Nanoimaging for protein misfolding and related diseases

Misfolding and aggregation of proteins is a common thread linking a number of important human health problems. The misfolded and aggregated proteins are inducers of cellular stress and activators of immunity in neurodegenerative diseases. They might possess clear cytotoxic properties, being responsible for the dysfunction and loss of cells in the affected organs. Despite the crucial importance of protein misfolding and abnormal interactions, very little is currently known about the molecular mechanism underlying these processes. Factors that lead to protein misfolding and aggregation in vitro are poorly understood, not to mention the complexities involved in the formation of protein nanoparticles with different morphologies (e.g., the nanopores) in vivo. A better understanding of the molecular mechanisms of misfolding and aggregation might facilitate development of the rational approaches to prevent pathologies mediated by protein misfolding. The conventional tools currently available to researchers can only provide an averaged picture of a living system, whereas much of the subtle or short-lived information is lost. We believe that the existing and emerging nanotools might help solving these problems by opening the entirely novel pathways for the development of early diagnostic and therapeutic approaches. This article summarizes recent advances of the nanoscience in detection and characterization of misfolded protein conformations. Based on these findings, we outline our view on the nanoscience development towards identification intracellular nanomachines and/or multicomponent complexes critically involved in protein misfolding.     

Structure of Three-Way DNA Junctions 1. Non-Planar DNA Geometry

Abstract

Three-way junctions were obtained by annealing two synthetic DNA-oligomers. One of the strands contains a short palindrome sequence, leading to the formation of a hairpin with four base pairs in the stem and four bases in the loop. Another strand is complementary to the linear arms of the first hairpin-containing strand. Both strands were annealed to form a three-way branched structure with sticky ends on the linear arms. The branched molecules were ligated, and the ligation mixture was analysed on a two-dimensional gel in conditions which separated linear and circular molecules. Analysis of 2D-electrophoresis data shows that circular molecules with high mobility are formed. Formation of circular molecules is indicative of bends between linear arms. We estimate the magnitude of the angle between linear arms from the predominant size of the circular molecules formed. When the junction-to-junction distance is 20–21 bp, trimers and tetramers are formed predominately, giving an angle between linear arms as small as 60–90°. Rotation of the hairpin position in the three- way junction allowed us to measure angles between other arms, yielding similar values. These results led us to conclude that the three-way DNA junction possesses a non-planar pyramidal geometry with 60–90° between the arms. Computer modeling of the three-way junction with 60° pyramidal geometry showed a predominantly B-form structure with local distortions at the junction points that diminish towards the ends of the helices. The size distributions of circular molecules are rather broad indicating a dynamic flexibility of three-way DNA junctions.     

Vertical stratification of an avian community in New Guinean tropical rainforest

Vertical stratification of avian communities has been studied in both temperate and tropical forests; however, the majority of studies used ground-based methods. In this study we used ground-to-canopy mist nets to collect detailed data on vertical bird distribution in primary rain forest in Wanang Conservation Area in Papua New Guinea (Madang Province). In total 850 birds from 86 species were caught. Bird abundance was highest in the canopy followed by the understory and lowest in the midstory. Overall bird diversity increased towards the canopy zone. Insectivorous birds represented the most abundant and species-rich trophic guild and their abundances decreased from the ground to canopy. The highest diversity of frugivorous and omnivorous birds was confined to higher vertical strata. Insectivorous birds did not show any pattern of diversity along the vertical gradient. Further, insectivores preferred strata with thick vegetation, while abundance and diversity of frugivores increased with decreasing foliage density. Our ground-to-canopy (0–27 m) mist netting, when compared to standard ground mist netting (0–3 m), greatly improved bird diversity assessment and revealed interesting patterns of avian community stratification along vertical forest strata.     

Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants

Cellular and Molecular Neurobiology - The opioid receptor (OPR) family comprises the mu-, delta-, and kappa-opioid, and nociceptin receptors that belong to the superfamily of 7-transmembrane...     

Structural basis for μ-opioid receptor binding and activation

Opioids that stimulate the μ-opioid receptor (MOR1) are the most frequently prescribed and effective analgesics. Here we present a structural model of MOR1. Molecular dynamics simulations show a ligand-dependent increase in the conformational flexibility of the third intracellular loop that couples with the G protein complex. These simulations likewise identified residues that form frequent contacts with ligands. We validated the binding residues using site-directed mutagenesis coupled with radioligand binding and functional assays. The model was used to blindly screen a library of ～1.2 million compounds. From the 34 compounds predicted to be strong binders, the top three candidates were examined using biochemical assays. One compound showed high efficacy and potency. Post hoc testing revealed this compound to be nalmefene, a potent clinically used antagonist, thus further validating the model. In summary, the MOR1 model provides a tool for elucidating the structural mechanism of ligand-initiated cell signaling and for screening novel analgesics.     

