Space-Time Structured Plasma Waves

Electrostatic waves play a critical role in nearly every branch of plasma physics from fusion to advanced accelerators, to astro, solar, and ionospheric physics. The properties of planar electrostatic waves are fully determined by the plasma conditions, such as density, temperature, ionization state, or details of the distribution functions. Here we demonstrate that electrostatic wave packets structured with space-time correlations can have properties that are independent of the plasma conditions. For instance, an appropriately structured electrostatic wave packet can travel at any group velocity, even backward with respect to its phase fronts, while maintaining a localized energy density. These linear, propagation-invariant wave packets can be constructed with or without orbital angular momentum by superposing natural modes of the plasma and can be ponderomotively excited by space-time structured laser pulses like the flying focus.

Dephasingless laser wakefield acceleration in the bubble regime

Laser wakefield accelerators (LWFAs) have electric fields that are orders of magnitude larger than those of conventional accelerators, promising an attractive, small-scale alternative for next-generation light sources and lepton colliders. The maximum energy gain in a single-stage LWFA is limited by dephasing, which occurs when the trapped particles outrun the accelerating phase of the wakefield. Here, we demonstrate that a single space-time structured laser pulse can be used for ionization injection and electron acceleration over many dephasing lengths in the bubble regime. Simulations of a dephasingless laser wakefield accelerator driven by a 6.2-J laser pulse show 25 pC of injected charge accelerated over 20 dephasing lengths (1.3 cm) to a maximum energy of 2.1 GeV. The space-time structured laser pulse features an ultrashort, programmable-trajectory focus. Accelerating the focus, reducing the focused spot-size variation, and mitigating unwanted self-focusing stabilize the electron acceleration, which improves beam quality and leads to projected energy gains of 125 GeV in a single, sub-meter stage driven by a 500-J pulse.

Programmable-trajectory ultrafast flying focus pulses

"Flying focus" techniques produce laser pulses with dynamic focal points that travel distances much greater than a Rayleigh length. The implementation of these techniques in laser-based applications requires the design of optical configurations that can both extend the focal range and structure the radial group delay. This article describes a method for designing optical configurations that produce ultrashort flying focus pulses with programmable-trajectory focal points. The method is illustrated by several examples that employ an axiparabola for extending the focal range and either a reflective echelon or a deformable mirror-spatial light modulator pair for structuring the radial group delay. The latter configuration enables rapid exploration and optimization of flying foci, which could be ideal for experiments.

Model-scale jet noise analysis with a single-point, frequency-domain nonlinearity indicator

A single-point, frequency-domain nonlinearity indicator is calculated and analyzed for noise from a model-scale jet at Mach 0.85, Mach 1.8, and Mach 2.0. The nonlinearity indicator, ν_N, has been previously derived from an ensemble-averaged, frequency-domain version of the generalized Burgers equation (GBE) from Reichman, Gee, Neilsen, and Miller [J. Acoust. Soc. Am. 139, 2505-2513 (2016)]. The indicator gives the spatial rate of change due to nonlinear processes in sound pressure level (SPL) spectrum, and two other indicators from the GBE-ν_S and ν_α-give the same quantity due to geometric spreading and absorption, respectively. Trends with frequency, angle, distance, and jet condition-supported both by spectral analysis and by calculation of the GBE-derived indicators-reveal a concentration of nonlinear effects along radials close to the plume with large overall SPLs. The calculated indicators for nonlinearity and absorption effects far from the source combine to give the same decay predicted by nonlinear theory for monofrequency sources. Trends in the ν_N indicator are compared with trends observed for other indicators such as pressure-derivative skewness and bicoherence, revealing both the qualitative and quantitative advantages of the ν_N indicator.

Asymptotic behavior of a frequency-domain nonlinearity indicator for solutions to the generalized Burgers equation

A frequency-domain nonlinearity indicator has previously been characterized for two analytical solutions to the generalized Burgers equation (GBE) [Reichman, Gee, Neilsen, and Miller, J. Acoust. Soc. Am. 139, 2505-2513 (2016)], including an analytical, asymptotic expression for the Blackstock Bridging Function. This letter gives similar old-age analytical expressions of the indicator for the Mendousse solution and a computational solution to the GBE with spherical spreading. The indicator can be used to characterize the cumulative nonlinearity of a waveform with a single-point measurement, with suggested application to noise waveforms as well.

