Comparison of the optical quality vision between real post-LASIK myopic laser surgery and the simulated implantation of a phakic IOL in low myopia

A phakic intraocular lens (PIOL) of - 4.5 D was characterized from its wavefront aberration profile. A preclinical study was conducted using pre- and post-surgery data from four patients that had undergone myopic laser refractive surgery. All these patients would have needed a PIOL of - 4.5 D. Pre-surgery data were used to simulate the effect of a PIOL implantation. Post myopic refractive surgery data were used to calculate the post-LASIK eye model. Modulation transfer function (MTF), point spread function (PSF) and simulation of optotypes vision were obtained and compared. The PIOL did not worsen the optical quality of the eyes evaluated. High order Aberrations were always higher in the post-LASIK eye model. Optics quality trended to be better in PIOL implantation than post-LASIK surgery as pupil size increased.

MET-Induced CD73 Restrains STING-Mediated Immunogenicity of EGFR-Mutant Lung Cancer

Immunotherapy has shown limited efficacy in patients with EGFR-mutated lung cancer. Efforts to enhance the immunogenicity of EGFR-mutated lung cancer have been unsuccessful to date. Here, we discover that MET amplification, the most common mechanism of resistance to third-generation EGFR tyrosine kinase inhibitors (TKI), activates tumor cell STING, an emerging determinant of cancer immunogenicity (1). However, STING activation was restrained by ectonucleosidase CD73, which is induced in MET-amplified, EGFR-TKI-resistant cells. Systematic genomic analyses and cell line studies confirmed upregulation of CD73 in MET-amplified and MET-activated lung cancer contexts, which depends on coinduction of FOSL1. Pemetrexed (PEM), which is commonly used following EGFR-TKI treatment failure, was identified as an effective potentiator of STING-dependent TBK1-IRF3-STAT1 signaling in MET-amplified, EGFR-TKI-resistant cells. However, PEM treatment also induced adenosine production, which inhibited T-cell responsiveness. In an allogenic humanized mouse model, CD73 deletion enhanced immunogenicity of MET-amplified, EGFR-TKI-resistant cells, and PEM treatment promoted robust responses regardless of CD73 status. Using a physiologic antigen recognition model, inactivation of CD73 significantly increased antigen-specific CD8+ T-cell immunogenicity following PEM treatment. These data reveal that combined PEM and CD73 inhibition can co-opt tumor cell STING induction in TKI-resistant EGFR-mutated lung cancers and promote immunogenicity.

SIGNIFICANCE

MET amplification upregulates CD73 to suppress tumor cell STING induction and T-cell responsiveness in TKI-resistant, EGFR-mutated lung cancer, identifying a strategy to enhance immunogenicity and improve treatment.

Activation of Tumor-Cell STING Primes NK-Cell Therapy

Activation of the stimulator of interferon genes (STING) pathway promotes antitumor immunity but STING agonists have yet to achieve clinical success. Increased understanding of the mechanism of action of STING agonists in human tumors is key to developing therapeutic combinations that activate effective innate antitumor immunity. Here, we report that malignant pleural mesothelioma cells robustly express STING and are responsive to STING agonist treatment ex vivo. Using dynamic single-cell RNA sequencing of explants treated with a STING agonist, we observed CXCR3 chemokine activation primarily in tumor cells and cancer-associated fibroblasts, as well as T-cell cytotoxicity. In contrast, primary natural killer (NK) cells resisted STING agonist-induced cytotoxicity. STING agonists enhanced migration and killing of NK cells and mesothelin-targeted chimeric antigen receptor (CAR)-NK cells, improving therapeutic activity in patient-derived organotypic tumor spheroids. These studies reveal the fundamental importance of using human tumor samples to assess innate and cellular immune therapies. By functionally profiling mesothelioma tumor explants with elevated STING expression in tumor cells, we uncovered distinct consequences of STING agonist treatment in humans that support testing combining STING agonists with NK and CAR-NK cell therapies.

