Complete Genome Sequences of Chop, DelRio, and GrandSlam, Three Gordonia Phages Isolated from Soil in Central Arkansas.

Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.

Impact of Extralegal and Community Factors on Police Officers' Decision to Book Arrests for Minor Offenses.

Booked arrests carry greater harms than non-booked arrests. When booked following an arrest, individuals are confined without guilt and an official criminal record forms that carries several negative consequences. Even with these greater harms, police decision to book arrests is understudied with little research on what factors influence this decision. This study utilizes official booking data to determine if suspect extralegal and community factors affect officers' decisions to book arrests across minor offenses. The study uses data from the Chandler Police Department in Arizona and the American Community Survey from 2013 to 2019. These data include suspect legal/extralegal, officer, time, and block-group level factors. Using a cross-classified modeling approach, we examine factors associated with booking arrests across five offenses (cannabis possession, drug paraphernalia, shoplifting, criminal damage, and non-DUI-traffic). Results suggest that legal factors, particularly felony charges, are associated with higher odds of booking after arrest. However, we also demonstrate how extralegal factors significantly impact police decision to book arrests. Native Americans, Blacks, older individuals, and those with prior records had higher odds of booked arrests. While the odds of booked arrest varied across officers and communities, few officer or community factors were related to the decision to book arrests. Results suggest extralegal factors remain significant across minor offenses. These findings highlight the need to examine disparities on police post-arrest outcomes, expand racial categories studied, and incorporate less utilized variables like prior record. Supplementary Information: The online version contains supplementary material available at 10.1007/s12103-022-09669-6.

Multiplexed TEM Specimen Preparation and Analysis of Plasmonic Nanoparticles.

We describe a system for rapidly screening hundreds of nanoparticle samples using transmission electron microscopy (TEM). The system uses a liquid handling robot to place up to 96 individual samples onto a single standard TEM grid at separate locations. The grid is then transferred into the TEM and automated software is used to acquire multiscale images of each sample. The images are then analyzed to extract metrics on the size, shape, and morphology of the nanoparticles. The system has been used to characterize plasmonically active nanomaterials.

Understanding the dark and light-enhanced bactericidal action of cationic conjugated polyelectrolytes and oligomers.

A multiscale investigation was carried out to study the dark and light-enhanced bactericidal mechanisms of poly(phenylene ethynylene) (PPE)-based cationic conjugated polyelectrolytes (CPEs) and oligo-phenylene ethynylenes (OPEs). On the morphological scale, Gram-negative E. coli cells exposed to CPE and OPE compounds in the dark show damage to the cell envelope, plasma membrane, and in some cases the cytoplasm, while with UV-irradiation, E. coli sustained catastrophic damages to both the cell envelope and cytoplasm. In contrast, the Gram-positive S. epi bacteria appeared intact when exposed to CPE and OPE compounds in the dark but showed damages to the cell envelope with UV-irradiation. To better understand the molecular basis of CPE- and OPE-induced morphological changes and damages to bacteria, we investigated the effect of these compounds on model bacterial plasma membrane and bacterial proteins and plasmid DNA. Measurements of dark membrane perturbation activity of the CPEs and OPEs using model lipid membranes support a carpet or detergent-like mechanism by which the antimicrobial compounds induce membrane collapse and phase transitions. Under UV-irradiation, E. coli bacteria exposed to CPEs and OPEs showed covalent modifications and damages to both cellular protein and plasmid DNA, likely through oxidative pathways mediated by singlet oxygen and subsequent reactive oxygen species sensitized by the CPE and OPE compounds. Our finding thus show that the antimicrobial polymers and oligomers exert toxicity toward Gram-negative bacteria by disrupting the morphology and structures of cell envelope and cytoplasm, including cellular components such as proteins and DNA, while exert toxicity toward Gram-positive bacteria by binding to and disrupting just the cell wall.

Electron tomographic analysis of synaptic ultrastructure.