Construction of a Global Pain Systems Network Highlights Phospholipid Signaling as a Regulator of Heat Nociception

The ability to perceive noxious stimuli is critical for an animal''s survival in the face of environmental danger, and thus pain perception is likely to be under stringent evolutionary pressure. Using a neuronal-specific RNAi knock-down strategy in adult Drosophila, we recently completed a genome-wide functional annotation of heat nociception that allowed us to identify α2δ3 as a novel pain gene. Here we report construction of an evolutionary-conserved, system-level, global molecular pain network map. Our systems map is markedly enriched for multiple genes associated with human pain and predicts a plethora of novel candidate pain pathways. One central node of this pain network is phospholipid signaling, which has been implicated before in pain processing. To further investigate the role of phospholipid signaling in mammalian heat pain perception, we analysed the phenotype of PIP5Kα and PI3Kγ mutant mice. Intriguingly, both of these mice exhibit pronounced hypersensitivity to noxious heat and capsaicin-induced pain, which directly mapped through PI3Kγ kinase-dead knock-in mice to PI3Kγ lipid kinase activity. Using single primary sensory neuron recording, PI3Kγ function was mechanistically linked to a negative regulation of TRPV1 channel transduction. Our data provide a systems map for heat nociception and reinforces the extraordinary conservation of molecular mechanisms of nociception across different species.     

Variable optimization for the formation of three-dimensional self-organized heart muscle

Cardiac tissue-engineering research is focused on the development of functional three-dimensional (3D) heart muscle in vitro. These models allow the detailed study of critical events in organogenesis, such as the establishment of cell–cell communication and construction and modification of the extracellular matrix. We have previously described a model for 3D heart muscle, termed cardioids, formed by the spontaneous delamination of a cohesive monolayer of primary cells in the absence of any synthetic scaffolding material. In an earlier publication, we have shown that, upon electrical stimulation, cardioids generate a twitch force in the range of 200–300 μN, generate a specific force (twitch force normalized to total cross-sectional area) of 2–4 kN/m², and can be electrically paced at frequencies of up to 10 Hz without any notable fatigue. We have two objectives for the current study: model development and model optimization. Our model development efforts are focused on providing additional characterization of the cardioid model. In this study, we show for the first time that cardioids show a pattern of gene expression comparable to that of cells cultured in two dimensions on tissue culture plastic and normal mammalian heart muscle. Compared with primary cardiac cells cultured on tissue culture plastic, the expression of α-myosin heavy chain (MHC), β-MHC, SERCA2, and phospholamban was significantly higher in cardioids. Our second objective, model optimization, is focused on evaluating the effect of several cell culture variables on cardioid formation and function. Specifically, we looked at the effect of plating density (1.0–4.0 × 10⁶ cells per cardioid), concentration of two adhesion proteins (laminin at 0.2–2.0 μg/cm² and fibronectin at 1–10 μg/cm²), myocyte purity (using preplating times of 15 and 60 min), and ascorbic acid stimulation (1–100 μl/ml). For our optimization studies, we utilized twitch force in response to electrical stimulation as our endpoint metric. Based on these studies, we found that cardioids formed with a plating density in the range 3–4 × 10⁶ cells per cardioid generated the maximum twitch force, whereas increasing the surface adhesion protein (using either laminin or fibronectin) and increasing the myocyte purity both resulted in a decrease in twitch force. In addition, increasing the ascorbic acid concentration resulted in an increase in the baseline force of cardioids, which was recorded in the absence of electrical stimulation. Based on the model development studies, we have shown that cardioids do indeed exhibit a gene expression pattern similar to normal mammalian heart muscle. This provides further validity for the cardioid model. Based on the model optimization studies, we have identified specific cell culture regimes which support cardioid formation and function. These results are specific to the cardioid model; however, they may be translated and applied to other tissue-engineering models. Collectively, the work described in this study provides insight into the formation of functional 3D heart muscle and the effect of several cell culture variables on tissue formation and function.     

洛南盆地槐树坪地点2013年出土的石制品

洛南盆地槐树坪旧石器地点最初发现于1999年,该地点位于南洛河左岸(北部)支流石门河及石门河的二级支流东麻坪河(石门河一级支流为麻坪河)之间的第四级阶地上,是洛南盆地高阶地旷野旧石器地点群的代表性遗址之一。2004年4~5月和2006年6~7月,槐树坪地点曾历经两次小规模试掘。2013年4~6月,我们对该遗址进行了较大规模的系统发掘,发掘面积56 m~2,出土石锤、石料、石核、石片、工具、断块、碎屑等不同类型石制品830件。本文对2013年发掘出土的石制品进行了初步研究,统计分析结果显示,槐树坪地点加工石制品的原料来自遗址附近河流阶地砾石层中的砾石,其中以石英和石英岩为主,石英砂岩和细砂岩也有使用。剥片方式主要采用锤击法,偶见砸击法和碰砧法。石制品以中型和小型为主。工具多为石片加工而成的刮削器,偶见手斧、薄刃斧、石刀等大型工具。石器加工方向以正向居多。光释光测年数据表明,槐树坪地点埋藏石制品地层堆积物形成年代大约为距今8~9万年到1.3万年之间,其中7~8万年段的地层堆积物中包含石制品较多。槐树坪地点发现的石制品丰富了洛南盆地旧石器遗址的材料,可以使我们更深刻的了解洛南盆地高阶地旧石器遗址群的地层埋藏情况、遗址年代和石器工业内涵。