Quantitative analysis of a frequency-domain nonlinearity indicator

In this paper, quantitative understanding of a frequency-domain nonlinearity indicator is developed. The indicator is derived from an ensemble-averaged, frequency-domain version of the generalized Burgers equation, which can be rearranged in order to directly compare the effects of nonlinearity, absorption, and geometric spreading on the pressure spectrum level with frequency and distance. The nonlinear effect is calculated using pressure-squared-pressure quadspectrum. Further theoretical development has given an expression for the role of the normalized quadspectrum, referred to as Q/S by Morfey and Howell [AIAA J. 19, 986-992 (1981)], in the spatial rate of change of the pressure spectrum level. To explore this finding, an investigation of the change in level for initial sinusoids propagating as plane waves through inviscid and thermoviscous media has been conducted. The decibel change with distance, calculated through Q/S, captures the growth and decay of the harmonics and indicates that the most significant changes in level occur prior to sawtooth formation. At large distances, the inviscid case results in a spatial rate of change that is uniform across all harmonics. For thermoviscous media, large positive nonlinear gains are observed but offset by absorption, which leads to a greater overall negative spatial rate of change for higher harmonics.

Intestinal smooth muscle phenotype determines enteric neuronal survival via GDNF expression

Intestinal inflammation causes initial axonal degeneration and neuronal death, as well as the proliferation of intestinal smooth muscle cells (ISMC), but subsequent axonal outgrowth leads to re-innervation. We recently showed that expression of glial cell-derived neurotrophic factor (GDNF), the critical neurotrophin for the post-natal enteric nervous system (ENS) is upregulated in ISMC by inflammatory cytokines, leading us to explore the relationship between ISMC growth and GDNF expression. In co-cultures of myenteric neurons and ISMC, GDNF or fetal calf serum (FCS) was equally effective in supporting neuronal survival, with neurons forming extensive axonal networks among the ISMC. However, only GDNF was effective in low-density cultures where neurons lacked contact with ISMC. In early-passage cultures of colonic circular smooth muscle cells (CSMC), polymerase chain reaction (PCR) and western blotting showed that proliferation was associated with expression of GDNF, and the successful survival of neonatal neurons co-cultured on CSMC was blocked by vandetanib or siGDNF. In tri-nitrobenzene sulfonic acid (TNBS)-induced colitis, immunocytochemistry showed the selective expression of GDNF in proliferating CSMC, suggesting that smooth muscle proliferation supports the ENS in vivo as well as in vitro. However, high-passage CSMC expressed significantly less GDNF and failed to support neuronal survival, while expressing reduced amounts of smooth muscle marker proteins. We conclude that in the inflamed intestine, smooth muscle proliferation supports the ENS, and thus its own re-innervation, by expression of GDNF. In chronic inflammation, a compromised smooth muscle phenotype may lead to progressive neural damage. Intestinal stricture formation in human disease, such as inflammatory bowel disease (IBD), may be an endpoint of failure of this homeostatic mechanism.

An in vitro biofilm model to examine the effect of antibiotic ointments on biofilms produced by burn wound bacterial isolates

PURPOSE

Topical treatment of burn wounds is essential as reduced blood supply in the burned tissues restricts the effect of systemic antibiotics. On the burn surface, microorganisms exist within a complex structure termed a biofilm, which enhances bacterial resistance to antimicrobial agents significantly. Since bacteria differ in their ability to develop biofilms, the susceptibility of these biofilms to topically applied antibiotics varies, making it essential to identify which topical antibiotics efficiently disrupt or prevent biofilms produced by these pathogens. Yet, a simple in vitro assay to compare the susceptibility of biofilms produced by burn wound isolates to different topical antibiotics has not been reported.

METHODS

Biofilms were developed by inoculating cellulose disks on agar plates with burn wound isolates and incubating for 24h. The biofilms were then covered for 24h with untreated gauze or gauze coated with antibiotic ointment and remaining microorganisms were quantified and visualized microscopically.

RESULTS

Mupirocin and triple antibiotic ointments significantly reduced biofilms produced by the Staphylococcus aureus and Pseudomonas aeruginosa burn wound isolates tested, as did gentamicin ointment, with the exception of one P. aeruginosa clinical isolate.

CONCLUSIONS

The described assay is a practical and reproducible approach to identify topical antibiotics most effective in eliminating biofilms produced by burn wound isolates.

Deep drilling into the Chesapeake Bay impact structure

Samples from a 1.76-kilometer-deep corehole drilled near the center of the late Eocene Chesapeake Bay impact structure (Virginia, USA) reveal its geologic, hydrologic, and biologic history. We conducted stratigraphic and petrologic analyses of the cores to elucidate the timing and results of impact-melt creation and distribution, transient-cavity collapse, and ocean-water resurge. Comparison of post-impact sedimentary sequences inside and outside the structure indicates that compaction of the crater fill influenced long-term sedimentation patterns in the mid-Atlantic region. Salty connate water of the target remains in the crater fill today, where it poses a potential threat to the regional groundwater resource. Observed depth variations in microbial abundance indicate a complex history of impact-related thermal sterilization and habitat modification, and subsequent post-impact repopulation.