Synaptic function depends on interactions among sets of proteins that assemble into complex supramolecular machines. Molecular biology, electrophysiology, and live-cell imaging studies have provided tantalizing glimpses into the inner workings of the synapse, but fundamental questions remain regarding the functional organization of these "nano-machines." Electron tomography reveals the internal structure of synapses in three dimensions with exceptional spatial resolution. Here we report results from an electron tomographic study of axospinous synapses in neocortex and hippocampus of the adult rat, based on aldehyde-fixed material stabilized with tannic acid in lieu of postfixation with osmium tetroxide. Our results provide a new window into the structural basis of excitatory synaptic processing in the mammalian brain.

Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM.

Over the last three decades, Cryo-TEM has developed into a powerful technique for high-resolution imaging of biological macromolecules in their native vitrified state. However, the method for vitrifying specimens onto EM grids is essentially unchanged - application of ∼3 µL sample to a grid, followed by blotting and rapid plunge freezing into liquid ethane. Several trials are often required to obtain suitable thin (few hundred nanometers or less) vitrified layers amenable for cryo-TEM imaging, which results in waste of precious sample and resources. While commercially available instruments provide some level of automation to control the vitrification process in an effort to increase quality and reproducibility, obtaining satisfactory vitrified specimens remains a bottleneck in the Cryo-TEM pipeline. We describe here a completely novel method for EM specimen preparation based on small volume (picoliter to nanoliter) dispensing using inkjet technology. A first prototype system (Spotiton v0.5) demonstrates feasibility of this new approach for specimen vitrification. A piezo-electric inkjet dispenser is integrated with optical real-time cameras (100 Hz frame rate) to analyze picoliter to nanoliter droplet profiles in-flight and spreading dynamics on the grid, and thus provides a method to optimize timing of the process. Using TEM imaging and biochemical assays we demonstrate that the piezo-electric inkjet mechanism does not disrupt the structural or functional integrity of macromolecules. These preliminary studies provide insight into the factors and components that will need further development to enable a robust and repeatable technique for specimen vitrification using this novel approach.

Direct restriction of virus release and incorporation of the interferon-induced protein BST-2 into HIV-1 particles.

Investigation of the Vpu protein of HIV-1 recently uncovered a novel aspect of the mammalian innate response to enveloped viruses: retention of progeny virions on the surface of infected cells by the interferon-induced, transmembrane and GPI-anchored protein BST-2 (CD317; tetherin). BST-2 inhibits diverse families of enveloped viruses, but how it restricts viral release is unclear. Here, immuno-electron microscopic data indicate that BST-2 is positioned to directly retain nascent HIV virions on the plasma membrane of infected cells and is incorporated into virions. Virion-incorporation was confirmed by capture of infectivity using antibody to the ectodomain of BST-2. Consistent with a direct tethering mechanism, we confirmed that proteolysis releases restricted virions and further show that this removed the ectodomain of BST-2 from the cell surface. Unexpectedly, enzymatic cleavage of GPI anchors did not release restricted virions, weighing against models in which individual BST-2 molecules span the virion and host cell membranes. Although the exact molecular topology of restriction remains unsolved, we suggest that the incorporation of BST-2 into viral envelopes underlies its broad restrictive activity, whereas its relative exclusion from virions and sites of viral assembly by proteins such as HIV-1 Vpu may provide viral antagonism of restriction.

Comparative, three-dimensional anterior sensory reconstruction of Aphelenchus avenae (nematoda: Tylenchomorpha).

