Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives.

BACKGROUND: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. RESULTS: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). CONCLUSIONS: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.

Phantom rivers filter birds and bats by acoustic niche.

Natural sensory environments, despite strong potential for structuring systems, have been neglected in ecological theory. Here, we test the hypothesis that intense natural acoustic environments shape animal distributions and behavior by broadcasting whitewater river noise in montane riparian zones for two summers. Additionally, we use spectrally-altered river noise to explicitly test the effects of masking as a mechanism driving patterns. Using data from abundance and activity surveys across 60 locations, over two full breeding seasons, we find that both birds and bats avoid areas with high sound levels, while birds avoid frequencies that overlap with birdsong, and bats avoid higher frequencies more generally. We place 720 clay caterpillars in willows, and find that intense sound levels decrease foraging behavior in birds. For bats, we deploy foraging tests across 144 nights, consisting of robotic insect-wing mimics, and speakers broadcasting bat prey sounds, and find that bats appear to switch hunting strategies from passive listening to aerial hawking as sound levels increase. Natural acoustic environments are an underappreciated niche axis, a conclusion that serves to escalate the urgency of mitigating human-created noise.

Influence of the Turing instability on the motion of domain boundaries.

Turing's theory of pattern formation has provided crucial insights into the behavior of various biological, geographical, and chemical systems over the last few decades. Existing studies have focused on moving-boundary Turing systems for which the motion of the boundary is prescribed by an external agent. In this paper, we present an extension of this theory to a class of systems in which the front motion is governed by the physical processes that occur within the domain. Biological systems exhibiting apically dominant growth and corrosion of metals and alloys highlight some of the noteworthy examples of such systems. In this study, we characterize the nature of interaction between the moving front and the Turing-instability for both an activator-inhibitor and an activator-substrate model. Behavioral regimes of periodic, as well as nonperiodic (nonconstant), growth rates are obtained. Furthermore, the trends in the first show striking similarities with the cyclic-boundary-kinetics observed in experimental systems. In general, a stationary, periodic structure is also left behind the moving front. If the periodicity of the boundary kinetics agrees with the allowed range of the stable-periodic solutions, the pattern formed tends to persist. Otherwise, it evolves to a nearby energy-minimum either by peak-splitting, peak-decay, or by settling down to a spatially homogeneous state.

Indentation of an elastic half space with material properties varying with depth.

We consider the effect of an elastic modulus that decreases with depth on the load-displacement relation for indentation of a graded half space by a rigid indenter. A closed-form approximation incorporating features of the plate on an elastic substrate and the Hertzian contact theory is compared with finite element results for the case of a uniform stiff layer on a homogeneous substrate. Some general results are presented for the case where the grading has inverse power-law form and the effects of truncation to a finite surface value are investigated numerically. Finally, a more practical error-function grading is considered. In all cases, the load-displacement relation is closer to linear than in the homogeneous case. We conclude that the experimental data can be used to determine parameters in a predetermined form of grading, but that comparative insensitivity to the exact form of the grading would make it difficult to distincguish experimentally between different models based on indentation experiments alone.

The role of adhesion in contact mechanics.

Adhesive (e.g. van der Waals) forces were not generally taken into account in contact mechanics until 1971, when Johnson, Kendall and Roberts (JKR) generalized Hertz' solution for an elastic sphere using an energetic argument which we now recognize to be analogous to that used in linear elastic fracture mechanics. A significant result is that the load-displacement relation exhibits instabilities in which approaching bodies 'jump in' to contact, whereas separated bodies 'jump out' at a tensile 'pull-off force'. The JKR approach has since been widely used in other geometries, but at small length scales or for stiffer materials it is found to be less accurate. In conformal contact problems, other instabilities can occur, characterized by the development of regular patterns of regions of large and small traction. All these instabilities result in differences between loading and unloading curves and consequent hysteretic energy losses. Adhesive contact mechanics has become increasingly important in recent years with the focus on soft materials (which generally permit larger areas of the interacting surfaces to come within the range of adhesive forces), nano-devices and the analysis of bio-systems. Applications are found in nature, such as insect attachment forces, in nano-manufacturing, and more generally in industrial systems involving rubber or polymer contacts. In this paper, we review the strengths and limitations of various methods for analysing contact problems involving adhesive tractions, with particular reference to the effect of the inevitable roughness of the contacting surfaces.

