Strain Modulation of Si Vacancy Emission from SiC Micro- and Nanoparticles.

Single-photon emitting point defects in semiconductors have emerged as strong candidates for future quantum technology devices. In the present work, we exploit crystalline particles to investigate relevant defect localizations, emission shifting, and waveguiding. Specifically, emission from 6H-SiC micro- and nanoparticles ranging from 100 nm to 5 µm in size is collected using cathodoluminescence (CL), and we monitor signals attributed to the Si vacancy (VSi) as a function of its location. Clear shifts in the emission wavelength are found for emitters localized in the particle center and at the edges. By comparing spatial CL maps with strain analysis carried out in transmission electron microscopy, we attribute the emission shifts to compressive strain of 2-3% along the particle a-direction. Thus, embedding VSi qubit defects within SiC nanoparticles offers an interesting and versatile opportunity to tune single-photon emission energies while simultaneously ensuring ease of addressability via a self-assembled SiC nanoparticle matrix.

Reply to Comment on 'Nanoscale mapping of optical band gaps using monochromated electron energy loss spectroscopy'.

We respond to the comment by Thomas Walther and reaffirm the findings of our original article.

Nanoscale mapping of optical band gaps using monochromated electron energy loss spectroscopy.

Using monochromated electron energy loss spectroscopy in a probe-corrected scanning transmission electron microscope we demonstrate band gap mapping in ZnO/ZnCdO thin films with a spatial resolution below 10 nm and spectral precision of 20 meV.

Characterization of Giardia lamblia genotypes in dogs from Tucson, Arizona using SSU-rRNA and ß-giardin sequences.

The objective of this study was to determine if human genotypes of Giardia lamblia could be found in canine companion animals from urban and peri-urban environments in Tucson, Arizona. Canine fecal samples collected from the Humane Society of Southern Arizona between July 2006 and April 2009 were screened for G. lamblia infection using immunofluorescent microscopy and confirmed by polymerase chain reaction (PCR). Of the 672 samples screened, 196 were found positive by IFA and 185 of those positive were successfully amplified through PCR. Sequencing analysis showed samples were primarily of the C or D genotypes (n =154), or showing a mix of the C and D genotypes (n =10). One sample showed a mixed infection of a human genotype (A) and a dog-specific genotype (C). These data are consistent with previous studies showing dog specific genotypes to be dominant in environments where dog-to-dog transmission is likely to occur, and provides further evidence that multiple genes should be targeted for more accurate genotype characterization.

Optical signatures of single ion tracks in ZnO.

The optical properties of single ion tracks have been studied in ZnO implanted with Ge by combining depth-resolved hyperspectral cathodoluminescence (CL) and photoluminescence (PL) spectroscopy techniques. The results indicate that ZnO is susceptible to implantation doses as low as 108 to 109 cm-2. We demonstrate that the intensity ratio of ionized and neutral donor bound exciton emissions [D+X/D0X] can be used as a tracer for a local band bending both at the surface as well as in the crystal bulk along the ion tracks. The hyperspectral CL imaging performed at 80 K with 50 nm resolution over the regions with single ion tracks permitted direct assessment of the minority carrier diffusion length. The radii of distortion and space charge surrounding single ion tracks were estimated from the 2D distributions of defect-related green emission (GE) and excitonic D+X emission, both normalized with regard to neutral D0X emission, i.e., from the [GE/D0X] and [D+X/D0X] ratio maps. Our results indicate that single ion tracks in ZnO can be resolved up to ion doses of the order of 5 × 109 cm-2, in which defect aggregation along the extended defects obstructs signatures of individual tracks.

Experimental exploration of the amphoteric defect model by cryogenic ion irradiation of a range of wide band gap oxide materials.

The evolution of electrical resistance as function of defect concentration is examined for the unipolarn-conducting oxides CdO,ß-Ga2O3, In2O3, SnO2and ZnO in order to explore the predictions of the amphoteric defect model. Intrinsic defects are introduced by ion irradiation at cryogenic temperatures, and the resistance is measured in-situ by current-voltage sweeps as a function of irradiation dose. Temperature dependent Hall effect measurements are performed to determine the carrier concentration and mobility of the samples before and after irradiation. After the ultimate irradiation step, the Ga2O3and SnO2samples have both turned highly resistive. In contrast, the In2O3and ZnO samples are ultimately found to be less resistive than prior to irradiation, however, they both show an increased resistance at intermediate doses. Based on thermodynamic defect charge state transitions computed by hybrid density functional theory, a model expanding on the current amphoteric defect model is proposed.

Differential glycosylation of tractin and LeechCAM, two novel Ig superfamily members, regulates neurite extension and fascicle formation.

