Report - Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State
Contributors: Yoshiki Tanaka, Yasunori Sugano, Mizuki Takemoto, Takaharu Mori, Arata Furukawa, Tsukasa Kusakizako, Kaoru Kumazaki, Ayako Kashima, Ryuichiro Ishitani, Yuji Sugita
... The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal structures of intact SecYEG at 2.7-Å resolution and of peptide-bound SecYEG at 3.6-Å resolution. The higher-resolution structure revealed that the cytoplasmic loop of SecG covers the hourglass-shaped channel, which was confirmed to also occur in the membrane by disulfide bond formation analysis and molecular dynamics simulation. The cytoplasmic loop may be involved in protein translocation. In addition, the previously unknown peptide-bound crystal structure of SecYEG implies that interactions between the cytoplasmic side of SecY and signal peptides are related to lateral gate opening at the first step of protein translocation. These SecYEG structures therefore provide a number of structural insights into the Sec machinery for further study.
Sulphur-cycling bacteria and ciliated protozoans in a Beggiatoaceae mat covering organically enriched sediments beneath a salmon farm in a southern Chilean fjord
Contributors: Carlos P. Aranda, Cristian Valenzuela, Yessica Matamala, Félix A. Godoy, Nicol Aranda
... The colourless mat covering organically enriched sediments underlying an intensive salmon farm in Estero Pichicolo, southern Chile, was surveyed by combined 454 PyroTag and conventional Sanger sequencing of 16S/18S ribosomal RNA genes for Bacteria and Eukarya. The mat was dominated by the sulphide-oxidizing bacteria (SOB) Candidatus Isobeggiatoa, Candidatus Parabeggiatoa and Arcobacter. By order of their abundances, sulphate-reducing bacteria (SRB) were represented by diverse deltaproteobacterial Desulfobacteraceae, but also within Desulfobulbaceae, Desulfuromonadaceae and Desulfovibrionaceae. The eukaryotic PyroTags were dominated by polychaetes, copepods and nematodes, however, ciliated protozoans were highly abundant in microscopy observations, and were represented by the genera Condylostoma, Loxophyllum and Peritromus. Finally, the abundant Sulfurimonas/Sulfurovum also suggest the occurrence of zero-valence sulphur oxidation, probably derived from Beggiatoaceae as a result of bacteriovorus infaunal activity or generated as free S0 by the Arcobacter bacteria. The survey suggests an intense and complex sulphur cycle within the surface of salmon-farm impacted sediments.
Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation
Contributors: Xiaofei Cheng, Ping Deng, Hongguang Cui, Aiming Wang
... Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells.
The V-ATPase accessory protein Atp6ap1b mediates dorsal forerunner cell proliferation and left–right asymmetry in zebrafish
Contributors: Jason J. Gokey, Agnik Dasgupta, Jeffrey D. Amack
... Asymmetric fluid flows generated by motile cilia in a transient ‘organ of asymmetry’ are involved in establishing the left–right (LR) body axis during embryonic development. The vacuolar-type H+-ATPase (V-ATPase) proton pump has been identified as an early factor in the LR pathway that functions prior to cilia, but the role(s) for V-ATPase activity are not fully understood. In the zebrafish embryo, the V-ATPase accessory protein Atp6ap1b is maternally supplied and expressed in dorsal forerunner cells (DFCs) that give rise to the ciliated organ of asymmetry called Kupffer’s vesicle (KV). V-ATPase accessory proteins modulate V-ATPase activity, but little is known about their functions in development. We investigated Atp6ap1b and V-ATPase in KV development using morpholinos, mutants and pharmacological inhibitors. Depletion of both maternal and zygotic atp6ap1b expression reduced KV organ size, altered cilia length and disrupted LR patterning of the embryo. Defects in other ciliated structures—neuromasts and olfactory placodes—suggested a broad role for Atp6ap1b during development of ciliated organs. V-ATPase inhibitor treatments reduced KV size and identified a window of development in which V-ATPase activity is required for proper LR asymmetry. Interfering with Atp6ap1b or V-ATPase function reduced the rate of DFC proliferation, which resulted in fewer ciliated cells incorporating into the KV organ. Analyses of pH and subcellular V-ATPase localizations suggested Atp6ap1b functions to localize the V-ATPase to the plasma membrane where it regulates proton flux and cytoplasmic pH. These results uncover a new role for the V-ATPase accessory protein Atp6ap1b in early development to maintain the proliferation rate of precursor cells needed to construct a ciliated KV organ capable of generating LR asymmetry.
Contributors: Mathilde Flamand, Bastien Herlin, Smaranda Leu-Semenescu, Valérie Attali, Claire Launois, Isabelle Arnulf
... Choking during sleep may be caused by various respiratory and non-respiratory problems.
