Ecomorphology of Neotropical Electric Fishes: An Integrative Approach to Testing the Relationships between Form, Function, and Trophic Ecology

The relationship between form and function is thought to play an integral role in structuring broad-scale patterns of morphological evolution and resource utilization. In ecomorphological studies, mechanical performance is widely understood to constrain the evolution of form and function. However, the relationship between form, function, and resource utilization is less clear. Additionally, seasonal fluctuations in resource availability may further complicate patterns of resource use. How organisms cope with these complexities, and the effect of these factors on broadscale patterns of morphological evolution is also poorly understood. Here we use three-dimensional geometric morphometrics, biomechanics, stable isotope analysis, and gut-content analysis to study trophic evolution in a clade of riverine-adapted electric fishes from a region with high seasonal variability; the Amazon River. We find significant and phylogenetically structured relationships among measures of trophic ecology and skull shape. We also recover a significant relationship between the mechanical advantage of the mandible and trophic position, where species feeding at higher trophic levels have narrower jaws with lower mechanical advantages, and species feeding at lower trophic levels have deeper jaws with higher mechanical advantages. Our results indicate that selection is driving the evolution of mandible shape and performance toward specialization on different trophic ecologies.

Routine determination of ice thickness for cryo-EM grids

Recent advances in instrumentation and automation have made cryo-EM a popular method for producing near-atomic resolution structures of a variety of proteins and complexes. Sample preparation is still a limiting factor in collecting high quality data. Thickness of the vitreous ice in which the particles are embedded is one of the many variables that need to be optimized for collection of the highest quality data. Here we present two methods, using either an energy filter or scattering outside the objective aperture, to measure ice thickness for potentially every image collected. Unlike geometrical or tomographic methods, these can be implemented directly in the single particle collection workflow without interrupting or significantly slowing down data collection. We describe the methods as implemented into the Leginon/Appion data collection workflow, along with some examples from test cases. Routine monitoring of ice thickness should prove helpful for optimizing sample preparation, data collection, and data processing.

Publisher Correction: Controllable molecular motors engineered from myosin and RNA

An incorrect Supplementary Information file was originally published. The file has been replaced with the correct one.

High resolution single particle cryo-electron microscopy using beam-image shift

Automated data acquisition is used widely for single-particle reconstruction of three-dimensional (3D) volumes of biological complexes preserved in vitreous ice and imaged in a transmission electron microscope. Automation has become integral to this method because of the very large number of particle images required in order to overcome the typically low signal-to-noise ratio of these images. For optimal efficiency, automated data acquisition software packages typically employ some beam-image shift targeting as this method is both fast and accurate (±0.1 µm). In contrast, using only stage movement, relocation to a targeted area under low-dose conditions can only be achieved in combination with multiple iterations or long relaxation times, both reducing efficiency. Nevertheless it is well known that applying beam-image shift induces beam-tilt and with it a potential structure phase error with a phase error π/4 the highest acceptable value. This theory has been used as an argument against beam-image shift for high resolution data collection. Nevertheless, in practice many small beam-image shift datasets have resulted in 3D reconstructions beyond the π/4 phase error limit. To address this apparent contradiction, we performed cryo-EM single-particle reconstructions on a T20S proteasome sample using applied beam-image shifts corresponding to beam tilts from 0 to 10 mrad. To evaluate the results we compared the FSC values, and examined the water density peaks in the 3D map. We conclude that the phase error does not limit the validity of the 3D reconstruction from single-particle averaging beyond the π/4 resolution limit.

Benchmarking cryo-EM Single Particle Analysis Workflow

Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase.

Routine single particle CryoEM sample and grid characterization by tomography

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.

Controllable molecular motors engineered from myosin and RNA

Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems ¹ or in living cells ² . Previously, synthetic nucleic acid motors ^3-5 and modified natural protein motors ^6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors ^11-15 . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure ^7,9 . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing ¹⁶ . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement ¹⁷ reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s^-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.

Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity

Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.

Like miniature motors, proteins called myosins generate the forces needed for cells to move and for muscles to contract. Myosins use the energy stored in a chemical called ATP to move along filaments made from another protein called actin and produce force. The same part of the myosin protein that binds to and uses ATP also contacts actin. As a myosin protein consumes ATP, it cycles through a series of shape changes to drive the motor protein forward, altering how it interacts with the actin filament in the process.