Analysis and comparison of monofocal, extended depth of focus and trifocal intraocular lens profiles

To test the feasibility of using profilometers to extract information about IOL surfaces design. A standard monofocal IOL (Tecnis 1), a monofocal IOL that provided some depth of focus (Eyhance), an extended depth of focus IOL based on refractive optics (Mini Well) and a trifocal IOL based on diffractive optics were used in this study (Tecnis Synergy). The surface topography of the IOLs was measured by using a multimode optical profilometer. Posterior surface of Tecnis 1 IOL was spherical and the anterior surface aspherical. In the Eyhance IOL, posterior surface was spherical and anterior surface did not fit to any of our reference surfaces, indicating a higher order aspheric surface design. In the Mini Well Ready IOL, a best-fit sphere surface was obtained for the second surface and a high order aspherical surface design was deduced for the first surface. The anterior surface of the Synergy IOL was aspherical and the base curve of the diffractive structure fitted very well to a spherical surface. To consider an aspheric surface as possible best-fit surface provided more information than if only best-fit spherical surface was considered. The high order aspheric surface designs employed in the IOLs studied presented differences, regarding best-fit asphere surface, higher than 1 micron. These differences were correlated with the generation of spherical aberration complex profiles (with Zernike terms higher than 4th order) and with the production of distinct amounts of depth of focus. This method was also useful to deduce the base curve of diffractive surfaces.

Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade

Resistance to oncogene-targeted therapies involves discrete drug-tolerant persister cells, originally discovered through in vitro assays. Whether a similar phenomenon limits efficacy of programmed cell death 1 (PD-1) blockade is poorly understood. Here, we performed dynamic single-cell RNA-Seq of murine organotypic tumor spheroids undergoing PD-1 blockade, identifying a discrete subpopulation of immunotherapy persister cells (IPCs) that resisted CD8+ T cell-mediated killing. These cells expressed Snai1 and stem cell antigen 1 (Sca-1) and exhibited hybrid epithelial-mesenchymal features characteristic of a stem cell-like state. IPCs were expanded by IL-6 but were vulnerable to TNF-α-induced cytotoxicity, relying on baculoviral IAP repeat-containing protein 2 (Birc2) and Birc3 as survival factors. Combining PD-1 blockade with Birc2/3 antagonism in mice reduced IPCs and enhanced tumor cell killing in vivo, resulting in durable responsiveness that matched TNF cytotoxicity thresholds in vitro. Together, these data demonstrate the power of high-resolution functional ex vivo profiling to uncover fundamental mechanisms of immune escape from durable anti-PD-1 responses, while identifying IPCs as a cancer cell subpopulation targetable by specific therapeutic combinations.

New method to improve the quality of vision in cataractous keratoconus eyes

To analyze using optical simulations if the proper use of a segmented intraocular lens (IOL) can improve the visual outcomes compared to the implantation of a spherical monofocal IOL. The wavefront profile of the Mplus (Oculentis) and a monofocal IOLs with the phase transformation introduced by each IOL were calculated using a Hartmann-Shack wavefront sensor. In addition, the wavefront profile of schematic eye models of various keratoconus conditions was obtained and was propagated to the IOLs. The optical performance of such combination was obtained after combining ray tracing and Fourier optics. A pre-clinical validation was also evaluated incorporating clinical data from three different keratoconus eyes of three patients. The implantation of the Mplus IOL can compensate or reduce the overall coma of the eye with keratoconus improving the quality of vision compared with a spherical monofocal IOL due to lower displacements of the retinal image or tilting in keratoconus. All theoretical simulations were confirmed afterwards by mean of a preclinical validation. The use of a standard toric segmented IOL with a proper orientation and selection of the addition can improve the optical quality of the keratoconus eye compared to the use of a monofocal spherical IOL.

