Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

The instability of fluids with time dependent heating

The stability of a fluid having a non-uniform temperature stratification is examined analytically for the response of infinitesimal disturbances. The growth rates of disturbances have been established for a semi-infinite fluid for Rayleigh numbers of 10³, 10⁴, and 10⁵ and for Prandtl numbers of 7.0 and 0.7.

The critical Rayleigh number for a semi-infinite fluid, based on the effective fluid depth, is found to be 32, while it is shown that for a finite fluid layer the critical Rayleigh number depends on the rate of heating. The minimum critical Rayleigh number, based on the depth of a fluid layer, is found to be 1340.

The stability of a finite fluid layer is examined for two special forms of heating. The first is constant flux heating, while in the second, the temperature of the lower surface is increased uniformly in time. In both cases, it is shown that for moderate rates of heating the critical Rayleigh number is reduced, over the value for very slow heating, while for very rapid heating the critical Rayleigh number is greatly increased. These results agree with published experimental observations.

The question of steady, non-cellular convection is given qualitative consideration. It is concluded that, although the motion may originate from infinitesimal disturbances during non-uniform heating, the final flow field is intrinsically non-linear.

Effects of atmosphere visibility on performances of non-line-of-sight ultraviolet communication systems

Dependence of performances of non-line-of-sight (NLOS) solar-blind ultraviolet (UV) communication systems on atmosphere visibility is investigated numerically by correlating the propagation of UV radiation with the visibility. A simplified solar-blind UV atmospheric propagation model is introduced, and the NLOS UV communication system model is constituted based on the single scattering assumption. Using the model, numerical simulation is conducted for two typical geometry configurations and different modulation formats. The results indicate that the performance of the NLOS UV communication system is insensitive to variation of visibility in quite a large range, and deteriorates significantly only in very low-visibility weather, and is also dependent on the geometry configuration of the system. The results also show that the pulse position modulation (PPM) is preferable due to its high-power efficiency to improve the system performance. (c) 2007 Elsevier GmbH. All rights reserved.

Results on proximal and generalized weak proximal contractions including the case of iteration-dependent range sets

This paper presents some further results on proximal and asymptotic proximal contractions and on a class of generalized weak proximal contractions in metric spaces. The generalizations are stated for non-self-mappings of the forms for and , or , subject to and , such that converges uniformly to T, and the distances are iteration-dependent, where , , and are non-empty subsets of X, for , where is a metric space, provided that the set-theoretic limit of the sequences of closed sets and exist as and that the countable infinite unions of the closed sets are closed. The convergence of the sequences in the domain and the image sets of the non-self-mapping, as well as the existence and uniqueness of the best proximity points, are also investigated if the metric space is complete. Two application examples are also given, being concerned, respectively, with the solutions through pseudo-inverses of both compatible and incompatible linear algebraic systems and with the parametrical

Adenylate Cyclase Toxin promotes bacterial internalisation into non phagocytic cells

Bordetella pertussis causes whooping cough, a respiratory infectious disease that is the fifth largest cause of vaccine-preventable death in infants. Though historically considered an extracellular pathogen, this bacterium has been detected both in vitro and in vivo inside phagocytic and non-phagocytic cells. However the precise mechanism used by B. pertussis for cell entry, or the putative bacterial factors involved, are not fully elucidated. Here we find that adenylate cyclase toxin (ACT), one of the important toxins of B. pertussis, is sufficient to promote bacterial internalisation into non-phagocytic cells. After characterization of the entry route we show that uptake of "toxin-coated bacteria" proceeds via a clathrin-independent, caveolae-dependent entry pathway, allowing the internalised bacteria to survive within the cells. Intracellular bacteria were found inside non-acidic endosomes with high sphingomyelin and cholesterol content, or "free" in the cytosol of the invaded cells, suggesting that the ACT-induced bacterial uptake may not proceed through formation of late endolysosomes. Activation of Tyr kinases and toxin-induced Ca2+-influx are essential for the entry process. We hypothesize that B. pertussis might use ACT to activate the endocytic machinery of non-phagocytic cells and gain entry into these cells, in this way evading the host immune system.

