Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation

Intraflagellar transport (IFT), the bi-directional movement of particles along the length of flagella, is required for flagellar assembly. The IFT particles are moved by kinesin II from the base to the tip of the flagellum, where flagellar assembly occurs. The IFT particles are then moved in the retrograde direction by cytoplasmic dynein 1b/2 to the base of the flagellum. The IFT particles of Chlamydomonas are composed of ~16 proteins, organized into complexes A and B. Alhough IFT is believed to transport cargoes into flagella, few cargoes have been identified and little is known about how the cargos are transported. To study the mechanism of IFT and how IFT is involved in flagellar assembly, this thesis focuses on two questions. 1) In addition to a heavy chain, DHC1b, and a light chain, LC8, what other proteins are responsible for the retrograde movement of IFT particles? 2) What is the specific function of an individual IFT-particle protein? To address these two questions, I screened for Chlamydomonas mutants either defective in retrograde IFT by immunofluorescence microscopy, or defective in IFT-particle proteins and D1bLIC, a dynein light intermediate chain possibly involved in retrograde IFT, by Southern blotting. I identified several mutants defective in retrograde IFT and one of them is defective in the D1bLIC gene. I also identified several mutants defective in several IFT-particle protein genes. I then focused on the mutant defective in D1bLIC and the one defective in IFT46, which was briefly reported as an IFT complex B protein. My results show that as a subunit of the retrograde IFT motor, D1bLIC is required for the stability of DHC1b and is involved in the attachment of IFT particles to the retrograde motor. The P-loop in D1bLIC is not necessary for the function of D1bLIC in retrograde IFT. My results also show that as a complex B protein, IFT46 is necessary for complex B stability and is required for the transport of outer dynein arms into flagella. IFT46 is phosphorylated in vivo and the phosphorylation is not critical for IFT46’s function in flagellar assembly

The N-terminus of IFT46 mediates intraflagellar transport of outer arm dynein and its cargo-adaptor ODA16

Cilia are assembled via intraflagellar transport (IFT). The IFT machinery is composed of motors and multi-subunit particles, termed IFT-A and IFT-B, that carry cargo into the cilium. Knowledge of how the IFT subunits interact with their cargo is of critical importance for understanding how the unique ciliary domain is established. We previously reported a Chlamydomonas mutant, ift46-1, that fails to express the IFT-B protein IFT46, has greatly reduced levels of other IFT-B proteins, and assembles only very short flagella. A spontaneous suppression of ift46-1 restored IFT-B levels and enabled growth of longer flagella, but the flagella lacked outer dynein arms. Here, we show that the suppression is due to insertion of the transposon MRC1 into the ift46-1 allele, causing the expression of a fusion protein including the IFT46 C-terminal 240 amino acids. The IFT46 C-terminus can assemble into and stabilize IFT-B, but does not support transport of outer arm dynein into flagella. ODA16, a cargo adaptor specific for outer arm dynein, also fails to be imported into the flagella in the absence of the IFT46 N-terminus. We conclude that IFT46, ODA16, and the outer dynein arm interact for IFT of the latter

TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions

Proteome of the central apparatus of a ciliary axoneme

Nearly all motile cilia have a 9+2 axoneme containing a central apparatus (CA), consisting of two central microtubules with projections, that is essential for motility. To date, only 22 proteins are known to be CA components. To identify new candidate CA proteins, we used mass spectrometry to compare axonemes of wild-type Chlamydomonas and a CA-less mutant. We identified 44 novel candidate CA proteins, of which 13 are conserved in humans. Five of the latter were studied more closely, and all five localized to the CA; therefore, most of the other candidates are likely to also be CA components. Our results reveal that the CA is far more compositionally complex than previously recognized and provide a greatly expanded knowledge base for studies to understand the architecture of the CA and how it functions. The discovery of the new conserved CA proteins will facilitate genetic screening to identify patients with a form of primary ciliary dyskinesia that has been difficult to diagnose

A dynamic simulation model for financing strategy management of infrastructure PPP projects