Abstract 5543: TAK1 deficiency in tumor cells enhances sensitivity to CTL-mediated killing via TNF-α

The clinical successes achieved by different immunotherapies have resulted in a paradigm shift in treatment modalities. Despite these significant advances, not all patients benefit from the use of these therapies, creating a need to develop additional approaches to enhance and broaden their clinical application. To identify genes whose products can increase or decrease the sensitivity of tumor cells to the immune system, we used a CTL assay to screen a whole genomic CRISPR library. We co-culture a mouse cell line, ID8, expressing a model antigen (Ova) with transgenic CD8 T cells (OT-I) recognizing this antigen. A set of controls that enhance or decrease CTL activity behaved as expected. Comparison of the CRISPR score identified several hits that increased or decreased the sensitivity of the tumor cells to CTL killing. Subsets of these hits belong to two pathways involved in CTL-mediated killing: the IFN-γ and the TNF-α signaling pathways. We evaluated which of these hits would be amenable to therapeutic modulation, and decided to focus on the kinase TAK1 for confirmation and validation studies. A TAK1 deficient cell line was more sensitive to CTL killing, which was prevented by expression of TAK1, confirming the role of TAK1 in this process. A TAK1 gene carrying an inactivation mutation K63W did not rescue the effects of TAK1 KO, indicating that TAK1 enzymatic activity was necessary. Several pathways mediate CTL killing: Perforin/Granzyme B, IFN-γ, TNF-α, Fas & TRAIL pathways. To determine TAK1 MOA, we studied the effects of a Perforin/Granzyme B inhibitor CMA. CMA inhibited CTL activity in a dose-dependent manner on WT cells, but did not inhibit CTL activity on TAK1 deficient cells, indicating TAK1 effects are independent of this pathway. We then tested the sensitivity of TAK1 KO cells to TNF-α. TAK1 KO cells were more sensitive to TNF-α mediated killing, and similar results were observed with several additional cell lines (MC38, EMT6, KP). TNF-α can activate the JNK, p38, and NF-κB pathways, and the apoptosis extrinsic pathway to regulate cell growth and cell death. Kinetics studies monitoring pathway activity upon TNF-α stimulation showed that TAK1 KO cell lines induced cFLIP degradation before observing PARP cleavage, and that the NF-κB pathway, which has been observed to mediate cFLIP synthesis, was not activated. We proceeded to evaluate the effects of TAK1 deficiency in a mouse syngeneic model. TAK1 deficiency resulted in reduced growth and increased survival in the MC38 in vivo model. In summary, by screening a CRISPR library against a CTL assay, we identified TAK1 as a novel potential target for immunotherapies. TAK1 deficiency enhances CTL killing and results in decreased tumor growth and increased survival in vivo. This results support the development of TAK1 inhibitors to enhance the anti-tumor action of the immune system.

Citation Format: Juan J. Miret, Troy A. Luster, Patrick Lizotte, Min Wu, Sarah Nzikoba, Luke Taus J. Taus, Prafulla C. Gokhale, Paul Kirschmeier, David Barbie, Cloud P. Paweletz. TAK1 deficiency in tumor cells enhances sensitivity to CTL-mediated killing via TNF-α [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5543.

Suppression of Myeloid Cell Arginase Activity leads to Therapeutic Response in a NSCLC Mouse Model by Activating Anti-Tumor Immunity

BACKGROUND

Tumor orchestrated metabolic changes in the microenvironment limit generation of anti-tumor immune responses. Availability of arginine, a semi-essential amino acid, is critical for lymphocyte proliferation and function. Levels of arginine are regulated by the enzymes arginase 1,2 and nitric oxide synthase (NOS). However, the role of arginase activity in lung tumor maintenance has not been investigated in clinically relevant orthotopic tumor models.

METHODS

RNA sequencing (RNA-seq) of sorted cell populations from mouse lung adenocarcinomas derived from immunocompetent genetically engineered mouse models (GEMM)s was performed. To complement mouse studies, a patient tissue microarray consisting of 150 lung adenocarcinomas, 103 squamous tumors, and 54 matched normal tissue were stained for arginase, CD3, and CD66b by multiplex immunohistochemistry. Efficacy of a novel arginase inhibitor compound 9 in reversing arginase mediated T cell suppression was determined in splenocyte ex vivo assays. Additionally, the anti-tumor activity of this compound was determined in vitro and in an autochthonous immunocompetent KrasG12D GEMM of lung adenocarcinoma model.