Role of transglutaminase-mediated cross-linking of protein in the temperature-dependent setting of Alaska pollack surimi

During the low temperature setting of fish paste, myosin heavy chain (MHC) is polymerized to cross-linked myosin heavy chain (CMHC), which is considered to occur by the action of endogenous transglutaminase (TGase). In this study the contribution of TGase on the setting of Alaska pollack surimi at different temperatures was studied. Alaska pollack surimi was ground with 3% NaCl, 30% h2o and with or without ethylene glycol bis (β-aminoethylether) N, N, N¹,N¹- tetra acetic acid (EGTA), an inhibitor of TGase. Among the pastes without EGTA, highest TGase activity was observed at 25°C but breaking force of the gel set at 25°C was lower than that set at 30°, 35°, and 40°C. Addition of EGTA (5m mol/kg) to the paste suppressed TGase activity at all setting temperatures from 20° to 40°C. Gelation of the pastes and cross-linking of MHC on addition of EGTA were suppressed completely at 20° and 25°C, partially at 30° and 35°C, and not at all at 40°C. The findings suggested that during the setting of Alaska pollack surimi TGase mediated cross-linking of MHC was strong at around 25°C but the thermal aggregation of MHC by non-covalent bonds was strong at above 35°C. Setting of surimi at 40°C and cross-linking of its MHC did not involve TGase.

Acute rejection is associated with antibodies to non-Gal antigens in baboons using Gal-knockout pig kidneys

We transplanted kidneys from alpha 1,3-galactosyltransferase knockout (GalT-KO) pigs into six baboons using two different immunosuppressive regimens, but most of the baboons died from severe acute humoral xenograft rejection. Circulating induced antibodies to non-Gal antigens were markedly elevated at rejection, which mediated strong complement-dependent cytotoxicity against GaIT-KO porcine target cells. These data suggest that antibodies to non-Gal antigens will present an additional barrier to transplantation of organs from GaIT-KO pigs to humans.

Glucocorticoid receptor and protein/RNA synthesis-dependent mechanisms underlie the control of synaptic plasticity by stress

Learning and memory are exquisitely sensitive to behavioral stress, but the underlying mechanisms are still poorly understood. Because activity-dependent persistent changes in synaptic strength are believed to mediate memory processes in brain areas such as the hippocampus we have examined the means by which stress affects synaptic plasticity in the CA1 region of the hippocampus of anesthetized rats, Inescapable behavioral stress (placement on an elevated platform for 30 min) switched the direction of plasticity, favoring low frequency stimulation-induced decreases in synaptic transmission (long-term depression, LTD), and opposing the induction of long-term potentiation by high frequency stimulation, We have discovered that glucocorticoid receptor activation mediates these effects of stress on LTD and longterm potentiation in a protein synthesis-dependent manner because they were prevented by the glucocorticoid receptor antagonist RU 38486 and the protein synthesis inhibitor emetine. Consistent with this, the ability of exogenously applied corticosterone in non-stressed rats to mimic the effects of stress on synaptic plasticity was also blocked by these agents, The enablement of low frequency stimulation-induced LTD by both stress and exogenous corticosterone was also blocked by the transcription inhibitor actinomycin D, Thus, naturally occurring synaptic plasticity is liable to be reversed in stressful situations via glucocorticoid receptor activation and mechanisms dependent on the synthesis of new protein and RNA, This indicates that the modulation of hippocampus-mediated learning by acute inescapable stress requires glucocorticoid receptor-dependent initiation of transcription and translation.

Alternating current loss of second-generation high-temperature superconducting coils with magnetic and non-magnetic substrate

It is widely believed that the second-generation high-temperature superconducting (2G HTS) tapes with magnetic substrates suffer higher transport loss compared to those with non-magnetic substrates. To test this, we prepared two identical coils with magnetic and non-magnetic substrates, respectively. The experimental result was rather surprising that they generated roughly the same amount of transport loss. We used finite element method to understand this result. It is found that, unlike in the single tape where the magnetic field-dependent critical current characteristic can be neglected and the effect of magnetic substrate dominates, the magnetic field-dependent critical current characteristic of 2G tape plays as an equally important role as magnetic substrate in terms of HTS coils. © 2012 American Institute of Physics.

Temperature-Dependent Growth and Life Cycle of Nemoura sichuanensis (Plecoptera: Nemouridae) in a Chinese Mountain Stream

Plecoptera constitute a numerically and ecologically significant component in mountain streams all over the world, but little is known of their life cycles in Asia. The life cycle of Nemoura sichuanensis and its relationship to water temperature was investigated during a 4-year study in a headwater stream (known as the Jiuchong torrent) of the Xiangxi River in Central China. Size structure histograms suggest that the life cycle was univoltine, and the relationships between the growth of Nemoura sichuanensis, physiological time, and effective accumulated water temperature were described using logistic regressions. The growth pattern was generally similar within year classes but growth rates did vary between year-classes. Our field data suggest a critical thermal threshold for emergence in Nemoura sichuanensis, that was close to 9 degrees C. The total number of physiological days required for completing larval development was 250 days. The effective accumulated water temperature was 2500 degree-days in the field. Development during the life cycle increased somewhat linearly with the physiological time and the effective accumulated water temperature, but some non-linear relationships were best developed by logistic equations.