The anterior sensory anatomy (not including amphids) of the nematode Aphelenchus avenae (Tylenchomorpha) has been three-dimensionally reconstructed from serial, transmission electron microscopy thin sections. Models, showing detailed morphology and spatial relationships of cuticular sensilla and internal sensory receptors, are the first computerized reconstruction of sensory structures of a Tylenchomorpha nematode. Results are analyzed with respect to similarly detailed reconstructions of Rhabditida outgroup nematodes, Acrobeles complexus (Cephalobomorpha) and Caenorhabditis elegans (Rhabditomorpha). Homologies identified in A. avenae demonstrate the general conservation of the anterior sensory system between freeliving nematodes and the largely plant parasitic Tylenchomorpha. A higher degree of similarity is shown between A. avenae and A. complexus, with common features including: the presence of a second, internal outer labial dendrite (OL1); a second cephalic dendrite in the female (CEP2/CEM); an accessory process loop of inner labial dendrite 1; and terminus morphology and epidermal associations of internal sensory receptors BAG and URX. Unique to A. avenae is a pair of peripheral, lateral neurons of unknown homology but with axial positions and intercellular relationships nearly identical to the "posterior branches" of URX in A. complexus. Knowledge of homologies and connectivity of anterior sensory structures provides a basis for expansion of the experimental behavioral model of C. elegans to the economically important nematodes of Tylenchomorpha.

Phosphorylation of highly conserved neurofilament medium KSP repeats is not required for myelin-dependent radial axonal growth.

Neurofilament medium (NF-M) is essential for the acquisition of normal axonal caliber in response to a myelin-dependent "outside-in" trigger for radial axonal growth. Removal of the tail domain and lysine-serine-proline (KSP) repeats of NF-M, but not neurofilament heavy, produced axons with impaired radial growth and reduced conduction velocities. These earlier findings supported myelin-dependent phosphorylation of NF-M KSP repeats as an essential component of axonal growth. As a direct test of whether phosphorylation of NF-M KSP repeats is the target for the myelin-derived signal, gene replacement has now been used to produce mice in which all serines of NF-M's KSP repeats have been replaced with phosphorylation-incompetent alanines. This substitution did not alter accumulation of the neurofilaments or their subunits. Axonal caliber and motor neuron conduction velocity of mice expressing KSP phospho-incompetent NF-M were also indistinguishable from wild-type mice. Thus, phosphorylation of NF-M KSP repeats is not an essential component for the acquisition of normal axonal caliber mediated by myelin-dependent outside-in signaling.

Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure.

Organismal colour can be created by selective absorption of light by pigments or light scattering by photonic nanostructures. Photonic nanostructures may vary in refractive index over one, two or three dimensions and may be periodic over large spatial scales or amorphous with short-range order. Theoretical optical analysis of three-dimensional amorphous nanostructures has been challenging because these structures are difficult to describe accurately from conventional two-dimensional electron microscopy alone. Intermediate voltage electron microscopy (IVEM) with tomographic reconstruction adds three-dimensional data by using a high-power electron beam to penetrate and image sections of material sufficiently thick to contain a significant portion of the structure. Here, we use IVEM tomography to characterize a non-iridescent, three-dimensional biophotonic nanostructure: the spongy medullary layer from eastern bluebird Sialia sialis feather barbs. Tomography and three-dimensional Fourier analysis reveal that it is an amorphous, interconnected bicontinuous matrix that is appropriately ordered at local spatial scales in all three dimensions to coherently scatter light. The predicted reflectance spectra from the three-dimensional Fourier analysis are more precise than those predicted by previous two-dimensional Fourier analysis of transmission electron microscopy sections. These results highlight the usefulness, and obstacles, of tomography in the description and analysis of three-dimensional photonic structures.

Three-dimensional reconstruction of the amphid sensilla in the microbial feeding nematode, Acrobeles complexus (Nematoda: Rhabditida).

Amphid sensilla are the primary olfactory, chemoreceptive, and thermoreceptive organs in nematodes. Their function is well described for the model organism Caenorhabditis elegans, but it is not clear to what extent we can generalize these findings to distantly related nematodes of medical, economic, and agricultural importance. Current detailed descriptions of anatomy and sensory function are limited to nematodes that recent molecular phylogenies would place in the same taxonomic family, the Rhabditidae. Using serial thin-section transmission electron microscopy, we reconstructed the anatomy of the amphid sensilla in the more distantly related nematode, Acrobeles complexus (Cephalobidae). Amphid structure is broadly conserved in number and arrangement of cells. Details of cell anatomy differ, particularly for the sensory neurite termini. We identify an additional sensory neuron not found in the amphid of C. elegans and propose homology with the C. elegans interneuron AUA. Hypotheses of homology for the remaining sensory neurons are also proposed based on comparisons between C. elegans, Strongyloides stercoralis, and Haemonchus contortus.