RESULTS

Analysis of RNA-seq of sorted myeloid cells suggested that arginase expression is elevated in myeloid cells in the tumor as compared to the normal lung tissue. Accordingly, in the patient samples arginase 1 expression was mainly localized in the granulocytic myeloid cells and significantly elevated in both lung adenocarcinoma and squamous tumors as compared to the controls. Our ex vivo analysis demonstrated that myeloid derived suppressor cell (MDSC)s cause T cell suppression by arginine depletion, and suppression of arginase activity by a novel ARG1/2 inhibitor, compound 9, led to restoration of T cell function by increasing arginine. Treatment of KrasG12D GEMM of lung cancer model with compound 9 led to a significant tumor regression associated with increased T cell numbers and function, while it had no activity across several murine and human non-small cell (NSCLC) lung cancer lines in vitro.

CONCLUSIONS

We show that arginase expression is elevated in mouse and patient lung tumors. In a KRASG12D GEMM arginase inhibition diminished growth of established tumors. Our data suggest arginase as an immunomodulatory target that should further be investigated in lung tumors with high arginase activity.

Abstract 4065: Suppression of myeloid cell arginase activity leads to therapeutic response in Kras mutant lung cancer by activating anti-tumor immunity

Metabolic changes in the tumor microenvironment impair the generation of an efficient anti-tumor immune response. Reduction of specific amino acids like arginine and tryptophan limit anti-tumor immune responses, contributing to a tumor generated immune suppressive environment. Arginine levels are critical for lymphocyte proliferation and function, and they are regulated by arginase 1 & 2 and nitric oxide synthase. Arginase 1 activity has been associated with most of the immunosuppressive effects resulting from arginine depletion and the role of arginase activity in lung tumor maintenance has not been investigated in clinically relevant established tumor models. RNA sequencing of sorted cell populations from immunocompetent genetically engineered KRAS G12D mutant mouse lung tumors, showed that arginase 1 expression is elevated in the myeloid cell population in the tumor microenvironment. Ex vivo analysis demonstrated that myeloid derived suppressor cell (MDSCs) from mouse tumors hindered T cell function by depleting arginine. These MDSCs expressed elevated levels of arginase 1, and inhibition of its activity by an Arg1/2 inhibitor, compound 9, restored effector T cell function. Treatment of a genetically engineered KRAS mutant mouse model with compound 9 increased arginine levels in blood and tumor and led to an increased number of tumor T cells and a significant reduction in tumor volume after 1 week of treatment. Compound 9 had no growth inhibitory activity across several murine and human KRAS mutant lung cancer cell lines in vitro. We also determined by immunohistochemistry that elevated levels of arginase 1 were expressed in granulocytic myeloid cells from KRAS mutant lung cancer patient samples. Given the data reported here and by others, an arginase inhibitor with excellent potency and in vivo target engagement could represent an important new immunotherapeutic agent. We have recently discovered and are fully characterizing molecules that demonstrate excellent potency and selectivity along with oral bioavailability in rodents that provide good arginase target coverage at modest doses.

Citation Format: Juan J. Miret, Paul Kirschmeier, Min Wu, Wei Huang, William Walker, Sangeetha Palakurti, Nick Saccomano, Peter S. Hammerman, Kwok-kin Wong, Esra Akbay. Suppression of myeloid cell arginase activity leads to therapeutic response in Kras mutant lung cancer by activating anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4065.

Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery

Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy. Here we summarize our efforts to further validate ChoKα as an oncogenic target and explore the activity of novel small molecule inhibitors of ChoKα. Starting from weakly binding fragments, we describe a structure based lead discovery approach, which resulted in novel highly potent inhibitors of ChoKα. In cancer cell lines, our lead compounds exhibit a dose-dependent decrease of phosphocholine, inhibition of cell growth, and induction of apoptosis at low micromolar concentrations. The druglike lead series presented here is optimizable for improvements in cellular potency, drug target residence time, and pharmacokinetic parameters. These inhibitors may be utilized not only to further validate ChoKα as antioncogenic target but also as novel chemical matter that may lead to antitumor agents that specifically interfere with cancer cell metabolism.