Genomic sequence of mandarin fish rhabdovirus with an unusual small non-transcriptional ORF

The complete genome of mandarin fish Siniperca chuatsi rhabdovirus (SCRV) was cloned and sequenced. It comprises 11,545 nucleotides and contains five genes encoding the nucleoprotein N, the phosphoprotein P, the matrix protein M, the glycoprotein G, and the RNA-dependent RNA polymerase protein L. At the 3' and 5' termini of SCRV genome, leader and trailer sequences show inverse complementarity. The N, P, M and G proteins share the highest sequence identities (ranging from 14.8 to 41.5%) with the respective proteins of rhabdovirus 903/87, the L protein has the highest identity with those of vesiculoviruses, especially with Chandipura virus (44.7%). Phylogenetic analysis of L proteins showed that SCRV clustered with spring vireamia of carp virus (SVCV) and was most closely related to viruses in the genus Vesiculovirus. In addition, an overlapping open reading frame (ORF) predicted to encode a protein similar to vesicular stomatitis virus C protein is present within the P gene of SCRV. Furthermore, an unoverlapping small ORF downstream of M ORF within M gene is predicted (tentatively called orf4). Therefore, the genomic organization of SCRV can be proposed as 3' leader-N-P/C-M-(orf4)-G-L-trailer 5'. Orf4 transcription or translation products could not be detected by northern or Western blot, respectively, though one similar mRNA band to M mRNA was found. This is the first report on one small unoverlapping ORF in M gene of a fish rhabdovirus. (c) 2007 Elsevier B.V. All rights reserved.

Quantum master equation scheme of time-dependent density functional theory to time-dependent transport in nanoelectronic devices

In this work a practical scheme is developed for the first-principles study of time-dependent quantum transport. The basic idea is to combine the transport master equation with the well-known time-dependent density functional theory. The key ingredients of this paper include (i) the partitioning-free initial condition and the consideration of the time-dependent bias voltages which base our treatment on the Runge-Gross existence theorem; (ii) the non-Markovian master equation for the reduced (many-body) central system (i.e., the device); and (iii) the construction of Kohn-Sham master equations for the reduced single-particle density matrix, where a number of auxiliary functions are introduced and their equations of motion (EOMs) are established based on the technique of spectral decomposition. As a result, starting with a well-defined initial state, the time-dependent transport current can be calculated simultaneously along with the propagation of the Kohn-Sham master equation and the EOMs of the auxiliary functions.

Strain gradient theory based on a new framework of non-local model

A new framework of non-local model for the strain energy density is proposed in this paper. The global strain energy density of the representative volume element is treated as a non-local variable and can be obtained through a special integral of the local strain energy density. The local strain energy density is assumed to be dependent on both the strain and the rotation-gradient. As a result of the non-local model, a new strain gradient theory is derived directly, in which the first and second strain gradients, as well as the triadic and tetradic stress, are introduced in the context of work conjugate. For power law hardening materials, size effects in thin metallic wire torsion and ultra-thin cantilever beam bend are investigated. It is found that the result predicted by the theoretical model is well consistent with the experimental data for the thin wire torsion. On the other hand, the calculation result for the micro-cantilever beam bend clearly shows the size effect.

Non-commutative oscillator with Kepler-type dynamical symmetry

A 3-dimensional non-commutative oscillator with no mass term but with an appropriate momentum-dependent potential admits a conserved Runge-Lenz vector, derived from the dual description in momentum space. The trajectories lie on ellipses. The dynamical symmetry allows for an algebraic determination of the bound-state spectrum and extends to o(4,2). (c) 2010 Elsevier B.V. All rights reserved.

Time-dependent DNA condensation induced by amyloid beta-peptide

The major protein component of the amyloid deposition in Alzheimer's disease is a 39-43 residue peptide, amyloid beta (A beta). A beta is toxic to neurons, although the mechanism of neurodegeneration is uncertain. Evidence exists for non-B DNA conformation in the hippocampus of Alzheimer's disease brains, and A beta was reportedly able to transform DNA conformation in vitro. In this study, we found that DNA conformation was altered in the presence of A beta, and A beta induced DNA condensation in a time-dependent manner. Furthermore, A beta sheets, serving as condensation nuclei, were crucial for DNA condensation, and Cu2+ and Zn2+ ions inhibited A beta sheet-induced DNA condensation. Our results suggest DNA condensation as a mechanism of A beta toxicity.