HIV serodiscordant sex partners and the prevalence of human herpesvirus 8 infection among HIV negative men who have sex with men: baseline data from the EXPLORE Study

OBJECTIVES

Human herpesvirus 8 (HHV-8) infection is common among men who have sex with men (MSM), especially those infected with HIV, and is frequently detected in saliva. We sought to determine whether oral or anogenital contact with HIV discordant, or unknown serostatus sexual partners is associated with HHV-8 seroprevalence among HIV negative MSM.

METHODS

HIV negative MSM participating in a behavioural intervention trial for the prevention of HIV infection (the EXPLORE study) were recruited from the Seattle and Denver areas for participation in this cross sectional study. Participants completed detailed questionnaires regarding sexual behaviour, focusing on activities with possible exposure to the oropharynx. Serum samples from study enrollment were tested for the presence of HHV-8 antibodies using whole virus enzyme immunoassay and immunofluorescence assay to latent and lytic proteins.

RESULTS

198/819 MSM (24.3%) were HHV-8 antibody positive. Exposure to saliva with HIV positive and HIV unknown serostatus sex partners was reported by 83% and 90% of all men, respectively. In a multivariate model, reporting more than the median number of lifetime sex partners (OR 2.2, p = 0.03) or lifetime sex partners of unknown HIV status (OR 1.7, p = 0.03), and the performance of oro-anal sex ("rimming") on partners whose HIV status is unknown (OR 2.7, p = 0.04) were independently associated with HHV-8 infection.

CONCLUSIONS

The oropharynx may be an important anatomical site in HHV-8 acquisition, and contact with HIV serodiscordant or unknown sex partners is associated with higher HHV-8 seroprevalence among HIV negative MSM.

A role for RIC-8 (Synembryn) and GOA-1 (G(o)alpha) in regulating a subset of centrosome movements during early embryogenesis in Caenorhabditis elegans

RIC-8 (synembryn) and GOA-1 (G(o)alpha) are key components of a signaling network that regulates neurotransmitter secretion in Caenorhabditis elegans. Here we show that ric-8 and goa-1 reduction of function mutants exhibit partial embryonic lethality. Through Nomarski analysis we show that goa-1 and ric-8 mutant embryos exhibit defects in multiple events that involve centrosomes, including one-cell posterior centrosome rocking, P(1) centrosome flattening, mitotic spindle alignment, and nuclear migration. In ric-8 reduction of function backgrounds, the embryonic lethality, spindle misalignments and delayed nuclear migration are strongly enhanced by a 50% reduction in maternal goa-1 gene dosage. Several other microfilament- and microtubule-mediated events, as well as overall embryonic polarity, appear unperturbed in the mutants. In addition, our results suggest that RIC-8 and GOA-1 do not have roles in centrosome replication, in the diametric movements of daughter centrosomes along the nuclear membrane, or in the extension of microtubules from centrosomes. Through immunostaining we show that GOA-1 (G(o)alpha) localizes to cell cortices as well as near centrosomes. Our results demonstrate that two components of a neuronal signal transduction pathway also play a role in centrosome movements during early embryogenesis.

Class VI unconventional myosin is required for spermatogenesis in Drosophila

We have identified partial loss of function mutations in class VI unconventional myosin, 95F myosin, which results in male sterility. During spermatogenesis the germ line precursor cells undergo mitosis and meiosis to form a bundle of 64 spermatids. The spermatids remain interconnected by cytoplasmic bridges until individualization. The process of individualization involves the formation of a complex of cytoskeletal proteins and membrane, the individualization complex (IC), around the spermatid nuclei. This complex traverses the length of each spermatid resolving the shared membrane into a single membrane enclosing each spermatid. We have determined that 95F myosin is a component of the IC whose function is essential for individualization. In wild-type testes, 95F myosin localizes to the leading edge of the IC. Two independent mutations in 95F myosin reduce the amount of 95F myosin in only a subset of tissues, including the testes. This reduction of 95F myosin causes male sterility as a result of defects in spermatid individualization. Germ line transformation with the 95F myosin heavy chain cDNA rescues the male sterility phenotype. IC movement is aberrant in these 95F myosin mutants, indicating a critical role for 95F myosin in IC movement. This report is the first identification of a component of the IC other than actin. We propose that 95F myosin is a motor that participates in membrane reorganization during individualization.

The Source and Fate of Massive Carbon Input During the Latest Paleocene Thermal Maximum

Lithologic, faunal, seismic, and isotopic evidence from the Blake Nose (subtropical western North Atlantic) links a massive release of biogenic methane approximately 55.5 million years ago to a warming of deep-ocean and high-latitude surface waters, a large perturbation in the combined ocean-atmosphere carbon cycle (the largest of the past 90 million years), a mass extinction event in benthic faunas, and a radiation of mammalian orders. The deposition of a mud clast interval and seismic evidence for slope disturbance are associated with intermediate water warming, massive carbon input to the global exogenic carbon cycle, pelagic carbonate dissolution, a decrease in dissolved oxygen, and a benthic foraminiferal extinction event. These events provide evidence to confirm the gas hydrate dissociation hypothesis and identify the Blake Nose as a site of methane release.