Although all myosins use ATP in fundamentally the same way, individual members of this protein family have specialized properties that enable them to carry out different roles. It is not clear whether each type of myosin makes unique contacts with the actin filament, which could help determine these properties. Furthermore, mechanical forces can control the activity of myosin motors in ways that are poorly understood.

Gurel et al. have now looked at a family member called myosin VI, which moves in the opposite direction along actin filaments relative to other myosins, to better understand the properties of these proteins. An imaging technique called cryo-electron microscopy (cryo-EM) was used to determine the three-dimensional structure of myosin VI bound to actin at two steps in its cycle. Gurel et al. found that myosin VI formed specific interactions with actin that were very different from another myosin family member called myosin IIc, whose structure bound to actin was already known. In addition, the structural changes observed between the two stages of myosin VI’s cycle provided insight into how force could be used to control the motor.

Together these findings give a more detailed picture of how myosins work. They suggest that the surface of myosin that contacts actin can evolve to change the properties of a specific myosin. Studies of other myosins bound to actin will provide further insight into how distinct interactions relate to motor-specific properties. Future studies could also help scientists to understand how mutations in genes for myosins – which have been linked to a number of diseases in humans – alter the way in which myosins interact with actin filaments. This in turn could give insight into how these mutations disrupt the proteins’ activities.

Effect of relative humidity on preeclampsia

PURPOSE OF INVESTIGATION

The authors aimed to determine the relationship between meteorological variables and hypertension in pregnancy by using data from a national weather database.

MATERIALS AND METHODS

For this population-based observational study, the database of the Korea National Health Insurance (KNHI) Claims of the Health Insurance Review and Assessment Service (HIRA) and Korea Meteorological Administration was used. The 48,275 women with preeclampsia among 2,495,383 women who gave birth were included. Monthly meteorological factors and preeclampsia prevalence for five years were statistically analyzed.

RESULTS

Among temperature, relative humidity, sunlight duration, and rainfall, only relative humidity had a significant inverse correlation with the preeclampsia prevalence (p < 0.001). The other meteorological factors were not associated with preeclampsia.

CONCLUSION

Relative humidity may be a significant factor for of the development of preeclampsia. Further monitoring of weather parameters during the entire pregnancy period may be the best method for verifying the present results in the development of preeclampsia.

The Structural Basis of Actin Organization by Vinculin and Metavinculin

Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal "strap" and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1' helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies.

Screening for two-dimensional crystals by transmission electron microscopy of negatively stained samples

Structural studies of soluble and membrane proteins by electron crystallography include several critical steps. While the two-dimensional (2D) crystallization arguably may be described as the major bottleneck of electron crystallography, the screening by transmission electron microscopy (EM) to identify 2D crystals requires great care as well as practice. Both sample preparation and EM are skills that are relatively easily acquired, compared to the identification of the first ordered arrays. Added to this, membranes may have a variety of morphologies and sizes. Here we describe all steps involved in the screening for 2D crystals as well as the evaluation of samples.

Two-dimensional crystallization of membrane proteins by reconstitution through dialysis

Studies of membrane proteins by two-dimensional (2D) crystallization and electron crystallography have provided crucial information on the structure and function of a rapidly growing number of these intricate proteins within a close-to-native lipid bilayer. Here we provide protocols for planning and executing 2D crystallization trials by detergent removal through dialysis, including the preparation of phospholipids and the dialysis setup. General factors to be considered, such as the protein preparation, solubilizing detergent, lipid for reconstitution, and buffer conditions are discussed. Several 2D crystallization conditions are highlighted that have shown great promise to grow 2D crystals within a surprisingly short amount of time. Finally, conditions for optimizing order and size of 2D crystals are outlined.