By immunoaffinity purification with the mAb Lan3-2, we have identified two novel Ig superfamily members, Tractin and LeechCAM. LeechCAM is an NCAM/FasII/ApCAM homologue, whereas Tractin is a cleaved protein with several unique features that include a PG/YG repeat domain that may be part of or interact with the extracellular matrix. Tractin and LeechCAM are widely expressed neural proteins that are differentially glycosylated in sets and subsets of peripheral sensory neurons that form specific fascicles in the central nervous system. In vivo antibody perturbation of the Lan3-2 glycoepitope demonstrates that it can selectively regulate extension of neurites and filopodia. Thus, these experiments provide evidence that differential glycosylation can confer functional diversity and specificity to widely expressed neural proteins.

The notch gene product is a glycoprotein expressed on the cell surface of both epidermal and neuronal precursor cells during Drosophila development.

The Notch locus of Drosophila melanogaster is one of a small number of zygotically acting "neurogenic" genes involved in the correct segregation of neural from epidermal lineages during embryogenesis as well as in other postembryonic developmental events. We have generated antibody probes against three regions of the Notch protein to study the expression of Notch and begin a biochemical characterization of the protein. Consistent with predictions based on DNA sequence data, here we gather evidence showing that Notch encodes a large, glycosylated surface protein with an apparent molecular mass of 300 kD: (a) all three antibodies detect Notch on Western blots as a high molecular mass, primarily full-length product; (b) immunoelectron microscopy localizes the Notch protein to the cell membrane; and (c) lentil lectin column binding demonstrates that the protein is glycosylated, indicative of its surface protein nature. In general, the distribution of the Notch protein coincides with that of the Notch transcript determined previously by in situ hybridizations. Notch is expressed in a much wider range of tissue types than those disrupted in the neurogenic mutant, as determined by antibody localization. Early labeling in the blastoderm appears ubiquitous except for the pole cells, but as development proceeds some distinctive features emerge: stronger staining is seen within the germ band layer where neuroblast delamination occurs, and the developing embryonic nervous system shows pronounced axonal staining. In third instar larvae, Notch is expressed in imaginal disks and in the central nervous system. Based on these results, certain models for how Notch controls the neuroblast cell fate choice are eliminated. We discuss how Notch may function in this choice as well as in other lineage fate determinations.

JIL-1, a chromosomal kinase implicated in regulation of chromatin structure, associates with the male specific lethal (MSL) dosage compensation complex.

JIL-1 is a novel chromosomal kinase that is upregulated almost twofold on the male X chromosome in Drosophila. Here we demonstrate that JIL-1 colocalizes and physically interacts with male specific lethal (MSL) dosage compensation complex proteins. Furthermore, ectopic expression of the MSL complex directed by MSL2 in females causes a concomitant upregulation of JIL-1 to the female X that is abolished in msl mutants unable to assemble the complex. Thus, these results strongly indicate JIL-1 associates with the MSL complex and further suggests JIL-1 functions in signal transduction pathways regulating chromatin structure.

Calsensin: a novel calcium-binding protein expressed in a subset of peripheral leech neurons fasciculating in a single axon tract.

The mAb lan3-6 recognizes a cytosolic antigen which is selectively expressed in the growth cones and axons of a small subset of peripheral sensory neurons fasciculating in a single tract common to all hirudinid leeches. We have used this antibody to clone a novel EF-hand calcium-binding protein, calsensin, by screening an expression vector library. A full-length clone of 1.1 kb identified by the antibody was isolated and sequenced. In situ hybridizations with calsensin probes and antibody staining using new polyclonal antisera generated against calsensin sequence demonstrate that calsensin indeed corresponds to the lan3-6 antigen. Calsensin consists of 83 residues with a calculated molecular mass of 9.1 kD that contains two helix-loop-helix domains. The calcium-binding domains are likely to be functional in vivo since a fusion protein derived from the calsensin clone binds 45Ca2+ in vitro. Immunoaffinity purification experiments with the lan3-6 antibody shows that a large 200,000 M(r) protein selectively copurifies with calsensin in two different leech species. These results suggest that calsensin may be functioning as a trigger protein which interacts with the larger protein. These data are consistent with the hypothesis that calsensin may mediate calcium-dependent signal transduction events in the growth cones and axons of this small group of sensory neurons which fasciculate in a single axon tract.

Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix.