The actin cytoskeleton is required for maintenance of posterior pole plasm components in the Drosophila embryo

Localization of mRNAs is one of many aspects of cellular organization that requires the cytoskeleton. In Drosophila, microtubules are known to be required for correct localization of developmentally important mRNAs and proteins during oogenesis; however, the role of the actin cytoskeleton in localization is less clear. Furthermore, it is not known whether either of these cytoskeletal systems are necessary for maintenance of RNA localization in the early embryo. We have examined the contribution of the actin and microtubule cytoskeletons to maintenance of RNA and protein localization in the early Drosophila embryo. We have found that while microtubules are not necessary, the actin cytoskeleton is needed for stable association of nanos, oskar, germ cell-less and cyclin B mRNAs and Oskar and Vasa proteins at the posterior pole in the early embryo. In contrast, bicoid RNA, which is located at the anterior pole, does not require either cytoskeletal system to remain at the anterior.

A class VI unconventional myosin is associated with a homologue of a microtubule-binding protein, cytoplasmic linker protein-170, in neurons and at the posterior pole of Drosophila embryos

Coordination of cellular organization requires the interaction of the cytoskeletal filament systems. Recently, several lines of investigation have suggested that transport of cellular components along both microtubules and actin filaments is important for cellular organization and function. We report here on molecules that may mediate coordination between the actin and microtubule cytoskeletons. We have identified a 195-kD protein that coimmunoprecipitates with a class VI myosin, Drosophila 95F unconventional myosin. Cloning and sequencing of the gene encoding the 195-kD protein reveals that it is the first homologue identified of cytoplasmic linker protein (CLIP)-170, a protein that links endocytic vesicles to microtubules. We have named this protein D-CLIP-190 (the predicted molecular mass is 189 kD) based on its similarity to CLIP-170 and its ability to cosediment with microtubules. The similarity between D-CLIP-190 and CLIP-170 extends throughout the length of the proteins, and they have a number of predicted sequence and structural features in common. 95F myosin and D-CLIP-190 are coexpressed in a number of tissues during embryogenesis in Drosophila. In the axonal processes of neurons, they are colocalized in the same particulate structures, which resemble vesicles. They are also colocalized at the posterior pole of the early embryo, and this localization is dependent on the actin cytoskeleton. The association of a myosin and a homologue of a microtubule-binding protein in the nervous system and at the posterior pole, where both microtubule and actin-dependent processes are known to be important, leads us to speculate that these two proteins may functionally link the actin and microtubule cytoskeletons.

A genetic selection for Caenorhabditis elegans synaptic transmission mutants

We have isolated 165 Caenorhabditis elegans mutants, representing 21 genes, that are resistant to inhibitors of cholinesterase (Ric mutants). Since mutations in 20 of the genes appear not to affect acetylcholine reception, we suggest that reduced acetylcholine release contributes to the Ric phenotype of most Ric mutants. Mutations in 15 of the genes lead to defects in a gamma-aminobutyric acid-dependent behavior; these genes are likely to encode proteins with general, rather than cholinergic-specific, roles in synaptic transmission. Ten of the genes have been cloned. Seven encode homologs of proteins that function in the synaptic vesicle cycle: two encode cholinergic-specific proteins, while five encode general presynaptic proteins. Two other Ric genes encode homologs of G-protein signaling molecules. Our assessment of synaptic function in Ric mutants, combined with the homologies of some Ric mutants to presynaptic proteins, suggests that the analysis of Ric genes will continue to yield insights into the regulation and functioning of synapses.

The LYS5 gene of Saccharomyces cerevisiae

The LYS2 and LYS5 genes of Saccharomyces cerevisiae together encode the 180-kDa alpha-aminoadipate reductase (AAR) in the biosynthetic pathway of lysine. The 4.8-kb LYS2 gene encodes the 155-kDa subunit of AAR. The complete nucleotide (nt) sequence of the 1.1-kb LYS5 gene is presented in this report. It contains a single continuous open reading frame of 816 nt encoding a 272-amino-acid, 30.6-kDa polypeptide.

Actin organization, bristle morphology, and viability are affected by actin capping protein mutations in Drosophila

Regulation of actin filament length and orientation is important in many actin-based cellular processes. This regulation is postulated to occur through the action of actin-binding proteins. Many actin-binding proteins that modify actin in vitro have been identified, but in many cases, it is not known if this activity is physiologically relevant. Capping protein (CP) is an actin-binding protein that has been demonstrated to control filament length in vitro by binding to the barbed ends and preventing the addition or loss of actin monomers. To examine the in vivo role of CP, we have performed a molecular and genetic characterization of the beta subunit of capping protein from Drosophila melanogaster. We have identified mutations in the Drosophila beta subunit-these are the first CP mutations in a multicellular organism, and unlike CP mutations in yeast, they are lethal, causing death during the early larval stage. Adult files that are heterozygous for a pair of weak alleles have a defect in bristle morphology that is correlated to disorganized actin bundles in developing bristles. Our data demonstrate that CP has an essential function during development, and further suggest that CP is required to regulate actin assembly during the development of specialized structures that depend on actin for their morphology.