Ultrathin high-index metasurfaces for shaping focused beams

The volume size of a converging wave, which plays a relevant role in image resolution, is governed by the wavelength of the radiation and the numerical aperture (NA) of the wavefront. We designed an ultrathin (λ/8 width) curved metasurface that is able to transform a focused field into a high-NA optical architecture, thus boosting the transverse and (mainly) on-axis resolution. The elements of the metasurface are metal-insulator subwavelength gratings exhibiting extreme anisotropy with ultrahigh index of refraction for TM polarization. Our results can be applied to nanolithography and optical microscopy.

Engineered surface waves in hyperbolic metamaterials

We analyzed surface-wave propagation that takes place at the boundary between a semi-infinite dielectric and a multilayered metamaterial, the latter with indefinite permittivity and cut normally to the layers. Known hyperbolization of the dispersion curve is discussed within distinct spectral regimes, including the role of the surrounding material. Hybridization of surface waves enable tighter confinement near the interface in comparison with pure-TM surface-plasmon polaritons. We demonstrate that the effective-medium approach deviates severely in practical implementations. By using the finite-element method, we predict the existence of long-range oblique surface waves.

Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors

Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. The inhibition of LDH-A by small molecules is therefore of interest for potential cancer treatments. We describe the identification and optimization of LDH-A inhibitors by fragment-based drug discovery. We applied ligand based NMR screening to identify low affinity fragments binding to LDH-A. The dissociation constants (K(d)) and enzyme inhibition (IC(50)) of fragment hits were measured by surface plasmon resonance (SPR) and enzyme assays, respectively. The binding modes of selected fragments were investigated by X-ray crystallography. Fragment growing and linking, followed by chemical optimization, resulted in nanomolar LDH-A inhibitors that demonstrated stoichiometric binding to LDH-A. Selected molecules inhibited lactate production in cells, suggesting target-specific inhibition in cancer cell lines.

Crizotinib-resistant mutants of EML4-ALK identified through an accelerated mutagenesis screen

Activating gene rearrangements of anaplastic lymphoma kinase (ALK) have been identified as driver mutations in non-small-cell lung cancer, inflammatory myofibroblastic tumors, and other cancers. Crizotinib, a dual MET/ALK inhibitor, has demonstrated promising clinical activity in patients with non-small-cell lung cancer and inflammatory myofibroblastic tumors harboring ALK translocations. Inhibitors of driver kinases often elicit kinase domain mutations that confer resistance, and such mutations have been successfully predicted using in vitro mutagenesis screens. Here, this approach was used to discover an extensive set of ALK mutations that can confer resistance to crizotinib. Mutations at 16 residues were identified, structurally clustered into five regions around the kinase active site, which conferred varying degrees of resistance. The screen successfully predicted the L1196M, C1156Y, and F1174L mutations, recently identified in crizotinib-resistant patients. In separate studies, we demonstrated that crizotinib has relatively modest potency in ALK-positive non-small-cell lung cancer cell lines. A more potent ALK inhibitor, TAE684, maintained substantial activity against mutations that conferred resistance to crizotinib. Our study identifies multiple novel mutations in ALK that may confer clinical resistance to crizotinib, suggests that crizotinib's narrow selectivity window may underlie its susceptibility to such resistance and demonstrates that a more potent ALK inhibitor may be effective at overcoming resistance.

Nondiffracting Bessel plasmons

We report on the existence of nondiffracting Bessel surface plasmon polaritons (SPPs), advancing at either superluminal or subluminal phase velocities. These wave fields feature deep subwavelength FWHM, but are supported by high-order homogeneous SPPs of a metal/dielectric (MD) superlattice. The beam axis can be relocated to any MD interface, by interfering multiple converging SPPs with controlled phase matching. Dissipative effects in metals lead to a diffraction-free regime that is limited by the energy attenuation length. However, the ultra-localization of the diffracted wave field might still be maintained by more than one order of magnitude.

Three-dimensional point spread function and generalized amplitude transfer function of near-field flat lenses

We derive a nonsingular, polarization-dependent, 3D impulse response that provides unambiguously the wave field scattered by a negative-refractive-index layered lens and distributed in its image volume. By means of a 3D Fourier transform, we introduce the generalized amplitude transfer function in order to gain a deep insight into the resolution power of the optical element. In the near-field regime, fine details containing some depth information may be transmitted through the lens. We show that metamaterials with moderate absorption are appropriate for subwavelength resolution keeping a limited degree of depth discrimination.