A spindle matrix has been proposed to help organize and stabilize the microtubule spindle during mitosis, though molecular evidence corroborating its existence has been elusive. In Drosophila, we have cloned and characterized a novel nuclear protein, skeletor, that we propose is part of a macromolecular complex forming such a spindle matrix. Skeletor antibody staining shows that skeletor is associated with the chromosomes at interphase, but redistributes into a true fusiform spindle structure at prophase, which precedes microtubule spindle formation. During metaphase, the spindle, defined by skeletor antibody labeling, and the microtubule spindles are coaligned. We find that the skeletor-defined spindle maintains its fusiform spindle structure from end to end across the metaphase plate during anaphase when the chromosomes segregate. Consequently, the properties of the skeletor-defined spindle make it an ideal substrate for providing structural support stabilizing microtubules and counterbalancing force production. Furthermore, skeletor metaphase spindles persist in the absence of microtubule spindles, strongly implying that the existence of the skeletor-defined spindle does not require polymerized microtubules. Thus, the identification and characterization of skeletor represents the first direct molecular evidence for the existence of a complete spindle matrix that forms within the nucleus before microtubule spindle formation.

Tract formation and axon fasciculation of molecularly distinct peripheral neuron subpopulations during leech embryogenesis.

In leech, the central projections of peripheral sensory neurons segregate into specific axonal tracts, which are distinguished by differential expression of surface antigens recognized by the monoclonal antibodies Lan3-2 and Lan4-2. Lan3-2 recognizes an epitope expressed on axons that segregate into three distinct axon fascicles. In contrast, the Lan4-2-positive axons selectively project into only one of the Lan3-2-positive axon tracts. These observations provide evidence for a hierarchy of guidance cues mediating specific pathway formation in this system. Since the Lan3-2 antibody has been shown to perturb this process and since, as shown here, the Lan3-2 and Lan4-2 antigens are closely molecularly interrelated, these antibodies may help define molecules and epitopes mediating neuronal recognition and axonal guidance.

Defect segregation and optical emission in ZnO nano- and microwires.

The spatial distribution of defect related deep band emission has been studied in zinc oxide (ZnO) nano- and microwires using depth resolved cathodoluminescence spectroscopy (DRCLS) in a hyperspectral imaging (HSI) mode within a UHV scanning electron microscope (SEM). Three sets of wires were examined that had been grown by pulsed laser deposition or vapor transport methods and ranged in diameter from 200 nm-2.7 µm. This data was analyzed by developing a 3D DRCLS simulation and using it to estimate the segregation depth and decay profile of the near surface defects. We observed different dominant defects from each growth process as well as diameter-dependent defect segregation behavior.

Antibody identification, chromosome map assignment, and sequence analysis of a Rab escort protein homolog in Drosophila1.

Using a polyclonal antiserum a cDNA encoding a Rab escort protein (REP) homolog in Drosophila has been identified and sequenced. The gene encodes a 511 residue protein with a predicted molecular mass of 56855 Da. Antibody labeling demonstrates that Drosophila REP protein is present in the early embryo and that it is being apportioned uniformly throughout the embryo in a process likely to be linked to the syncytial nuclear divisions. In situ hybridization to polytene chromosomes reveals that the Drosophila REP gene is located in the 56E region on the second chromosome. Drosophila REP is the first invertebrate REP homolog to be identified and characterized.

Differential glycosylation and proteolytical processing of LeechCAM in central and peripheral leech neurons.

LeechCAM is a recently described member of the Ig-superfamily which has five Ig-domains, two FNIII-domains, a transmembrane domain, and a cytoplasmic domain. Phylogenetic analysis indicated that LeechCAM is the leech homolog of apCAM, FasII, and vertebrate NCAM. Using a leechCAM-specific monoclonal antibody we show by immunoblot analysis and by Triton X-114 phase separation experiments that in addition to existing in a transmembrane version LeechCAM is likely to be proteolytically cleaved into a secreted form without the transmembrane domain and the intracellular tail. Furthermore, by immunoprecipitation we demonstrate that LeechCAM is glycosylated with the Laz2-369 glycoepitope, an epitope that has been specifically implicated in regulation of axonal outgrowth and synapse formation.

Posttranslational processing and differential glycosylation of Tractin, an Ig-superfamily member involved in regulation of axonal outgrowth.

Tractin is a novel member of the Ig-superfamily which has a highly unusual structure. It contains six Ig domains, four FNIII-like domains, an acidic domain, 12 repeats of a novel proline- and glycine-rich motif with sequence similarity to collagen, a transmembrane domain, and an intracellular tail with an ankyrin and a PDZ domain binding motif. By generating domain-specific antibodies, we show that Tractin is proteolytically processed at two cleavage sites, one located in the third FNIII domain, and a second located just proximal to the transmembrane domain resulting in the formation of four fragments. The most NH(2)-terminal fragment which is glycosylated with the Lan3-2, Lan4-2, and Laz2-369 glycoepitopes is secreted, and we present evidence which supports a model in which the remaining fragments combine to form a secreted homodimer as well as a transmembrane heterodimer. The extracellular domain of the dimers is mostly made up of the collagen-like PG/YG-repeat domain but also contains 11/2 FNIII domain and the acidic domain. The collagen-like PG/YG-repeat domain could be selectively digested by collagenase and we show by yeast two-hybrid analysis that the intracellular domain of Tractin can interact with ankyrin. Thus, the transmembrane heterodimer of Tractin constitutes a novel protein domain configuration where sequence that has properties similar to that of extracellular matrix molecules is directly linked to the cytoskeleton through interactions with ankyrin.