The cytoplasmic accumulations of the cataract-associated mutant, Connexin50P88S, are long-lived and form in the endoplasmic reticulum.

Mutant connexins have been linked to hereditary congenital cataracts. One such mutant causes a proline-to-serine substitution at position 88 in human connexin 50 (CX50P88S). In transfected cells, CX50P88S does not form gap junctions, but localizes in cytoplasmic multilamellar structures. We studied the dynamics of formation and the stability of these structures in HeLa cells stably transfected with CX50P88S containing a tetracysteine motif appended to its C-terminus (HeLa-CX50P88S(Cys)(4) cells). The tetracysteine motif binds the membrane-permeable biarsenical compounds, FlAsH and ReAsH, which become fluorescent upon binding allowing detection of CX50P88S(Cys)(4) by fluorescence microscopy or by transmission electron microscopy after the ReAsH-driven fluorescent photoconversion of diaminobenzidine. CX50P88S structures were long-lived. Pulse labeling of HeLa-CX50P88S(Cys)(4) cells with FlAsH followed by a chase and ReAsH labeling showed a differential distribution of the labels, with older CX50P88S surrounded by newly synthesized protein. Formation of CX50P88S accumulations was not affected by treatments that block ER-to-Golgi transport. Transmission electron microscopy and tomographic reconstruction revealed that CX50P88S accumulations corresponded to closely apposed circular or semicircular membrane stacks that were sometimes continuous with the rough endoplasmic reticulum. These results suggest that CX50P88S accumulations originate from the rough endoplasmic reticulum and that mutant protein is sequentially added resulting in long-lived cytoplasmic particles. The persistence of these particles in the lens may cause light scattering and the pulverulent cataracts observed in affected individuals.

Three-dimensional reconstruction of the stomatostylet and anterior epidermis in the nematode Aphelenchus avenae (Nematoda: Aphelenchidae) with implications for the evolution of plant parasitism.

A three-dimensional model of the stomatostylet and associated structures has been reconstructed from serial thin sections of Aphelenchus avenae, a representative of Tylenchomorpha, a group including most plant parasitic nematodes. The reconstruction is compared with previous work on bacteriovorous cephalobids and rhabditids to better understand the evolution of the stylet and its associated cells. Two arcade syncytia ("guide ring") line the stylet shaft, supporting the hypothesis that the stylet shaft and cone (into which the shaft extends and which is not lined by syncytia) are homologous with the gymnostom of cephalobids, the sister taxon of tylenchids. Epidermal syncytia, HypA, HypB, HypC, and HypE, line the cephalic framework, vestibule, and vestibule extension, congruent with the hypothesis that these components are homologous with the cephalobid cheilostom. Relative to outgroups, HypC is expanded in A. avenae, enclosing sensilla that fill most of the cephalic framework. The homolog of syncytium HypD in the cephalobid Acrobeles complexus is not observed in A. avenae. Arcade syncytia are reduced compared with those of cephalobids. Stylet protractor muscles in A. avenae are homologous with the most anterior set of radial muscles of cephalobids. Observations to date test and verify our previous hypotheses of homology of the stomatostylet with respect to the stoma of bacteriovorous outgroups. Reconstruction of the stegostom and pharynx will provide further tests of homology and evolution of feeding structure adaptations for plant parasitism.

Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy.

