Zebrafish: a vertebrate tool for studying basal body biogenesis, structure, and function.

Understanding the role of basal bodies (BBs) during development and disease has been largely overshadowed by research into the function of the cilium. Although these two organelles are closely associated, they have specific roles to complete for successful cellular development. Appropriate development and function of the BB are fundamental for cilia function. Indeed, there are a growing number of human genetic diseases affecting ciliary development, known collectively as the ciliopathies. Accumulating evidence suggests that BBs establish cell polarity, direct ciliogenesis, and provide docking sites for proteins required within the ciliary axoneme. Major contributions to our knowledge of BB structure and function have been provided by studies in flagellated or ciliated unicellular eukaryotic organisms, specifically Tetrahymena and Chlamydomonas. Reproducing these and other findings in vertebrates has required animal in vivo models. Zebrafish have fast become one of the primary organisms of choice for modeling vertebrate functional genetics. Rapid ex-utero development, proficient egg laying, ease of genetic manipulation, and affordability make zebrafish an attractive vertebrate research tool. Furthermore, zebrafish share over 80 % of disease causing genes with humans. In this article, we discuss the merits of using zebrafish to study BB functional genetics, review current knowledge of zebrafish BB ultrastructure and mechanisms of function, and consider the outlook for future zebrafish-based BB studies

A CEP104-CSPP1 Complex Is Required for Formation of Primary Cilia Competent in Hedgehog Signaling

CEP104 is an evolutionarily conserved centrosomal and ciliary tip protein. CEP104 loss-of-function mutations are reported in patients with Joubert syndrome, but their function in the etiology of ciliopathies is poorly understood. Here, we show that cep104 silencing in zebrafish causes cilia-related manifestations: shortened cilia in Kupffer's vesicle, heart laterality, and cranial nerve development defects. We show that another Joubert syndrome-associated cilia tip protein, CSPP1, interacts with CEP104 at microtubules for the regulation of axoneme length. We demonstrate in human telomerase reverse transcriptase-immortalized retinal pigmented epithelium (hTERT-RPE1) cells that ciliary translocation of Smoothened in response to Hedgehog pathway stimulation is both CEP104 and CSPP1 dependent. However, CEP104 is not required for the ciliary recruitment of CSPP1, indicating that an intra-ciliary CEP104-CSPP1 complex controls axoneme length and Hedgehog signaling competence. Our in vivo and in vitro analyses of CEP104 define its interaction with CSPP1 as a requirement for the formation of Hedgehog signaling-competent cilia, defects that underlie Joubert syndrome

Dynamic remodeling of the plastid envelope membranes - a tool for chloroplast envelope in vivo localizations

Breuers FKH, Bräutigam A, Geimer S, et al. Dynamic remodeling of the plastid envelope membranes - a tool for chloroplast envelope in vivo localizations. Frontiers in Plant Science. 2012;3: 7.Two envelope membranes delimit plastids, the defining organelles of plant cells. The inner and outer envelope membranes are unique in their protein and lipid composition. Several studies have attempted to establish the proteome of these two membranes; however, differentiating between them is difficult due to their close proximity. Here, we describe a novel approach to distinguish the localization of proteins between the two membranes using a straightforward approach based on live cell imaging coupled with transient expression. We base our approach on analyses of the distribution of GFP-fusions, which were aimed to verify outer envelope membrane proteomics data. To distinguish between outer envelope and inner envelope protein localization, we used AtTOC64-GFP and AtTIC40-GFP, as respective controls. During our analyses, we observed membrane proliferations and loss of chloroplast shape in conditions of protein over-expression. The morphology of the proliferations varied in correlation with the suborganellar distribution of the over-expressed proteins. In particular, while layers of membranes built up in the inner envelope membrane, the outer envelope formed long extensions into the cytosol. Using electron microscopy, we showed that these extensions were stromules, a dynamic feature of plastids. Since the behavior of the membranes is different and is related to the protein localization, we propose that in vivo studies based on the analysis of morphological differences of the membranes can be used to distinguish between inner and outer envelope localizations of proteins. To demonstrate the applicability of this approach, we demonstrated the localization of AtLACS9 to the outer envelope membrane. We also discuss protein impact on membrane behavior and regulation of protein insertion into membranes, and provide new hypotheses on the formation of stromules

Preparation and Evaluation of Rice Bran-Modified Urea Formaldehyde as Environmental Friendly Wood Adhesive

In this study, defatted rice bran (RB) is used to prepare an environmentally friendly adhesive through chemical modifications. The RB is mixed with distilled water with ratios of 1:5 and 1:4 to prepare Type A and Type B adhesives, respectively having pH of 6, 8 and 10. Type A adhesive is prepared by treating RB with 1% potassium permanganate and 4% poly(vinyl alcohol), whereas Type B is formulated by adding 17.3% formaldehyde and 5.7% urea to RB. Viscosity, gel time, solid content, shear strength, Fourier transform infrared (FTIR) spectroscopy is carried out, and glass transition temperature (T-g), and activation energy (E-a) are determined to evaluate the performance of the adhesives. E-a data reveal that adhesives prepared at mild alkaline (pH 8) form long-chain polymers. Gel time is higher in the fabricated adhesives than that of the commercial urea formaldehyde (UF). FTIR data suggest that functional groups of the raw RB are chemically modified, which enhances the bondability of the adhesives. Shear strength data indicates that bonding strength increases with increasing pH. Similar results are also observed for physical and mechanical properties of fabricated particleboards with the adhesives. The results demonstrate that RB-based adhesives can be used as a potential alternative to currently used UF-based resin