Molecular identification and sequence analysis of Hillarin, a novel protein localized at the axon hillock.

The monoclonal antibody Lan3-15 identifies a novel protein, Hillarin, that is localized to the axon hillock of leech neurons. Using this antibody we have identified a full length cDNA coding for leech Hillarin and determined its sequence. The gene encodes a 1274 residue protein with a predicted molecular mass of 144013 Da. Data base searches revealed that leech Hillarin has potential orthologues in fly and nematode and that these proteins share two novel protein domains. The W180 domain is characterized by five conserved tryptophans whereas the H domains share 21 invariant residues. In contrast to the arrangement in fly and nematode the cassette containing the W180 and H domains is repeated twice in leech Hillarin. This suggests that the leech Hillarin sequence originated from a duplication event of an ancestral protein with single cassette structure.

Molecular mechanisms mediating axon pathway formation.

During nervous system formation nerve cells extend axons in order to form precise patterns of neuronal connectivity. These connections are often established after the neuronal growth cones have pioneered or navigated through complex pathways to their target area both within the CNS and to and from the periphery. Recent studies have provided evidence that the process of specific pathway formation may rely on a number of molecular guidance mechanisms and cues such as selective adhesion, growth cone avoidance, surface gradients, guidepost cells, and chemotropism. Analysis of the molecular basis for these guidance mechanisms show that the molecules involved often belong to distinct multigene families and that they can provide both short- and long-range attractive as well as repulsive cues. Many of these molecules have a modular structure that is made up of different tandemly arranged domains that allow for multiple functional interactions with a range of other molecules. This allows the same molecule to be multifunctional, for example, by attracting certain neurons while repelling others. This review is an overview of the molecular structure, as it relates to function and mechanisms of action of some of the major gene families thought to be mediating specific axonal guidance and pathway formation.

Chromatin structure and nuclear remodeling.

Nuclear architecture is remodeled during interphase in response to changes in gene activity as well as to changing structural and functional requirements during cell division. Using the monoclonal antibody mAb2A, we have identified two proteins that appear to play important roles in these processes: JIL-1 is a tandem serine-threonine kinase implicated in the regulation of chromatin structure, whereas Skeletor is a novel protein participating in structural nuclear remodeling during the cell cycle. Antibody staining and live imaging of JIL-1-GFP transgenic flies show that JIL-1 localizes to the gene-rich interband regions of larval polytene chromosomes and is upregulated almost twofold on the hypertranscribed male X chromosome compared with autosomes. We propose that JIL-1 may play a role in transcriptional control potentially by regulating chromatin structure. The other mAb2A antigen, Skeletor, is distributed in a nuclear meshwork pattern that can be observed in stereo pair images to reorganize during the cell cycle to form a spindle-like structure at prometaphase that is distinct from the microtubule spindle apparatus. Taking advantage of the powerful molecular and genetic approaches offered in Drosophila, the study of these two proteins promises to yield new insight into what defines nuclear architecture at the molecular level and how its remodeling is regulated.

Initial formation and secondary condensation of nerve pathways in the medicinal leech.

Invertebrates have proved to be important experimental systems for examining questions related to growth cone navigation and nerve formation, in large part because of their simpler nervous systems. However, such apparent simplicity can be deceiving because the final stereotyped patterns may be the result of multiple developmental mechanisms and not necessarily the sole consequence of the pathway choices of individual growth cones. We have examined the normal sequence of events that are involved in the formation of the major peripheral nerves in leech embryos by employing (1) an antibody directed against acetylated tubulin to label neurons growing out from the central nervous system, (2) the Lan3-2 antibody to label a specific population of peripheral neurons growing into the central nervous system, and (3) intracellular dye filling of single cells. We found that the mature pattern of nerves was characterized by a pair of large nerve roots, each of which branched into two major tracts. The earliest axonal projections did not, however, establish this pattern definitively. Rather, each of the four nerves initially formed as discrete, roughly parallel tracts without bifurcation, with the final branching pattern of the nerve roots being generated by a secondary condensation. In addition, we found that some of the nerves were pioneered in different ways and by different groups of neurons. One of the nerves was established by central neurons growing peripherally, another by peripheral neurons growing centrally. These results suggest that the formation of common nerves and neuronal pathfinding in the leech involves multiple sets of growth cone guidance strategies and morphogenetic mechanisms that belie its apparent simplicity.