Amyloid fibril formation by the glaucoma-associated olfactomedin domain of myocilin

Myocilin is a protein found in the extracellular matrix of trabecular meshwork tissue, the anatomical region of the eye involved in regulating intraocular pressure. Wild-type (WT) myocilin has been associated with steroid-induced glaucoma, and variants of myocilin have been linked to early-onset inherited glaucoma. Elevated levels and aggregation of myocilin hasten increased intraocular pressure and glaucoma-characteristic vision loss due to irreversible damage to the optic nerve. In spite of reports on the intracellular accumulation of mutant and WT myocilin in vitro, cell culture, and model organisms, these aggregates have not been structurally characterized. In this work, we provide biophysical evidence for the hallmarks of amyloid fibrils in aggregated forms of WT and mutant myocilin localized to the C-terminal olfactomedin (OLF) domain. These fibrils are grown under a variety of conditions in a nucleation-dependent and self-propagating manner. Protofibrillar oligomers and mature amyloid fibrils are observed in vitro. Full-length mutant myocilin expressed in mammalian cells forms intracellular amyloid-containing aggregates as well. Taken together, this work provides new insights into and raises new questions about the molecular properties of the highly conserved OLF domain, and suggests a novel protein-based hypothesis for glaucoma pathogenesis for further testing in a clinical setting.

Mutagenicity studies of methyl-tert-butylether using the Ames tester strain TA102

Methyl-tert-butylether (MTBE) is an oxygenate widely used in the United States as a motor vehicle fuel additive to reduce emissions and as an octane booster [National Research Council, Toxicological and Performance Aspects of Oxygenated Motor Vehicle Fules, National Academy Press, Washington, DC, 1996]. But it is the potential for MTBE to enter drinking water supplies that has become an area of public concern. MTBE has been shown to induce liver and kidney tumors in rodents but the biochemical process leading to carcinogenesis is unknown. MTBE was previously shown to be non-mutagenic in the standard Ames plate incorporation test with tester strains that detect frame shift (TA98) and point mutations (TA100) and in a suspension assay using TA104, a strain that detects oxidative damage, suggesting a non-genotoxic mechanism accounts for its carcinogenic potential. These strains are deficient in excision repair due to deletion of the uvrB gene. We hypothesized that the carcinogenic activity of MTBE may be dependent upon a functional excision repair system that attempts to remove alkyl adducts and/or oxidative base damage caused by direct interaction of MTBE with DNA or by its metabolites, formaldehyde and tert-butyl alcohol (TBA), established carcinogens that are mutagenic in some Ames strains. To test our hypothesis, the genotoxicity of MTBE-induced DNA alterations was assayed using the standard Ames test with TA102, a strain similar to TA104 in the damage it detects but uvrB + and, therefore, excision repair proficient. The assay was performed (1) with and without Aroclor-induced rat S-9, (2) with and without the addition of formaldehyde dehydrogenase (FDH), and (3) with human S-9 homogenate. MTBE was weakly mutagenic when tested directly and moderately mutagenic with S-9 activation producing between 80 and 200 TA102 revertants/mg of compound. Mutagenicity was inhibited 25%-30% by FDH. TA102 revertants were also induced by TBA and by MTBE when human S-9 was substituted for rat S-9. We conclude that MTBE and its metabolites induce a mutagenic pathway involving oxidation of DNA bases and an intact repair system. These data are significant in view of the controversy surrounding public safety and the environmental release of MTBE and similar fuel additives.

The argon contact laser scalpel: a study of its effect on atherosclerosis

A new argon laser scalpel (ALS) that delivers radiation to tissue by direct contact was used to perform endarterectomies on atherosclerotic rabbit aortas in vivo. The resultant effects were compared to those induced by CO2 laser (CO2) and conventional surgical endarterectomy (END) to determine whether this instrument might be useful in the treatment of occlusive cerebrovascular disease. Light microscopy of the treated aortic segments revealed significantly more atheroma removed and less damage to the underlying media in the ALS segments compared to the CO2 segments. Electron microscopy showed that the ALS surface and distal intima-media interface were smoother and more even than those of the CO2 or END groups. Prostacyclin synthesis, as measured by 6-keto-prostaglandin F1a levels, was significantly reduced in the ALS compared to the END and control segments. These results indicate that the ALS is superior to CO2 in performing open laser endarterectomies, but such treatment places the atherosclerotic blood vessel at greater risk for thrombotic complications during the early postoperative period that does surgical endarterectomy. It is conceivable that a contact laser may be useful in the smooth welding of the distal edge of an atheroma (i.e., during carotid endarterectomy) and for the transcatheter ablation of surgically inaccessible obstructions of the cerebral circulation.

The argon "contact" laser scalpel: technical considerations

The authors describe the use of a new contact argon laser scalpel designed specifically for hand-controlled cutting and hemostasis. This instrument delivers energy precisely to targeted tissue and produces minimal damage to adjacent healthy structures. Potential clinical applications are discussed.