The 95F unconventional myosin is required for proper organization of the Drosophila syncytial blastoderm

The 95F myosin, a class VI unconventional myosin, associates with particles in the cytoplasm of the Drosophila syncytial blastoderm and is required for the ATP- and F-actin-dependent translocation of these particles. The particles undergo a cell cycle-dependent redistribution from domains that surround each nucleus in interphase to transient membrane invaginations that provide a barrier between adjacent spindles during mitosis. When 95F myosin function is inhibited by antibody injection, profound defects in syncytial blastoderm organization occur. This disorganization is seen as aberrant nuclear morphology and position and is suggestive of failures in cytoskeletal function. Nuclear defects correlate with gross defects in the actin cytoskeleton, including indistinct actin caps and furrows, missing actin structures, abnormal spacing of caps, and abnormally spaced furrows. Three-dimensional examination of embryos injected with anti-95F myosin antibody reveals that actin furrows do not invaginate as deeply into the embryo as do normal furrows. These furrows do not separate adjacent mitoses, since microtubules cross over them. These inappropriate microtubule interactions lead to aberrant nuclear divisions and to the nuclear defects observed. We propose that 95F myosin function is required to generate normal actin-based transient membrane furrows. The motor activity of 95F myosin itself and/or components within the particles transported to the furrows by 95F myosin may be required for normal furrows to form.

Transport of cytoplasmic particles catalysed by an unconventional myosin in living Drosophila embryos

Myosins are actin-activated ATPases that are able to translocate along actin filaments using energy derived from ATP hydrolysis. Non-muscle cells contain conventional myosins, which are similar in sequence and structure to muscle myosin, and a number of unconventional myosins whose head sequences are similar but tail sequences are unrelated to conventional myosins. The myosin superfamily currently consists of nine classes; Drosophila 95F is an unconventional myosin and the original member of class VI, which includes a homologue found in pig kidney. Some unconventional myosins have been suggested as mediators of some types of intracellular transport, but there is little direct evidence for this function (but see ref. 6). We have observed transport of cytoplasmic particles in live Drosophila embryos in three dimensions using computational optical sectioning microscopy. We present here evidence that this transport is actin-based, ATP-dependent and catalysed by one such unconventional myosin, the 95F myosin. This is, to our knowledge, the first direct observation of transport catalysed by an unconventional myosin in living cells.

Isolation of cytoskeletal proteins from Drosophila

In this summary of methods, we have attempted to present a series of protocols relevant to the study of proteins that associate with each other inside cells. These techniques have found their main application, in our hands, to cytoskeletal structures, but the utility of these techniques is limited to this application. As we learn more about the physiology and organization of eukaryotic cells, information from a variety of studies and systems indicates that many processes occur in a highly spatially organized manner in cells, using multiprotein complexes. The techniques described here will find application to the study of how organization and associations between proteins contribute to many of cellular processes.

Identification of a 34 kDa protein specific to synaptic vesicles

In this study, we used synaptic vesicles purified from the electric organ of marine electric rays to search for novel molecules which have important functions in synaptic transmission. Proteins that copurified with synaptic vesicles were used to immunize rats, and the resulting antisera were then used to further characterize the vesicle proteins. One of the antisera recognizes a protein of 34 kDa, p34, that has several characteristics which suggest it is a synaptic vesicle specific protein: (1) it copurifies exclusively with the synaptic vesicle peak during permeation chromatography on a controlled pore glass beads column, (2) it can be immunoprecipitated with intact synaptic vesicles and (3) it is specifically localized to the nervous system. The results suggest that p34 is a synaptic vesicle specific protein with a widespread distribution in the nervous system.

Casein kinase II phosphorylates the synaptic vesicle protein p65

p65 (synaptotagmin), an abundant synaptic vesicle protein, has been implicated in the processes of vesicle docking and fusion. To characterize further the properties of this important neuronal protein, we have investigated its phosphorylation in vitro. Immunoprecipitation of p65 results in coprecipitation of a protein kinase that phosphorylates p65 as well as syntaxin, a plasma membrane protein that interacts with p65. p65 is phosphorylated on a threonine residue (Thr-128) within the cytoplasmic domain near the transmembrane region. The coprecipitating protein kinase was identified as casein kinase II based on its catalytic properties, the sequence surrounding Thr-128, and Western blot analysis of the anti-p65 immunoprecipitates. Affinity chromatography utilizing bacterially expressed fragments of p65 demonstrated that casein kinase II interacts with a domain of p65 distinct from the phosphorylation site. In a synaptic vesicle fraction, the phosphorylation of p65 is stimulated by sphingosine and by detergent solubilization, suggesting that p65 phosphorylation may be subject to regulatory processes.

Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos

In the syncytial blastoderm stage of Drosophila embryogenesis, dome-shaped actin "caps" are observed above the interphase nuclei. During mitosis, this actin rearranges to participate in the formation of pseudocleavage furrows, transient membranous invaginations between dividing nuclei. Embryos laid by homozygous sponge mothers lack these characteristic actin structures, but retain other actin associated structures and processes. Our results indicate that the sponge product is specifically required for the formation of actin caps and metaphase furrows. The specificity of the sponge phenotype permits dissection of both the process of actin cap formation and the functions of actin caps and metaphase furrows. Our data demonstrate that the distribution of actin binding protein 13D2 is unaffected in sponge embryos and suggest that 13D2 is upstream of actin in cortical cap assembly. Although actin caps and metaphase furrows have been implicated in maintaining the fidelity of nuclear division and the positions of nuclei within the cortex, our observations indicate that these structures are dispensible during the early syncytial blastoderm cell cycles. A later requirement for actin metaphase furrows in preventing the nucleation of mitotic spindles between inappropriate centrosomes is observed. Furthermore, the formation of actin caps and metaphase furrows is not a prerequisite for the formation of the hexagonal array of actin instrumental in the conversion of the syncytial embryo into a cellular blastoderm.

An unconventional myosin heavy chain gene from Drosophila melanogaster

As part of a study of cytoskeletal proteins involved in Drosophila embryonic development, we have undertaken the molecular analysis of a 140-kD ATP-sensitive actin-binding protein (Miller, K. G., C. M. Field, and B. M. Alberts. 1989. J. Cell Biol. 109:2963-2975). Analysis of cDNA clones encoding this protein revealed that it represents a new class of unconventional myosin heavy chains. The amino-terminal two thirds of the protein comprises a head domain that is 29-33% identical (60-65% similar) to other myosin heads, and contains ATP-binding, actin-binding and calmodulin/myosin light chain-binding motifs. The carboxy-terminal tail has no significant similarity to other known myosin tails, but does contain a approximately 100-amino acid region that is predicted to form an alpha-helical coiled-coil. Since the unique gene that encodes this protein maps to the polytene map position 95F, we have named the new gene Drosophila 95F myosin heavy chain (95F MHC). The expression profile of the 95F MHC gene is complex. Examination of multiple cDNAs reveals that transcripts are alternatively spliced and encode at least three protein isoforms; in addition, a fourth isoform is detected on Western blots. Developmental Northern and Western blots show that transcripts and protein are present throughout the life cycle, with peak expression occurring during mid-embryogenesis and adulthood. Immunolocalization in early embryos demonstrates that the protein is primarily located in a punctate pattern throughout the peripheral cytoplasm. Most cells maintain a low level of protein expression throughout embryogenesis, but specific tissues appear to contain more protein. We speculate that the 95F MHC protein isoforms are involved in multiple dynamic processes during Drosophila development.

p65 fragments, homologous to the C2 region of protein kinase C, bind to the intracellular receptors for protein kinase C

Receptors for activated protein kinase C (RACKs) have been isolated from the particulate cell fraction of heart and brain. We previously demonstrated that binding of protein kinase C (PKC) to RACKs requires PKC activators and is via a site on PKC that is distinct from the substrate binding site. Here, we examine the possibility that the C2 region in the regulatory domain of PKC is involved in binding of PKC to RACKs. The synaptic vesicle-specific p65 protein contains two regions homologous to the C2 region of PKC. We found that three p65 fragments, containing either one or two of these PKC C2 homologous regions, bound to highly purified RACKs. Binding of the p65 fragments and PKC to RACKs was mutually exclusive; preincubation of RACKs with the p65 fragments inhibited PKC binding, and preincubation of RACKs with PKC inhibited binding of the p65 fragments. Preincubation of the p65 fragments with a peptide resembling the PKC binding site on RACKs also inhibited p65 binding to RACKs, suggesting that PKC and p65 bind to the same or nearby regions on RACKs. Since the only homologous region between PKC and the p65 fragments is the C2 region, these results suggest that the C2 region on PKC contains at least part of the RACK binding site.

Differential expression of the p65 gene family

The genome of the marine ray Discopyge ommata contains at least three p65-related genes. o-p65-A is 84% identical, o-p65-B is 78% identical, and o-p65-C is only 41% identical to a previously characterized rat p65. The cytoplasmic domain, particularly the two regions that are similar to the regulatory domain of protein kinase C, are most highly conserved. The three genes are expressed in different but overlapping patterns in the central nervous system. o-p65-A immunoreactivity is found predominantly in forebrain, cerebellum, and neuroendocrine cells, while o-p65-B immunoreactivity is predominantly localized to the spinal cord, brainstem, and midbrain. Many synaptic vesicle proteins are members of small gene families that are differentially expressed, resulting in several unique combinations of these molecules in specific brain regions.