Measurement of polarization transfer in the quasi-elastic 40Ca(e⃗,e′p⃗)^{40}{\rm Ca}(\vec{e},e' \vec{p}) process

Polarization transfer to a bound proton in polarized electron knock-out reactions, $\mathrm{A}(\vec{e},e^{\prime}\vec{p})$, is a powerful tool to look for in-medium modification of the bound proton. It requires comparison to calculations which consider the many-body effects accompanying the quasi-free process. We report here measured components $P_x^{\prime}$, $P_z^{\prime}$, and their ratio $P_x^{\prime}/P_z^{\prime}$, of polarization transfer to protons bound in $^{40}\mathrm{Ca}$, which is described well by the shell model and for which reliable calculations are available. While the calculations capture the essence of the data, our statistical precision allows us to observe deviations which cannot be explained by simple scaling, including by varying the proton electromagnetic form factor ratio $G_E/G_M$. We further explore the deviations of the ratio of the polarization transfer components from that of a free proton, $(P_x^{\prime}/P_z^{\prime})_{\rm A}/(P_x^{\prime}/P_z^{\prime})_{\rm H}$, and its dependence on the bound-proton virtuality

The Plastid Genome of Eutreptiella Provides a Window into the Process of Secondary Endosymbiosis of Plastid in Euglenids

Euglenids are a group of protists that comprises species with diverse feeding modes. One distinct and diversified clade of euglenids is photoautotrophic, and its members bear green secondary plastids. In this paper we present the plastid genome of the euglenid Eutreptiella, which we assembled from 454 sequencing of Eutreptiella gDNA. Comparison of this genome and the only other available plastid genomes of photosynthetic euglenid, Euglena gracilis, revealed that they contain a virtually identical set of 57 protein coding genes, 24 genes fewer than the genome of Pyramimonas parkeae, the closest extant algal relative of the euglenid plastid. Searching within the transcriptomes of Euglena and Eutreptiella showed that 6 of the missing genes were transferred to the nucleus of the euglenid host while 18 have been probably lost completely. Euglena and Eutreptiella represent the deepest bifurcation in the photosynthetic clade, and therefore all these gene transfers and losses must have happened before the last common ancestor of all known photosynthetic euglenids. After the split of Euglena and Eutreptiella only one additional gene loss took place. The conservation of gene content in the two lineages of euglenids is in contrast to the variability of gene order and intron counts, which diversified dramatically. Our results show that the early secondary plastid of euglenids was much more susceptible to gene losses and endosymbiotic gene transfers than the established plastid, which is surprisingly resistant to changes in gene content

Nuclear density dependence of polarization transfer in quasi-elastic A(e⃗,e′p⃗){\rm A}(\vec{e},e' \vec{p}) reactions

The ratio of the transverse and longitudinal component of polarization transfer to protons in quasi-elastic $(\vec{e}, e^{\prime} \vec{p}\,)$ reaction, $P^{\prime}_x/P^{\prime}_z$, is sensitive to the proton's electromagnetic form factor ratio, $G_E/G_M$. To explore density-dependent in-medium modifications, a comparison of polarization transfer ratios involving protons from distinct nuclear shells, each with different local nuclear densities, has been proposed. In this study, we present such comparisons between four shells, $1s_{1/2}$, $1p_{3/2}$ in $^{12}\mathrm{C}$ and $1d_{3/2}$, $2s_{1/2}$ in $^{40}\mathrm{Ca}$. In an effort to account for other many-body effects that may differ between shells, we use state-of-the-art relativistic distorted-wave impulse-approximation (RDWIA) calculation and present the double ratios, $(P^{\prime}_x/P^{\prime}_z)_{\rm Data}/(P^{\prime}_x/P^{\prime}_z)_{\rm RDWIA}$ as well as the super ratios, $\left[(P^{\prime}_x/P^{\prime}_z)_{\rm A}/(P^{\prime}_x/P^{\prime}_z)_{\rm B}\right]_{\rm Data}/\left[(P^{\prime}_x/P^{\prime}_z)_{\rm A}/(P^{\prime}_x/P^{\prime}_z)_{\rm B}\right]_{\rm RDWIA}$, for chosen shells A and B, as a function of effective local nuclear densities. We find that double ratios for individual shells show a dependence on the probed effective nuclear densities. Studying the ratios, we observed a systematic variation between pairs of higher- and lower-density shells

Erosion and illegibility of images: ‘beyond the immediacy of the present’

The focus of this special journal issue ‘Erosion and Illegibility of Images’ is to explore the relationship of erosion and visibility through contemporary artistic practices at a moment when everything, as Latour suggests, is smashed to pieces. The essays in this issue deploy the notion of erosion as a conceptual tool in order to explore the shifting and depositing of materials, which is observed both on a formal visual level (the breaking up of the image surface) and a critical revaluation of memory, visibility and artistic tools. From an instrumentalist understanding of tools and material, I set out to explore the impact of a radical restriction and limitation of traditional skills and craftsmanship on the artistic process. While recent research has focused predominantly on art theoretical understandings of ruins, the articles collected here aim to interrogate the relationship between artists, artistic tools and the materials of production in contemporary artistic practice by putting them in conversation with each other and scrutinizing interventions such as ‘preservation’, remaking, retro-recuperations and nostalgia work of several kinds