Age-related rise in parathyroid hormone in man: the use of intact and midmolecule antisera to distinguish hormone secretion from retention

Circulating levels of parathyroid hormone (PTH) rise with age in normal men and women. To resolve the basis for this observation we measured iPTH in 137 normal men and women, age 23 to 85 years, using two antisera which responded to different portions of the PTH molecule. A midmolecule assay (Mid-PTH) employed antiserum NG-5, which recognizes mid- and carboxy-terminal portions of hPTH, whereas antiserum CK-67, which recognizes determinants in the 1-34 hPTH sequence, was used to measure intact PTH (NH2-PTH). Two-hour fasting urine was collected for measurement of creatinine clearance and excretion indices of phosphorus and cyclic AMP. Serum was analyzed for 25-hydroxyvitamin D (25-OHD) in addition to iPTH. Mid-PTH rose significantly with age in the 72 women (r = 0.38, p less than 0.001) and in the 65 men (r = 0.40, p less than 0.001). NH2-PTH rose with age in women (r = 0.23, p less than 0.05), but a change in men was not significant (r = 0.19, n.s.). Cyclic AMP excretion rose significantly with age in both women (r = 0.42) and men (r = 0.41), whereas phosphorus excretion rose significantly in women only (r = 0.32, p less than 0.01). 25-OHD levels were 27.5 +/- 1.3 ng/ml for women and 26.1 +/- 1.2 ng/ml for men. No change in 25-OHD was observed with age in women, and a significant decrease in men was due entirely to extremely high values in three young subjects.(ABSTRACT TRUNCATED AT 250 WORDS)

Highly sensitive two-site immunoradiometric assay of parathyrin, and its clinical utility in evaluating patients with hypercalcemia

We have developed a highly sensitive, two-site immunoradiometric assay (IRMA) for human parathyrin (PTH) that is specific for the intact, secreted, biologically active 84-amino-acid peptide. This assay has several technical advantages: it does not detect even high concentrations of inactive carboxyl-terminal fragments, results are available within 24 h, and the detection limit for intact hormone is low (1 ng/L). The assay readily measures concentrations of PTH in all healthy subjects and distinguishes these values from low or undetectable PTH values observed in clinical situations in which PTH secretion is expected to be suppressed. We found complete separation of results from 37 patients with surgically proven hyperparathyroidism and those from 23 patients with hypercalcemia associated with malignancy, the latter having PTH values at or below the lower limits of normal for this assay. The sensitivity, specificity, and rapid turnaround time of this two-site IRMA should advance the laboratory evaluation of patients with disorders of calcium metabolism.

Highly sensitive two-site immunoradiometric assay of parathyrin, and its clinical utility in evaluating patients with hypercalcemia

We have developed a highly sensitive, two-site immunoradiometric assay (IRMA) for human parathyrin (PTH) that is specific for the intact, secreted, biologically active 84-amino-acid peptide. This assay has several technical advantages: it does not detect even high concentrations of inactive carboxyl-terminal fragments, results are available within 24 h, and the detection limit for intact hormone is low (1 ng/L). The assay readily measures concentrations of PTH in all healthy subjects and distinguishes these values from low or undetectable PTH values observed in clinical situations in which PTH secretion is expected to be suppressed. We found complete separation of results from 37 patients with surgically proven hyperparathyroidism and those from 23 patients with hypercalcemia associated with malignancy, the latter having PTH values at or below the lower limits of normal for this assay. The sensitivity, specificity, and rapid turnaround time of this two-site IRMA should advance the laboratory evaluation of patients with disorders of calcium metabolism.

Compression neuropathy of the radial nerve due to pentazocine-induced fibrous myopathy

Fibrous myopathy is a common, well-known side effect of repeated pentazocine injection. However, compression neuropathy due to fibrotic muscle affected by pentazocine-induced myopathy has not previously been reported. In a 37-year-old woman with documented pentazocine-induced fibrous myopathy of triceps and deltoid muscles bilaterally and a three-week history of right wrist drop, electrodiagnostic examination showed a severe but partial lesion of the right radial nerve distal to the branches to the triceps, in addition to the fibrous myopathy. Surgery revealed the right radial nerve to be severely compressed by the densely fibrotic lateral head of the triceps. Decompression and neurolysis were performed with good subsequent recovery of function.