Surface instability of an elastic half space with material properties varying with depth.

If a body with a stiffer surface layer is loaded in compression, a surface wrinkling instability may be developed. A bifurcation analysis is presented for determining the critical load for the onset of wrinkling and the associated wavelength for materials in which the elastic modulus is an arbitrary function of depth. The analysis leads to an eigenvalue problem involving a pair of linear ordinary differential equations with variable coefficients which are discretized and solved using the finite element method.The method is validated by comparison with classical results for a uniform layer on a dissimilar substrate. Results are then given for materials with exponential and error-function gradation of elastic modulus and for a homogeneous body with thermoelastically-induced compressive stresses.

Modification of fos proteins: phosphorylation of c-fos, but not v-fos, is stimulated by 12-tetradecanoyl-phorbol-13-acetate and serum.

We have investigated the covalent modification of the proteins encoded by the murine fos proto-oncogene (c-fos) and that of the corresponding gene product of FBJ murine osteosarcoma virus (v-fos). Both proteins are posttranslationally processed in the cell, resulting in forms with lower electrophoretic mobilities than that of the initial translation product on sodium dodecyl sulfate-polyacrylamide gels. Treatment with alkaline phosphatase indicates that most, if not all, of this electrophoretic shift is due to phosphoesterification of both proteins. These phosphoryl groups stoichiometrically modify the v-fos and c-fos proteins on serine residues and turn over rapidly in vivo in the presence of protein kinase inhibitors (half-life, less than 15 min). Direct quantitative comparison of steady-state labeling studies with L-[35S]methionine and [32P]phosphate reveals that the c-fos protein is four- to fivefold more highly phosphorylated than the v-fos protein is. Comparison of tryptic fragments from [32P]phosphate-labeled proteins indicates that although the two proteins have several tryptic phosphopeptides in common, the c-fos protein contains unique major tryptic phosphopeptides that the v-fos protein lacks. These unique sites of c-fos phosphorylation have been tentatively localized to the carboxy-terminal 20 amino acid residues of the protein. Phosphorylation of the c-fos protein, but not the v-fos protein, can be stimulated at least fivefold in vivo by the addition of either 12-tetradecanoyl-phorbol-13-acetate or serum. This increase in the steady-state degree of phosphorylation of c-fos appears to be independent of protein kinase C since phosphorylation is Ca2+ and diacylglycerol independent. The possible role of phosphorylation of these proteins in cellular transformation is discussed.

Involvement of proteasome alpha-subunit PSMA7 in hepatitis C virus internal ribosome entry site-mediated translation.

Ribozymes are small catalytic RNA molecules that can be engineered to enzymatically cleave RNA transcripts in a sequence-specific fashion and thereby inhibit expression and function of the corresponding gene product. With their simple structures and site-specific cleavage activity, they have been exploited as potential therapeutic agents in a variety of human disorders, including hepatitis C virus (HCV) infection. We have designed a hairpin ribozyme (Rz3'X) targeting the HCV minus-strand replication intermediate at position 40 within the 3'X tail. Surprisingly, Rz3'X was found to induce ganciclovir (GCV)-resistant colonies in a bicistronic cellular reporter system with HCV internal ribosome entry site (IRES)-dependent translation of herpes simplex virus thymidine kinase (TK). Rz3'X-transduced GCV-resistant HeLa reporter cells showed substantially reduced IRES-mediated HCV core protein translation compared with control vector-transduced cells. Since these reporter systems do not contain the HCV 3'X tail sequences, the results indicate that Rz3'X probably exerted an inhibitory effect on HCV IRES activity fortuitously through another gene target. A novel technique of ribozyme cleavage-based target gene identification (cleavage-specific amplification of cDNA ends) (M. Krüger, C. Beger, P. J. Welch, J. R. Barber, and F. Wong-Staal, Nucleic Acids Res. 29:e94, 2001) revealed that human 20S proteasome alpha-subunit PSMA7 mRNA was a target RNA recognized and cleaved by Rz3'X. We then showed that additional ribozymes directed against PSMA7 RNA inhibited HCV IRES activity in two assay systems: GCV resistance in the HeLa IRES TK reporter cell system and a transient transfection assay performed with a bicistronic Renilla-HCV IRES-firefly luciferase reporter in Huh7 cells. In contrast, ribozymes were inactive against IRES of encephalomyocarditis virus and human rhinovirus. Additionally, proteasome inhibitor MG132 exerted a dose-dependent inhibitory effect on HCV IRES-mediated translation but not on cap-dependent translation. These data suggest a principal role for PSMA7 in regulating HCV IRES activity, a function essential for HCV replication.