Virus assembly occurs in a complex environment and is dependent upon viral and cellular components being properly correlated in time and space. The simplicity of the flock house virus (FHV) capsid and the extensive structural, biochemical and genetic characterization of the virus make it an excellent system for studying in vivo virus assembly. The tetracysteine motif (CCPGCC), that induces fluorescence in bound biarsenical compounds (FlAsH and ReAsH), was genetically inserted in the coat protein, to visualize this gene product during virus infection. The small size of this modification when compared to those made by traditional fluorescent proteins minimizes disruption of the coat proteins numerous functions. ReAsH not only fluoresces when bound to the tetracysteine motif but also allows correlated electron microscopy (EM) of the same cell following photoconversion and osmium staining. These studies demonstrated that the coat protein was concentrated in discrete patches in the cell. High pressure freezing (HPF) followed by freeze substitution (FS) of infected cells showed that these patches were formed by virus particles in crystalline arrays. EM tomography (EMT) of the HPF/FS prepared samples showed that these arrays were proximal to highly modified mitochondria previously established to be the site of RNA replication. Two features of the mitochondrial modification are approximately 60 nm spherules that line the outer membrane and the large chamber created by the convolution induced in the entire organelle.

The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications.

The emergence of electron tomography as a tool for three dimensional structure determination of cells and tissues has brought its own challenges for the preparation of thick sections. High pressure freezing in combination with freeze substitution provides the best method for obtaining the largest volume of well-preserved tissue. However, for deeply embedded, heterogeneous, labile tissues needing careful dissection, such as brain, the damage due to anoxia and excision before cryofixation is significant. We previously demonstrated that chemical fixation prior to high pressure freezing preserves fragile tissues and produces superior tomographic reconstructions compared to equivalent tissue preserved by chemical fixation alone. Here, we provide further characterization of the technique, comparing the ultrastructure of Flock House Virus infected DL1 insect cells that were (1) high pressure frozen without fixation, (2) high pressure frozen following fixation, and (3) conventionally prepared with aldehyde fixatives. Aldehyde fixation prior to freezing produces ultrastructural preservation superior to that obtained through chemical fixation alone that is close to that obtained when cells are fast frozen without fixation. We demonstrate using a variety of nervous system tissues, including neurons that were injected with a fluorescent dye and then photooxidized, that this technique provides excellent preservation compared to chemical fixation alone and can be extended to selectively stained material where cryofixation is impractical.

Three-dimensional fine structural reconstruction of the nose sensory structures of Acrobeles complexus compared to Caenorhabditis elegans (Nematoda: Rhabditida).

Nematode sensory structures can be divided into two classes; cuticular sensillae, with dendrites ending outside the epidermis, and internal receptors, that typically are single dendrites terminating within the body cavity. Fine structure of the former has been described completely in more than a dozen nematode taxa, while the latter were previously only well understood in the microbial feeder Caenorhabditis elegans. The distantly related nematode Acrobeles complexus has a similar ecology and together the two span a clade representing a large proportion of nematode biodiversity. The cuticular sensillae and internal receptors of A. complexus are here shown to be remarkably similar in number, arrangement, and morphology to those of C. elegans. Several key differences are reported that likely relate to function, and suggest that this nematode has a cuticular sensillum morphology that is closer to that of the common ancestor of the two taxa. Internal sensory receptors have more elaborate termini than those of C. elegans. The existence of a novel form of mechanoreceptor in A. complexus and spatial relationships between sensillum dendrites suggest differences between two classes of sensillae in how a touch-response behavior may be mediated.

Three-dimensional reconstruction of the nose epidermal cells in the microbial feeding nematode, Acrobeles complexus (Nematoda: Rhabditida).

