Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM

Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera (Gatan K2), the latest K3 camera is faster, larger, and now offers a correlated-double sampling mode (CDS). Importantly this results in a higher DQE and improved throughput compared to its predecessor. In this study, we focused on optimizing camera data collection parameters for daily use within a cryo-EM facility and explored the balance between throughput and resolution. In total, eight data sets of murine heavy-chain apoferritin were collected at different dose rates and magnifications, using 9-hole image shift data collection strategies. The performance of the camera was characterized by the quality of the resultant 3D reconstructions. Our results demonstrated that the Gatan K3 operating in CDS mode outperformed standard (nonCDS) mode in terms of reconstruction resolution in all tested conditions with 8 electrons per pixel per second being the optimal dose rate. At low magnification (64kx) we were able to achieve reconstruction resolutions of 149% of the physical Nyquist limit (1.8 Å with a 1.346 Å physical pixel size). Low magnification allows more particles to be collected per image, aiding analysis of heterogeneous samples requiring large data sets. At moderate magnification (105kx, 0.834 Å physical pixel size) we achieved a resolution of 1.65 Å within 8-h of data collection, a condition optimal for achieving high-resolution on well behaved samples. Our results also show that for an optimal sample like apoferritin, one can achieve better than 2.5 Å resolution with 5 min of data collection. Together, our studies validate the most efficient ways of imaging protein complexes using the K3 direct detector and will greatly benefit the cryo-EM community.

Mechanistic insights into the protective roles of polyphosphate against amyloid cytotoxicity

This study provides novel insights into the mechanisms by which presence of polyP alters the formation, structural properties, and cytotoxic effects of α-synuclein fibers.

The universally abundant polyphosphate (polyP) accelerates fibril formation of disease-related amyloids and protects against amyloid cytotoxicity. To gain insights into the mechanism(s) by which polyP exerts these effects, we focused on α-synuclein, a well-studied amyloid protein, which constitutes the major component of Lewy bodies found in Parkinson’s disease. Here, we demonstrate that polyP is unable to accelerate the rate-limiting step of α-synuclein fibril formation but effectively nucleates fibril assembly once α-synuclein oligomers are formed. Binding of polyP to α-synuclein either during fibril formation or upon fibril maturation substantially alters fibril morphology and effectively reduces the ability of α-synuclein fibrils to interact with cell membranes. The effect of polyP appears to be α-synuclein fibril specific and successfully prevents the uptake of fibrils into neuronal cells. These results suggest that altering the polyP levels in the extracellular space might be a potential therapeutic strategy to prevent the spreading of the disease.

Balsamia (Sequestrate Helvellaceae, Ascomycota) in western North America

Balsamia, a hypogeous, sequestrate genus in the Helvellaceae, has been characterized variously as having three to eight species in North America, and these have been considered either different from or conspecific with European species. No available modern systematic treatment of Balsamia exists to allow for accurate identification at the species level. We sequenced DNA from recent western North American Balsamia collections, assessed relationships by sequence similarity, and identified molecular taxonomic units. From these data, we determined which matched descriptions and types of named species. ITS sequences supported 12 Balsamia species in western North America, five originally described by Harkness and Fischer and seven new species that we describe here. No sequences from Balsamia collections in western North America were nested among those of European species. We found no clear evidence for separation of Balsamia into multiple genera.

Glucocorticoid receptor function regulated by coordinated action of the Hsp90 and Hsp70 chaperone cycles

The glucocorticoid receptor (GR), like many signaling proteins, depends on the Hsp90 molecular chaperone for in vivo function. Although Hsp90 is required for ligand binding in vivo, purified apo GR is capable of binding ligand with no enhancement from Hsp90. We reveal that Hsp70, known to facilitate client delivery to Hsp90, inactivates GR through partial unfolding, whereas Hsp90 reverses this inactivation. Full recovery of ligand binding requires ATP hydrolysis on Hsp90 and the Hop and p23 cochaperones. Surprisingly, Hsp90 ATP hydrolysis appears to regulate client transfer from Hsp70, likely through a coupling of the two chaperone's ATP cycles. Such coupling is embodied in contacts between Hsp90 and Hsp70 in the GR:Hsp70:Hsp90:Hop complex imaged by cryoelectron microscopy. Whereas GR released from Hsp70 is aggregation prone, release from Hsp90 protects GR from aggregation and enhances its ligand affinity. Together, this illustrates how coordinated chaperone interactions can enhance stability, function, and regulation.