A novel functional genomics approach identifies mTERT as a suppressor of fibroblast transformation.

As a tool for functional genomics, a hairpin ribozyme gene library with randomized target recognition sequences was constructed in a retroviral vector. This library has the potential to target and cleave any possible RNA substrate. Mouse fibroblasts transduced with this ribozyme gene vector library were selected in a focus formation assay to isolate in vivo functional ribozymes that promote cell transformation in tissue culture. After two successive rounds of selection by focus formation assay, a transforming ribozyme (Rz007) was identified. The sequence of this ribozyme was used to identify the putative target genes responsible for the transformation. A candidate gene target for Rz007 encodes telomerase reverse transcriptase (mTERT). Both mRNA level and enzymatic activity of mTERT were down-regulated in Rz007-transformed cells. Furthermore, newly designed ribozymes, recognizing other potential ribozyme cleavage sites unique to the mTERT mRNA, also cause cell transformation, thus validating the role of mTERT in suppressing the transformation phenotype. These surprising results suggest that the commonly accepted role of telomerase in maintaining cellular immortalization is more complicated than previously thought. These studies also demonstrate the utility of this novel 'reverse' functional genomics approach, enabling the targeted discovery of genes, whether previously known or not, that are involved in any selectable phenotype.

C-SPACE (cleavage-specific amplification of cDNA ends): a novel method of ribozyme-mediated gene identification.

A hairpin ribozyme, RzCR2A, directed against position 323 of the hepatitis C virus 5'-untranslated region (HCV 5'-UTR) was used to establish and validate a novel method for the detection of cellular target molecules for hairpin ribozymes, termed C-SPACE (cleavage-specific amplification of cDNA ends). For C-SPACE, HeLa mRNA containing the transcript of interest was subjected to in vitro cleavage by RzCR2A in parallel with a control ribozyme, followed by reverse transcription using a modified SMART cDNA amplification method and cleavage-specific PCR analysis. C-SPACE allowed identification of the RzCR2A target transcript from a mixture containing the entire cellular mRNA while only requiring knowledge of the ribozyme binding sequence for amplification. In a similar approach, C-SPACE was used successfully to identify human 20S proteasome alpha-subunit PSMA7 mRNA as the cellular target RNA of Rz3'X, a ribozyme originally designed to cleave the negative strand HCV 3'-UTR. Rz3'X was found to substantially inhibit HCV internal ribosome entry site (IRES) activity and PSMA7 was subsequently confirmed to be involved in HCV IRES-mediated translation. Thereby, C-SPACE was validated as a powerful tool to rapidly identify unknown target RNAs recognized and cleaved by hairpin ribozymes.

Metabolism of S-adenosyl-L-methionine in intact human erythrocytes.

Freshly isolated human erythrocytes contain S-adenosyl-L-methionine (AdoMet) at a concentration of about 3.5 mumol/l cells. When such cells are incubated in a medium containing 30 microM L-methionine, 18 mM D-glucose and 118 mM sodium phosphate (pH 7.4), intracellular AdoMet levels continuously decrease to a value of about 0.1 microM after 24 h. This occurs in spite of the fact that the cellular concentrations of the substrates for the AdoMet synthetase reaction, ATP and L-methionine, remain relatively constant. In a search for incubation conditions that lead to stable levels of AdoMet in incubated cells, we have developed a sodium-Hepes-buffered medium which includes 1 mM adenine and a stoichiometric excess of MgCl2 over its ligand, phosphate. The inclusion of magnesium ion (and a reduction in phosphate) appears to increase intracellular free Mg2+, which is required for full activity of the erythrocyte AdoMet synthetase. Even in the presence of MgCl2, however, the AdoMet pool level can drop 4-6-fold within the first 2 h of incubation. We present evidence that suggests that this initial fall in the cellular AdoMet level may be due to the activation of AdoMet-dependent protein carboxyl methyltransferase, an enzyme which accounts for a large fraction of the total cellular AdoMet utilization. Adenine, or related compounds in the medium may prevent this activation, although the mechanism of this action is not clear at present.