The epidermis of the anterior end (nose) plays an important role in the evolution, development, and functional feeding morphology in nematodes, but information on this complex organ system is limited. Here, we produce a 3D model of 13 of the cells making up this organ system reconstructed from serial transmission electron micrographs of the microbial feeding nematode, Acrobeles complexus. Nose epidermal cells were found to be broadly similar to those of the distantly related model organism Caenorhabditis elegans in the number and arrangement of nuclei in these largely syncytial cells; this similarity demonstrates striking evolutionary conservation that allows for robust statements of homology between the taxa. Examining details of cell shape, however, revealed surprisingly complex subcellular specialization, which differed markedly from C. elegans in the number and arrangement of cell processes. Anterior toroid processes of the anterior arcade, posterior arcade, and HypB syncytia form a nested complex at the base of the labial probolae. Anterior toroid processes of HypC and the inner labial socket cells are associated with the base of the cephalic probolae and radial ridge processes. Extracellular filaments (tendon organs) and radiating cytoskeletal filaments of the posterior arcade syncytium form a connection between the body wall muscle cells and the pharynx. An epidermal cell with no known homolog in other nematodes is identified. Findings provide a basis to propose hypotheses related to the development and evolutionary origin of specialized feeding appendages (probolae) in the Cephalobinae (including Acrobeles), and hypotheses of homology are revised for epidermal cells in the nose of the closely related and primarily plant parasitic group, Tylenchida.

NF-M is an essential target for the myelin-directed "outside-in" signaling cascade that mediates radial axonal growth.

Neurofilaments are essential for acquisition of normal axonal calibers. Several lines of evidence have suggested that neurofilament-dependent structuring of axoplasm arises through an "outside-in" signaling cascade originating from myelinating cells. Implicated as targets in this cascade are the highly phosphorylated KSP domains of neurofilament subunits NF-H and NF-M. These are nearly stoichiometrically phosphorylated in myelinated internodes where radial axonal growth takes place, but not in the smaller, unmyelinated nodes. Gene replacement has now been used to produce mice expressing normal levels of the three neurofilament subunits, but which are deleted in the known phosphorylation sites within either NF-M or within both NF-M and NF-H. This has revealed that the tail domain of NF-M, with seven KSP motifs, is an essential target for the myelination-dependent outside-in signaling cascade that determines axonal caliber and conduction velocity of motor axons.

Depolarization redistributes synaptic membrane and creates a gradient of vesicles on the synaptic body at a ribbon synapse.

We used electron tomography of frog saccular hair cells to reconstruct presynaptic ultrastructure at synapses specialized for sustained transmitter release. Synaptic vesicles at inhibited synapses were abundant in the cytoplasm and covered the synaptic body at high density. Continuous maximal stimulation depleted 73% of the vesicles within 800 nm of the synapse, with a concomitant increase in surface area of intracellular cisterns and plasmalemmal infoldings. Docked vesicles were depleted 60%-80% regardless of their distance from the active zone. Vesicles on the synaptic body were depleted primarily in the hemisphere facing the plasmalemma, creating a gradient of vesicles on its surface. We conclude that formation of new synaptic vesicles from cisterns is rate limiting in the vesicle cycle.

Ultrastructural organization of lamprey reticulospinal synapses in three dimensions.

The giant reticulospinal synapse in lamprey provides a unique model to study synaptic vesicle traffic. The axon permits microinjections, and the active zones are often separated from each other, which makes it possible to track vesicle cycling at individual release sites. However, the proportion of reticulospinal synapses with individual active zones ("simple synapses") is unknown and a quantitative description of their organization is lacking. Here, we report such data obtained by serial section analysis, intermediate-voltage electron microscopy, and electron tomography. The simple synapse was the most common type (78%). It consisted of one active zone contacting one dendritic process. The remaining synapses were "complex," mostly containing one vesicle cluster and two to three active zones synapsing with distinct dendritic shafts. Occasional axosomatic synapses with multiple active zones forming synapses with the same cell were also observed. The vast majority of active zones in all synapse types contained both chemical and electrotonic synaptic specializations. Quantitative analysis of simple synapses showed that the majority had active zones with a diameter of 0.8-1.8 microm. The number of synaptic vesicles and the height of the vesicle cluster in middle sections of serially cut synapses correlated with the active zone length within, but not above, this size range. Electron tomography of simple synapses revealed small filaments between the clustered synaptic vesicles. A single vesicle could be in contact with up to 12 filaments. Another type of filament, also associated with synaptic vesicles, emerged from dense projections. Up to six filaments could be traced from one dense projection.