Actin-binding proteins from Drosophila embryos: a complex network of interacting proteins detected by F-actin affinity chromatography

By using F-actin affinity chromatography columns to select proteins solely by their ability to bind to actin filaments, we have identified and partially purified greater than 40 proteins from early Drosophila embryos. These proteins represent approximately 0.5% of the total protein present in soluble cell extracts, and 2 mg are obtained by chromatography of an extract from 10 g of embryos. As judged by immunofluorescence of fixed embryos, 90% of the proteins that we have detected in F-actin column eluates are actin-associated in vivo (12 of 13 proteins tested). The distributions of antigens observed suggest that groups of these proteins cooperate in generating unique actin structures at different places in the cell. These structures change as cells progress through the cell cycle and as they undergo the specializations that accompany development. The variety of different spatial localizations that we have observed in a small subset of the total actin-binding proteins suggests that the actin cytoskeleton is a very complex network of interacting proteins.

F-actin affinity chromatography: technique for isolating previously unidentified actin-binding proteins

We have developed stable and easy to use filamentous actin (F-actin) affinity-chromatography columns that selectively purify proteins that bind to actin filaments from cell extracts. Most traditional assays for actin-associated proteins screen for their effects on actin polymerization or actin filament crosslinking. Because our technique requires only actin-filament binding, it can identify additional types of proteins involved in the function of the actin cytoskeleton. By chromatographing extracts of several types of cells on these columns, we show that known actin-binding proteins are selectively retained as a subset of a larger group of actin-binding proteins that have not been identified previously.

Yeast actin-binding proteins: evidence for a role in morphogenesis

Three yeast actin-binding proteins were identified using yeast actin filaments as an affinity matrix. One protein appears to be a yeast myosin heavy chain; it is dissociated from actin filaments by ATP, it is similar in size (200 kD) to other myosins, and antibodies directed against Dictyostelium myosin heavy chain bind to it. Immunofluorescence experiments show that a second actin-binding protein (67 kD) colocalizes in vivo with both cytoplasmic actin cables and cortical actin patches, the only identifiable actin structures in yeast. The cortical actin patches are concentrated at growing surfaces of the yeast cell where they might play a role in membrane and cell wall insertion, and the third actin-binding protein (85 kD) is only detected in association with these structures. This 85-kD protein is therefore a candidate for a determinant of growth sites. The in vivo role of this protein was tested by overproduction; this overproduction causes a reorganization of the actin cytoskeleton which in turn dramatically affects the budding pattern and spatial growth organization of the yeast cell.

A complex control region of the mouse rRNA gene directs accurate initiation by RNA polymerase I

To determine the size and location of the mouse rDNA promoter, we constructed systematic series of deletion mutants approaching the initiation site from the 5' and 3' directions. These templates were transcribed in vitro under various conditions with S-100 and whole-cell extracts. Surprisingly, the size of the rDNA region that determines the level of transcription differed markedly, depending on the reaction conditions. In both kinds of cell extracts, the apparent 5' border of the promoter was at residue ca. -27 under optimal transcription conditions, but as reaction conditions became less favorable, the 5' border moved progressively out to residues -35, -39, and -45. The complete promoter, however, extends considerably further, for under other nonoptimal conditions, we observed major effects of promoter domains extending in the 5' direction to positions ca. -100 and -140. In contrast, the apparent 3' border of the mouse rDNA promoter was at residue ca. +9 under all conditions examined. We also show that the subcloned rDNA region from -39 to +9 contains sufficient information to initiate accurately and that the region between +2 and +9 can influence the specificity of initiation. These data indicate that, although the polymerase I transcription factors recognize and accurately initiate with only the sequences downstream of residue -40, sequences extending out to residue -140 greatly favor the initiation reaction; presumably, this entire region is involved in rRNA transcription in vivo.

Specific protein modifications are altered in a temperature-sensitive Drosophila developmental mutant

The temperature-sensitive Drosophila mutation l(3)c21RRW630 disturbs oogenesis and imaginal disc development and has a maternal effect on embryogenesis. Two-dimensional gel electrophoretic analysis of protein synthesis in mutant tissue at a restrictive temperature shows that the synthesis of three proteins is elevated and the synthesis of three other proteins is reduced, when compared to wild type. Each protein with increased synthesis is similar to a protein whose synthesis is reduced, as judged by comparison of partial proteolytic digests of these proteins. To explain these findings, we propose that the wild-type c21R gene codes for a protein-modifying enzyme. This enzyme catalyzes the acidic modification of three abundant proteins. The correct modification of these proteins is required for cell division, cell motility, and the formation of adult hairs and bristles. In the mutant at restrictive temperature, the enzyme does not function properly and so the unmodified substrate proteins accumulate. This study correlates the morphological defects in a Drosophila developmental mutant with an altered molecular process.