Strategic management is vital for significant infrastructure public-private partnership (PPP) projects characterised by a heavy and irreversible investment over a long period. In PPP projects, the financing strategy relates to the capital structure of the project and the coordination of the participants’ requirements. In this paper, a system dynamics (SD) model is described to analyse the impacts of two types of financing strategies on the needs of creditors, the government, and private investors, considering the dynamic and complex characteristics of infrastructure PPP projects. The proposed model has been implemented on a PPP highway project. A number of experiments were conducted over a 33-year strategic planning horizon as a means of assessing the long-term effects of different financing strategies. The experimental results reveal that the model is a useful tool that could support decision-makers in identifying the intervals with different management focus of financing risk and comparing different financing strategies to choose the optimal one. It is especially helpful for the government to select a financing strategy for infrastructure PPP projects with capital limitations

A microtubule-dynein tethering complex regulates the axonemal inner dynein f (I1)

Motility of cilia/flagella is generated by a coordinated activity of thousands of dyneins. Inner dynein arms (IDAs) are particularly important for the formation of ciliary/flagellar waveforms, but the molecular mechanism of IDA regulation is poorly understood. Here, we show using cryo-electron tomography and biochemical analyses of Chlamydomonas flagella that a conserved protein FAP44 forms a complex that tethers IDA f (I1 dynein) head domains to the A-tubule of the axonemal outer doublet microtubule. In wild-type flagella, IDA f showed little nucleotide-dependent movement except for a tilt in the fbeta head perpendicular to the microtubule-sliding direction. In the absence of the tether complex, however, addition of ATP and vanadate caused a large conformational change in the IDA f head domains, suggesting that the movement of IDA f is mechanically restricted by the tether complex. Motility defects in flagella missing the tether demonstrates the importance of the IDA f-tether interaction in the regulation of ciliary/flagellar beating

Locus coeruleus in the pathogenesis of Alzheimer's disease: A systematic review.

The locus coeruleus (LC) is a nucleus in the brain stem producing noradrenaline. While cognitive decline in Alzheimer's disease (AD) has primarily been related to cholinergic depletion, evidence indicates extensive LC degeneration as its earliest pathological marker. The current study aimed to systematically evaluate current evidence investigating the role of the LC in the pathogenesis of AD. A systematic search of the literature was performed on electronic databases including PubMed and Web of Science. Twelve animal, human post mortem, and human imaging studies were included in this review. Screening, data extraction, and quality assessment were undertaken following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for preferred reporting of systematic reviews. Significant associations were identified between LC changes and cognitive decline. Significant reductions in fiber density, neuronal number, and LC volume were seen to correlate with other pathological degenerative markers. Current evidence indicates an important role of the LC in pathogenesis of AD and suggests its potential in both diagnosis and treatment of AD. This systematic review advances our understanding of the role of the LC in AD by synthesizing available evidence, identifying research gaps, highlighting methodological challenges, and making recommendations for future work

Locus coeruleus in the pathogenesis of Alzheimer's disease: A systematic review.

The locus coeruleus (LC) is a nucleus in the brain stem producing noradrenaline. While cognitive decline in Alzheimer's disease (AD) has primarily been related to cholinergic depletion, evidence indicates extensive LC degeneration as its earliest pathological marker. The current study aimed to systematically evaluate current evidence investigating the role of the LC in the pathogenesis of AD. A systematic search of the literature was performed on electronic databases including PubMed and Web of Science. Twelve animal, human post mortem, and human imaging studies were included in this review. Screening, data extraction, and quality assessment were undertaken following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for preferred reporting of systematic reviews. Significant associations were identified between LC changes and cognitive decline. Significant reductions in fiber density, neuronal number, and LC volume were seen to correlate with other pathological degenerative markers. Current evidence indicates an important role of the LC in pathogenesis of AD and suggests its potential in both diagnosis and treatment of AD. This systematic review advances our understanding of the role of the LC in AD by synthesizing available evidence, identifying research gaps, highlighting methodological challenges, and making recommendations for future work