Diffraction-free beams in thin films

The propagation and transmission of Bessel beams through nano-layered structures has been discussed recently. Within this framework we recognize the formation of unguided diffraction-free waves with the spot size approaching and occasionally surpassing the limit of a wavelength when a Bessel beam of any order n is launched onto a thin material slab with grazing incidence. On the basis of the plane-wave representation of cylindrical waves, a simple model is introduced providing an exact description of the transverse pattern of this type of diffraction-suppressed localized wave. Potential applications in surface science are put forward for consideration.

Octave-spanning ultraflat supercontinuum with soft-glass photonic crystal fibers

We theoretically identify some photonic-crystal-fiber structures, made up of soft glass, that generate ultrawide (over an octave) and very smooth supercontinuum spectra when illuminated with femtosecond pulsed light. The design of the fiber geometry in order to reach a nearly ultraflattened normal dispersion behavior is crucial to accomplish the above goal. Our numerical simulations reveal that these supercontinuum sources show high stability and no significant changes are detected even for fairly large variations of the incident pulse.

Free-space delay lines and resonances with ultraslow pulsed Bessel beams

We investigate the ultraslow motion of polychromatic Bessel beams in unbounded, nondispersive media. Control over the group velocity is exercised by means of the angular dispersion of pulsed Bessel beams of invariant transverse spatial frequency, which spontaneously emerge from near-field generators. Temporal dynamics in transients and resonances over homogeneous delay lines (dielectric slabs) are also examined.

Angular spectrum of diffracted wave fields with apochromatic correction

We report on compensation of diffraction-induced angular dispersion of ultrashort pulses up to a second order. A strategy for chromatic correction profits from high dispersion of kinoform-type zone plates. Ultraflat dispersion curves rely on a saddle point that may be tuned at a prescribed wavelength. Validity of our approach may reach the few-cycles regime.

Differential toolbox to shape dispersion behavior in photonic crystal fibers

We present an analytical procedure to compute the first derivatives of the propagation constants with respect to several structural parameters in photonic crystal fibers (PCFs). From them we can easily evaluate the same derivatives of other directly related magnitudes. The above derivatives provide the trend of the magnitude at issue, which allows us to take advantage of a gradient-based algorithm to shape the properties of the guiding structure. In this way we implement an optimization process to carry out real inverse design in PCFs. We focus our attention on designing PCFs with a specific chromatic dispersion behavior. Likewise, the same approach makes it possible to analyze their fabrication tolerances.

Multiplexed G-protein-coupled receptor Ca2+ flux assays for high-throughput screening

An early drug discovery approach focusing on gene families can benefit from strategies that exploit common signaling mechanisms to more effectively identify and characterize novel chemical lead structures. Multiplexing, defined as the screening of multiple targets within the same experiment, is an example of this strategy. Here, the authors describe a technique that allows multiplexing of a common assay type used to study G-protein-coupled receptors: changes in intracellular Ca2+ levels as measured by Molecular Device's fluorometric imaging plate reader (FLIPR). The multiplexed FLIPR assays showed the expected pharmacological properties of single assays, with good reproducibility and Z* factors. The authors used them to screen large compound libraries in 2 multiplexed assay designs. The 1st used a single-cell line expressing 2 different receptors and the 2nd a mixture of 2 cell lines of the same type each expressing distinct receptors. Screening using these multiplexed assays produced significant savings in reagents, time, and human resources and allowed the authors to quickly identify specific and selective hits.

Analytical evaluation of chromatic dispersion in photonic crystal fibers

We present a two-dimensional modal approach for the evaluation, in an analytical manner, of chromatic dispersion in any kind of optical fiber. It combines an iterative Fourier technique to compute the propagation constant at any fixed wavelength and an analytical procedure to calculate its derivatives. The proposed formulation takes into account the effective anisotropy of the interfaces and allows us to deal with microstructured fibers, in general, and specifically with realistic photonic crystal fibers (PCFs), including arbitrary spatial refractive-index distributions of dispersive and absorbing materials. This fast and accurate numerical technique is extremely useful for both analysis and design. We show some results of analysis of PCFs with high anisotropy, and we also describe PCFs with new dispersive properties.