Dinucleotide primers facilitate convenient identification of the mouse ribosomal DNA transcription initiation site. A general method for analysis of transcription by RNA polymerases I and III

The in vitro initiation site for RNA polymerase I on the mouse rRNA gene was identified using a new method that is generally applicable to the study of other eukaryotic transcripts. First, the 5' end of mouse rRNA was located to an ApC . . . by high resolution S1 nuclease mapping. Dinucleotide primers were then used in transcription reactions to demonstrate that this position is the actual de novo initiation site, and not a rapid RNA processing site. For this analysis, initiation was inhibited by reduced rXTP concentration, and, upon supplementation with various dinucleotides, only ApC stimulated correct synthesis. Independently confirming its role as the initiating nucleotide, ATP was shown to be required at a much higher concentration than the other rXTPs for RNA initiation, but not for elongation. These results also demonstrate a marked sequence conservation of rRNA initiation sites between the mouse and frog, two species that violate the general rule of species specificity in RNA polymerase I initiation. Extending these studies to RNA polymerase III, the initiation site for 5 S RNA can be similarly located by dinucleotide analysis and confirmed from the concentration requirements of each rXTP. In addition to allowing initiation at suboptimal rXTP concentration, dinucleotide primers can also circumvent the need for a factor normally required for initiation, suggesting their potential value in dissecting the mechanism of eukaryotic transcription.

A homogeneous type II DNA topoisomerase from HeLa cell nuclei

Using kinetoplast DNA networks as a substrate in a decatenation assay, we have purified to apparent homogeneity a type II DNA topoisomerase from HeLa cell nuclei. The most pure preparations contain a single polypeptide of 172,000 daltons as determined by sodium dodecyl sulfate-gel electrophoresis. The molecular weight of the native protein, based on sedimentation and gel filtration analyses, is estimated to be 309,000. These results suggest that the enzyme is a dimer of 172,0090-dalton subunits. The enzyme is a type II topoisomerase as demonstrated by its ability to change the linking number of DNA circles in steps of two and to decatenate or unknot covalently closed DNA circles. No gyrase activity is detectable. ATP is required for the relaxation, decatenation, and unknotting of DNA, and a DNA-dependent ATPase activity is present in the most pure fractions. ATP is hydrolyzed to ADP in this properties to T4 DNA topoisomerase (Liu, L. F., Liu, C. C., and Alberts, B. M. (1979) Nature 281, 456-461).

Eukaryotic DNA topoisomerases: two forms of type I DNA topoisomerases from HeLa cell nuclei

Two type I DNA topoisomerases have been purified to homogeneity from the nuclei of HeLa cells. One topoisomerase has a peptide molecular weight of 100,000 and the other, a molecular weight of 67,000. Several lines of evidence indicate that these two topoisomerases are closely related, (a) Both exhibit similar enzymatic activities on DNA. (b) The chromatographic properties of the two topoisomerases during purification are similar. (c) Mild proteolysis of the purified molecular weight 100,000 topoisomerase in vitro generates a group of protein bands of molecular weight approximately 67,000, and these bands retain topoisomerase activity. (d) The peptides formed by partial proteolysis of the 67,000 topoisomerase in the presence of NaDodSO4 form a subset of those produced from the 100,000 enzyme. The 100,000 topoisomerase is the major type I enzyme in the cell. The 67,000 topoisomerase, which may be identical to the previously identified "nicking-closing" enzyme [Champoux, J. J. & Dulbecco, R. (1972) Proc. Natl. Acad. Sci. USA 69, 143-146], is probably formed by proteolysis of the 100,000 enzyme.

Decatenation of kinetoplast DNA by topoisomerases

Kinetoplast DNA is the mitochondrial DNA of trypanosomatids such as Crithidia fasciculata. This DNA is in the form of networks containing thousands of DNA circles which are apparently catenated (interlocked). Some topoisomerases, such as T4 phage topoisomerase and DNA gyrase, catalyze a decatenation of the networks to form individual covalently closed circles.

Screening for gonorrhea and syphilis in the gay baths--Denver, Colorado

During 33 screening sessions in Denver gay steambaths, 48 of 419 (11.5 per cent) men were found to have asymptomatic gonorrhea and six (1.4 per cent) had early latent syphilis. Questionnaires were administered to 160 men who reported a mean of 7.9 different male sex contacts per month. Female sex contacts were also reported by 30 per cent. The respondents used the baths an average of 2.2 times per month, having an average of 2.7 different sex contacts per visit, 84 per cent of whom were not previously known to the respondent. Gay steambaths are productive locations for detecting asymptomatic gonorrhea and syphilis.