Expression of ribozymes in gene transfer systems to modulate target RNA levels.

The possibility of designing ribozymes to cleave any specific target RNA has rendered them valuable tools in both basic research and therapeutic applications. In the therapeutics area, they have been exploited to target viral RNAs in infectious diseases, dominant oncogenes in cancers and specific somatic mutations in genetic disorders. Most notably, several ribozyme gene therapy protocols for HIV patients are already in Phase 1 trials. More recently, ribozymes have been used for transgenic animal research, gene target validation and pathway elucidation.

Cytotoxic T-lymphocyte induction in asymptomatic HIV-1-infected patients immunized with Retrovector-transduced autologous fibroblasts expressing HIV-1IIIB Env/Rev proteins.

OBJECTIVE: To demonstrate the safety and enhancement of HIV-1-specific immune responses in HIV-infected asymptomatic patients following treatment with retroviral vector (Retrovector)-transduced autologous fibroblasts (VTAF) expressing HIV-1IIIB Env/Rev proteins. DESIGN: A non-placebo-controlled, single arm Phase I study. PARTICIPANTS: Four HIV-1-seropositive asymptomatic volunteers were selected based on age (18-50 years), CD4/CD3 lymphocyte counts (> 600 x 10(6)/l or > 40%), and positive delayed-type hypersensitivity test to at least one recall antigen. INTERVENTIONS: Patients were treated at 2-week intervals with a total of three intramuscular injections of irradiated autologous fibroblasts transduced with a molecularly engineered, non-replicating amphotropic murine retrovector encoding the HIV-1IIIB Env/Rev proteins. MAIN OUTCOME MEASURES: The clinical status of patients was assessed by history, physical examination, serum chemistry and hematology, CD4/CD3 lymphocyte counts, HIV viral burden, and monitored throughout the study to detect potentially treatment-induced toxic or unwanted side-effects. In addition, HIV-1-specific cytotoxic T-lymphocyte (CTL) activity was measured to determine the biological activity of VTAF. RESULTS: No acute local or systemic adverse events occurred following three injections with VTAF. Furthermore, a statistically significant increase of CD8+ CTL activity against HIV-1IIIB Env/Rev-expressing targets was observed in peripheral blood mononuclear cells from two out of four patients. CONCLUSIONS: This is the first report of the administration of a gene transfer treatment to HIV-1-infected patients and provides initial support for the safety and activity of retrovector-transduced fibroblasts administered to asymptomatic patients. This treatment resulted in the detection of increased HIV-1IIIB Env/Rev-specific CTL activity in two HIV-seropositive patients and could provide a better understanding of the role of CTL activity in HIV disease progression.

Development of novel cell surface CD34-targeted recombinant adenoassociated virus vectors for gene therapy.

Recombinant adenoassociated virus (rAAV) type 2 vectors have been used to transduce a wide variety of cell types, including hematopoietic progenitor cells. For in vivo gene transfer, it is desirable to have an rAAV vector that specifically transduces selected target cells. As a first step toward generating an rAAV vector capable of targeting delivery in vivo, we have engineered a chimeric protein combining the AAV capsid protein and the variable region of a single-chain antibody against human CD34 molecules, a cell surface marker for hematopoietic stem/progenitor cells. Inclusion of the chimeric CD34 single-chain antibody-AAV capsid proteins within an rAAV virion significantly increased the preferential infectivity of rAAV for the CD34+ human myoleukemia cell line KG-1, which is normally refractory to rAAV transduction. Antibodies against the single-chain antibody and the CD34 protein blocked this transduction. This chimeric vector represents a significant improvement in the host range of rAAV and the first step toward specific gene delivery by rAAV vectors to cells of choice, in this case, hematopoietic progenitor cells, for the treatment of human disease.

Transduction of human melanoma cells with the gamma interferon gene enhances cellular immunity.