Application of network theory to potential mycorrhizal networks

The concept of a common mycorrhizal network implies that the arrangement of plants and mycorrhizal fungi in a community shares properties with other networks. A network is a system of nodes connected by links. Here we apply network theory to mycorrhizas to determine whether the architecture of a potential common mycorrhizal network is random or scale-free. We analyzed mycorrhizal data from an oak woodland from two perspectives: the phytocentric view using trees as nodes and fungi as links and the mycocentric view using fungi as nodes and trees as links. From the phytocentric perspective, the distribution of potential mycorrhizal links, as measured by the number of ectomycorrhizal morphotypes on trees of Quercus garryana, was random with a short tail, implying that all the individuals of this species are more or less equal in linking to fungi in a potential network. From the mycocentric perspective, however, the distribution of plant links to fungi was scale-free, suggesting that certain fungus species may act as hubs with frequent connections to the network. Parallels exist between social networks and mycorrhizas that suggest future lines of study on mycorrhizal networks.

Diversity of ectomycorrhizas associated with Quercus garryana in southern Oregon

We investigated diversity of ectomycorrhizas associated with Quercus garryana Dougl. ex Hook. (Oregon white oak, or Garry oak) at Whetstone Savanna Preserve in southern Oregon. Based on morphotyping and DNA restriction fragments, we described 39 ectomycorrhizas. The most common five morphotypes were found in 5% or more of 160 soil cores. Cenococcum geophilum, the most abundant morphotype, occurred in 75% of soil cores. Another common morphotype yielded a restriction fragment length polymorphism (RFLP) pattern similar to that of Tuber species. Uncommon morphotypes were responsible for the majority of ectomycorrhizal diversity on Q. garryana. Morphotype diversity of seedlings was more similar to that of their parent tree than to seedlings under other trees. Internal transcribed spacer (ITS) – RFLP patterns of ectomycorrhizas found beneath sporocarps did not match those of the sporocarps fruiting above ground. An understanding of the diversity of the ectomycorrhizal community on Q. garryana will enable us to compare ectomycorrhizas on other oak species and habitats; determine seasonality of ectomycorrhizal growth; evaluate treatments such as fire, grazing, invasion by exotic plants, and other anthropogenic disturbances; and aid restoration protocols.Key words: biocomplexity, biodiversity, ectomycorrhizas, hypogeous fungi, morphotypes, Peziza infossa, Tuber.

Morphology and Stomatal Function of Douglas Fir Needles Exposed to Climate Change: Elevated CO2 and Temperature

Climate change may have an impact on the productivity of conifer trees by influencing the morphology (size and surface characteristics) and function (capacity for gas exchange) of conifer needles. In order to test the responses of needles to climatic variables, Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), saplings were grown in sunlit controlled environment chambers at ambient or elevated (+200 parts per million above ambient) CO2 and at ambient or elevated temperature (+4 degrees C above ambient). Needle characteristics, including length, width, area, stomatal density (stomata per mm2), percentage of stomatal occlusion, and the morphology of epicuticular wax, were evaluated. Needle function was evaluated as stomatal conductance to water vapor and transpiration. Needle length increased significantly with elevated temperature but not with elevated CO2. Neither elevated CO2 nor elevated temperature affected stomatal density or stomatal number in these hypostomatous needles. Epicuticular wax was less finely granular at elevated than at ambient temperature and was similar in appearance at elevated and ambient CO2. Stomatal conductance and transpiration increased with elevated temperature and associated increased vapor pressure deficit; however, neither conductance nor transpiration was affected by elevated CO2. These results indicate that simulated climate change influences Douglas fir needle structure and function.