Contributors: Hisako Takigawa-Imamura, Ritsuko Morita, Takafumi Iwaki, Takashi Tsuji, Kenichi Yoshikawa
... In the early stage of tooth germ development, the bud of the dental epithelium is invaginated by the underlying mesenchyme, resulting in the formation of a cap-like folded shape. This bud-to-cap transition plays a critical role in determining the steric design of the tooth. The epithelial-mesenchymal interaction within a tooth germ is essential for mediating the bud-to-cap transition. Here, we present a theoretical model to describe the autonomous process of the morphological transition, in which we introduce mechanical interactions among cells. Based on our observations, we assumed that peripheral cells of the dental epithelium bound tightly to each other to form an elastic sheet, and mesenchymal cells that covered the tooth germ would restrict its growth. By considering the time-dependent growth of cells, we were able to numerically show that the epithelium within the tooth germ buckled spontaneously, which is reminiscent of the cap-stage form. The difference in growth rates between the peripheral and interior parts of the dental epithelium, together with the steric size of the tooth germ, were determining factors for the number of invaginations. Our theoretical results provide a new hypothesis to explain the histological features of the tooth germ.
Contributors: Markus Koppensteiner, Pia Stephan, Johannes Paul Michael Jäschke
... We collected short video clips of speakers and created five types of stimuli: (1) the original videos, (2) the audio tracks only, (3) single pictures only, (4) speech content, and (5) stick-figure animations displaying body motion. Participants rated these stimuli on a brief Big Five personality inventory. We then used ratings of the incomplete information conditions to predict ratings of the original video condition. Impressions in the audio track condition were strong predictors throughout all trait ratings. However, other cues were also non-negligible contributors to an overall impression. People even make sense of parsimonious cues, e.g., an animated stick-figure. Thus, presenters on a public stage are not only judged by what they say but also by how they move.
Letter to the Editor - Preoperative Echocardiography First Diagnosed and Intraoperative Echocardiography Altered the Surgical Plan in Intravenous Leiomyomatosis
Contributors: Ying-Hsuan Tai, Su-Man Lin, Chiao-Po Hsu, Wen-Chung Yu, Chun-Sung Sung
Absence of Dystrophin Related Protein-2 disrupts Cajal bands in a patient with Charcot–Marie–Tooth disease
Contributors: Kathryn M. Brennan, Yunhong Bai, Chiara Pisciotta, Suola Wang, Shawna M.E. Feely, Mark Hoegger, Laurie Gutmann, Steven A. Moore, Michael Gonzalez, Diane L. Sherman
... Using exome sequencing in an individual with Charcot–Marie–Tooth disease (CMT) we have identified a mutation in the X-linked dystrophin-related protein 2 (DRP2) gene. A 60-year-old gentleman presented to our clinic and underwent clinical, electrophysiological and skin biopsy studies. The patient had clinical features of a length dependent sensorimotor neuropathy with an age of onset of 50 years. Neurophysiology revealed prolonged latencies with intermediate conduction velocities but no conduction block or temporal dispersion. A panel of 23 disease causing genes was sequenced and ultimately was uninformative. Whole exome sequencing revealed a stop mutation in DRP2, c.805C>T (Q269*). DRP2 interacts with periaxin and dystroglycan to form the periaxin–DRP2–dystroglycan complex which plays a role in the maintenance of the well-characterized Cajal bands of myelinating Schwann cells. Skin biopsies from our patient revealed a lack of DRP2 in myelinated dermal nerves by immunofluorescence. Furthermore electron microscopy failed to identify Cajal bands in the patient's dermal myelinated axons in keeping with ultrastructural pathology seen in the Drp2 knockout mouse. Both the electrophysiologic and dermal nerve twig pathology support the interpretation that this patient's DRP2 mutation causes characteristic morphological abnormalities recapitulating the Drp2 knockout model and potentially represents a novel genetic cause of CMT.
Contributors: Alexander Dunkel
... Assessing information on aspects of identification, perception, emotion, and social interaction with respect to the environment is of particular importance to the fields of natural resource management. Our ability to visualize this type of information has rapidly improved with the proliferation of social media sites throughout the Internet in recent years. While many methods to extract information on human behavior from crowdsourced geodata already exist, this paper focuses on visualizing landscape perception for application to the fields of landscape and urban planning. Visualization of peoples’ perceptual responses to landscape is demonstrated with crowdsourced photo geodata from Flickr, a popular photo sharing community. A basic, general method to map, visualize, and evaluate perception and perceptual values is proposed. The approach utilizes common tools for spatial knowledge discovery and builds on existing research, but is specifically designed for implementation within the context of landscape perception analysis and particularly suited as a base for further evaluation in multiple scenarios. To demonstrate the process in application, three novel types of visualizations are presented: the mapping of sightlines in Yosemite Valley, the assessment of landscape change in the area surrounding the High Line in Manhattan, and individual location analysis for Coit Tower in San Francisco. The results suggest that analyzing crowdsourced data may contribute to a more balanced assessment of the perceived landscape, which provides a basis for a better integration of public values into planning processes.