Human tumor cells transduced with the gamma interferon (gamma IFN) gene are currently used in specific active immunotherapy protocols to enhance the antitumor immune responses of cancer patients. This in vitro study was undertaken to examine the initial events in the cellular immune response that may occur following the administration of the gamma IFN-transduced cell vaccine. Human melanoma tumor cell lines were transduced with a MoMLV-based retroviral vector carrying the human gamma IFN gene. The transduced cells expressed the cytokine gene, secreted biologically active gamma IFN, and exhibited enhanced expression of MHC class I and class II (HLA-DR), and ICAM-1 surface antigens. The gamma IFN-transduced and corresponding parental melanoma cells were used for the induction of short-term lymphocyte cultures. Peripheral blood lymphocytes or lymph node cells from 20 melanoma patients were stimulated for 5 to 15 days with autologous or MHC class I-matched allogeneic parental or gamma IFN-transduced melanoma cells. Seven of the 20 lymphocyte cultures showed substantial increases in lytic activity following stimulation with the transduced melanoma cells in comparison to control lymphocyte cultures stimulated with unmodified parental melanoma. The cytolytic activity stimulated with gamma IFN-modified melanomas was mediated partly by MHC-restricted cytotoxic T lymphocytes and partly by NK cells. Lymphocyte cultures that displayed increases in cytotoxicity after stimulation with the gamma IFN-transduced melanoma cells also exhibited enhanced expression or induction of one or more of the following lymphokines: IL-4, IL-1 alpha, IL-1 beta, gamma IFN, and TNF-alpha.(ABSTRACT TRUNCATED AT 250 WORDS)

Sustained cytokine production and immunophenotypic changes in human neuroblastoma cell lines transduced with a human gamma interferon vector.

The majority of human neuroblastomas express low to undetectable levels of major histocompatibility complex (MHC) class I and II antigens (MHC-I and -II). We studied the effects of gamma interferon (gamma-IFN) transduction on expression of these antigens in six human neuroblastoma cell lines with and without genomic amplification of the N-myc oncogene. All six were stably transduced with an MoMLV-based gamma-IFN retroviral vector (DAh gamma-IFN). G418-resistant cells were assayed for MHC-I, MHC-II, B7-1, and neuroblastoma-associated antigen expression, as well as for gamma-IFN levels in cell culture supernatants. Sustained gamma-IFN production, 2 to > 1000 units/10(6) cells/d, was attained for five of six transduced cell lines and persisted for up to 9 months. This resulted in marked upregulation of MHC-I and MHC-II expression in LA-N-1, LA-N-6, and CHLA-127 cells and moderate upregulation in SK-N-Fi and SK-N-AS cells. One cell line (LA-N-1) had marked induction of MHC-I and MHC-II despite marginal levels of gamma-IFN production. Expression of CD28 ligand B7-1 (as determined by BB1 antibody) remained unchanged in all gamma-IFN-transduced cell lines tested. Expression of several neuroblastoma-associated antigens (NKH1A, 126-4, HSAN 1.2, HNK, 459, and 390) was upregulated in some of the gamma-IFN-transduced cell lines. These results demonstrate that preparation of gamma-IFN expressing neuroblastoma cells for immunotherapeutic purposes is feasible and that gamma-IFN transduction results in phenotypic changes that may improve immunogenicity of human neuroblastoma cells.

Proto-oncogene fos: factors affecting expression and covalent modification of the gene product.

Expression of proto-oncogene fos is induced in response to a variety of growth factors and differentiation-specific agents. However, the induction of fos gene expression is not influenced by inhibition of protein synthesis. We, therefore, entertained the notion that expression of the fos gene may be governed by posttranslational modification of cellular transcriptional factors. We report here that transcription of the human c-fos gene is modulated by negatively and positively acting cellular factors. The nuclear protein products of the resident oncogene of the FBJ-murine osteosarcoma virus (v-fos) and its corresponding cellular proto-oncogene (c-fos) are stoichiometrically phosphorylated on serine and threonine residues. The c-fos protein is more highly phosphorylated than the v-fos protein due to the phosphorylation of unique sites tentatively localized to the c-terminal 20 amino acid residues. The protein kinase C agonist, TPA, stimulates phosphorylation of the c-fos, but not the v-fos protein.

Incremental stiffness and electrical contact conductance in the contact of rough finite bodies.

If two half spaces are in contact, there exists a formal mathematical relation between the electrical contact resistance and the incremental elastic compliance. Here, this relation is extended to the contact of finite bodies. In particular, it is shown that the additional resistance due to roughness of the contacting surfaces (the interface resistance) bears a similar relation to the additional compliance as that obtained for the total resistance in the half-space problem.