Comparison of flagellated and nonflagellated sperm in plants

Differences among flagellated and nonflagellated sperm in land plants are striking, but close examination reveals similarities in pattern of cytoskeleton and in nuclear structure. The microtubular cytoskeleton of flowering plant sperm consists of microtubule bundles arranged obliquely around the nucleus, terminating in cellular extensions. Microtubules are linked into bundles that branch and rejoin along the axis of the sperm cell, forming a cytoskeleton that determines cell shape but does not actively participate in cell movement. Generative cells and sperm share a pattern of microtubules not found in somatic cells. This pattern is initiated in the generative cell, one division before sperm formation, a situation parallel to spermatogenous cell development in vascular plants with flagellated sperm. Chromatin in flagellated and nonflagellated sperm is condensed by specialized histones.

Antibodies to pollen exines

A polyclonal antiserum and monoclonal antibodies have been prepared to purified pollen exines of Calocedrus decurrens Florin. The location of the antigen is in the exine, as shown by light-and electron-microscopic immunocytochemistry. The greatest reduction in antibody binding follows treatment of the exine with chemicals known to alter sporopollenin. These results provide evidence that sporopollenin is antigenic. Exines of ten species of gymnosperms and angiosperms also bound the polyclonal antiserum, indicating similarity of sporopollenin structure.

beta-1, 3-Glucan Synthase from Lilium longiflorum Pollen

A particulate fraction from pollen tubes and ungerminated pollen of Lilium longiflorum incorporated (14)C-glucose from UDP-glucose-(14)C into a lipid fraction and into beta-1, 3-glucan. Partial hydrolysis of the glucan yielded laminaribiose as the only radioactive disaccharide. The preferred substrate was UDP-glucose, and enzyme activity was stimulated by glucose and by beta-linked di- and trisaccharides. Enzyme from growing pollen tubes synthesized beta-1, 3-glucan more rapidly and produced a higher proportion of alkali-insoluble glucan than did enzyme from ungerminated pollen. The onset of pollen tube growth may be dependent on altered activity of beta-1, 3-glucan synthase.

Cytochemical reactivity of pollen walls

Cytochemical staining reactions in pollen grain walls of three species of Compositae, Ambrosia trifida, Artemisia pycnocephala and Gerbera jamesonii, were examined. The intine gives positive reactions for protein and for insoluble polysaccharides including pectic acid, callose and hemicellulose. The exine gives positive reactions for protein and for extractable lipids. In addition the structural material of the exine, sporopollenin, gives positive reactions for aliphatic double bonds and for closely packed anionic sites. Sporopollenin gives negative results to common cytochemical tests for lignin but reacts the same as lignin to metachromatic dyes. Some staining differences between exine-1 and exine-2 were noted.

Freeze-Etched Pollen Walls of Artemisia Pycnocephala and Lilium Humboldtii

Mature pollen was examined by freeze-etching. The fracture and etch faces of Artemisia ektexine are unstructured and homogeneous. The endexine fracture face contains particles in paired rows which correspond to the endexine lamellae with a central white line seen in osmium-stained thin sections. The intine fracture face in Artemisia is coarsely pitted and has very long fibrils. Small vesicles are observed on both sides of the plasmalemma. The fracture face of Lilium ektexine has radiating fibrils which end in a regular array near the surface; the etch face on the surface is smooth. In thin sections the staining of the Lilium ektexine differs from that of the core, giving evidence that the smooth ektexine surface is chemically distinct from the fibrillar core. The intine in Lilium shows no fibrils. Vesicles near the plasmalemma appear to be fusing with the plasmalemma creating smooth depressions in the particulate plasmalemma fracture face. The plasmalemma in both species is beset with particles in regular arrays.