCR assay was established for Leishmania species identification between Leishmania donovani and L. infantum for visceral leishmaniasis (VL) and among L. major, L. tropica and L. donovani/L. infantum for cutaneous leishmaniasis (CL), targeting hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and spermidine synthase (SPDSYN) gene with their species-specific single nucleotide polymorphisms (SNPs). The limit of detection of this assay was evaluated based on 8 repeated tests with intra-assay standard deviation < 0.5 and inter-assay coefficients of variability < 5%. The specificity of this assay was tested with DNA samples obtained from Plasmodium falciparum, Toxoplasma gondii, Brucella melitensis and Orientia tsutsugamushi. Total 42 clinical specimens were used to evaluate the ability of this assay for Leishmania species identification. The phylogenetic tree was constructed using HGPRT and SPDSYN gene fragments to validate the performance of this assay. Results: This new method was able to detect 3 and 12 parasites/reaction for VL and CL respectively, and exhibited no cross-reaction with P. falciparum, T. gondii, B. melitensis, O. tsutsugamushi and non-target species of Leishmania. Twenty-two samples from VL patients were identified as L. donovani (n = 3) and L. infantum (n = 19), and 20 specimens from CL patients were identified as L. major (n = 20), providing an agreement of 100% compared with sequencing results. For further validation, 29 sequences of HGPRT fragment from nine Leishmania species and 22 sequences from VL patients were used for phylogenetic analysis, which agreed with the results of this new method. Similar results were obtained with 43 sequences of SPDSYN fragment from 18 Leishmania species and 20 sequences from CL patients. Conclusions: Our assay provides a rapid and accurate tool for Leishmania species identification which is applicable for species-adapted therapeutic schedule and patient management. Graphical Abstract

Short-term prediction of PV output based on weather classification and SSA-ELM

In this paper, according to the power output characteristics of distributed photovoltaic users, the SSA-ELM (Sparrow Search Algorithm - Extreme Learning Machine) model based on weather type division is proposed for photovoltaic power day ahead prediction. Because the solar panel power generation sequence of photovoltaic users contains high frequency fluctuations, in this paper we use the power sequence convergence effect to make cluster prediction on all photovoltaic panels to reduce the randomness of distributed photovoltaic. The prediction accuracy is further improved by dividing weather types. The historical data of distributed PV users in a region of Gansu province is used for modeling verification, and the results show that the prediction error of the proposed method is lower. In bad weather, the root mean square error is at least 0.02 less than the comparison model, and the average annual accuracy rate is 93.2%, which proves the applicability of the proposed method in different output types

Immunoglobulin G Locus Events in Soft Tissue Sarcoma Cell Lines

Recently immunoglobulins (Igs) have been found to be expressed by cells other than B lymphocytes, including various human carcinoma cells. Sarcomas are derived from mesenchyme, and the knowledge about the occurrence of Ig production in sarcoma cells is very limited. Here we investigated the phenomenon of immunoglobulin G (IgG) expression and its molecular basis in 3 sarcoma cell lines. The mRNA transcripts of IgG heavy chain and kappa light chain were detected by RT-PCR. In addition, the expression of IgG proteins was confirmed by Western blot and immunofluorescence. Immuno-electron microscopy localized IgG to the cell membrane and rough endoplasmic reticulum. The essential enzymes required for gene rearrangement and class switch recombination, and IgG germ-line transcripts were also identified in these sarcoma cells. Chromatin immunoprecipitation results demonstrated histone H3 acetylation of both the recombination activating gene and Ig heavy chain regulatory elements. Collectively, these results confirmed IgG expression in sarcoma cells, the mechanism of which is very similar to that regulating IgG expression in B lymphocytes

Dynamical Jumping Real-Time Fault-Tolerant Routing Protocol for Wireless Sensor Networks

In time-critical wireless sensor network (WSN) applications, a high degree of reliability is commonly required. A dynamical jumping real-time fault-tolerant routing protocol (DMRF) is proposed in this paper. Each node utilizes the remaining transmission time of the data packets and the state of the forwarding candidate node set to dynamically choose the next hop. Once node failure, network congestion or void region occurs, the transmission mode will switch to jumping transmission mode, which can reduce the transmission time delay, guaranteeing the data packets to be sent to the destination node within the specified time limit. By using feedback mechanism, each node dynamically adjusts the jumping probabilities to increase the ratio of successful transmission. Simulation results show that DMRF can not only efficiently reduce the effects of failure nodes, congestion and void region, but also yield higher ratio of successful transmission, smaller transmission delay and reduced number of control packets.Comment: 22 pages, 9 figure

Robust Interfacial Exchange Bias and Metal-Insulator Transition Influenced by the LaNiO3 Layer Thickness in La0.7Sr0.3MnO3/LaNiO3 Superlattices

Artificial heterostructures based on LaNiO3 (LNO) have been widely investigated with the aim to realize the insulating antiferromagnetic state of LNO. In this work, we grew [(La0.7Sr0.3MnO3)5-(LaNiO3)n]12 superlattices on (001)-oriented SrTiO3 substrates by pulsed laser deposition and observed an unexpected exchange bias effect in field-cooled hysteresis loops. Through X-ray absorption spectroscopy and magnetic circular dichroism experiments, we found that the charge transfer at the interfacial Mn and Ni ions can induce a localized magnetic moment. A remarkable increase of exchange bias field and a transition from metal to insulator were simultaneously observed upon decreasing the thickness of the LNO layer, indicating the antiferromagnetic insulator state in 2 unit cells LNO ultrathin layers. The robust exchange bias of 745 Oe in the superlattice is caused by an interfacial localized magnetic moment and an antiferromagnetic state in the ultrathin LNO layer, pinning the ferromagnetic La0.7Sr0.3MnO3 layers together. Our results demonstrate that artificial interface engineering is a useful method to realize novel magnetic and transport properties