Functional expression of heteromeric calcitonin gene-related peptide and adrenomedullin receptors in yeast

The ability of G protein-coupled receptors (GPCRs) to form homo- and heteromeric complexes has important implications for the regulation of cellular events. A notable example of heteromer formation is the interaction of the calcitonin receptor-like receptor (CRLR) with different members of the receptor activity modifying protein (RAMP) family, which results in the formation of two different receptors, a calcitonin gene-related peptide (CGRP) receptor and an adrenomedullin receptor. To analyze the role of RAMPs in determining ligand specificity, we have co-expressed CRLR and RAMP proteins in the yeast Saccharomyces cerevisiae, which provides a null system to study the function of mammalian receptors. Co-expression of RAMP1 and CRLR reconstituted a CGRP receptor that was able to activate the pheromone-signaling pathway with pharmacological properties similar to those observed previously in mammalian cells. Co-expression of CRLR with RAMP2 or RAMP3 resulted in a response with the pharmacological properties of an adrenomedullin receptor. These data indicate that RAMPs are necessary and sufficient to determine ligand specificity of CRLR. Contrary to observations in mammalian cells, the glycosylation of CRLR was not affected by the presence of RAMPs in yeast, indicating that glycosylation of CRLR is not the prime determinant of ligand specificity. The first functional reconstitution of a heteromeric seven transmembrane receptor in yeast suggests this organism as a useful research tool to study the molecular nature of other heteromeric receptors.

Efficient repair of large DNA loops in Saccharomyces cerevisiae

Small looped mispairs are efficiently corrected by mismatch repair. The situation with larger loops is less clear. Repair activity on large loops has been reported as anywhere from very low to quite efficient. There is also uncertainty about how many loop repair activities exist and whether any are conserved. To help address these issues, we studied large loop repair in Saccharomyces cerevisiae using in vivo and in vitro assays. Transformation of heteroduplexes containing 1, 16 or 38 nt loops led to >90% repair for all three substrates. Repair of the 38 base loop occurred independently of mutations in key genes for mismatch repair (MR) and nucleotide excision repair (NER), unlike other reported loop repair functions in yeast. Correction of the 16 base loop was mostly independent of MR, indicating that large loop repair predominates for this size heterology. Similarities between mammalian and yeast large loop repair were suggested by the inhibitory effects of loop secondary structure and by the role of defined nicks on the relative proportions of loop removal and loop retention products. These observations indicate a robust large loop repair pathway in yeast, distinct from MR and NER, and conserved in mammals.

Cis-elements governing trinucleotide repeat instability in Saccharomyces cerevisiae

Trinucleotide repeat (TNR) instability in humans is governed by unique cis-elements. One element is a threshold, or minimal repeat length, conferring frequent mutations. Since thresholds have not been directly demonstrated in model systems, their molecular nature remains uncertain. Another element is sequence specificity. Unstable TNR sequences are almost always CNG, whose hairpin-forming ability is thought to promote instability by inhibiting DNA repair. To understand these cis-elements further, TNR expansions and contractions were monitored by yeast genetic assays. A threshold of approximately 15--17 repeats was observed for CTG expansions and contractions, indicating that thresholds function in organisms besides humans. Mutants lacking the flap endonuclease Rad27p showed little change in the expansion threshold, suggesting that this element is not altered by the presence or absence of flap processing. CNG or GNC sequences yielded frequent mutations, whereas A-T rich sequences were substantially more stable. This sequence analysis further supports a hairpin-mediated mechanism of TNR instability. Expansions and contractions occurred at comparable rates for CTG tract lengths between 15 and 25 repeats, indicating that expansions can comprise a significant fraction of mutations in yeast. These results indicate that several unique cis-elements of human TNR instability are functional in yeast.

Donor and acceptor guided modes in photonic crystal fibers

We present a triangular photonic-crystal-fiber structure that exhibits guided modes simultaneously above and below the first conduction band. We achieve this configuration by decreasing the size of one of the airholes (the defect) in a specific triangular lattice. More generally, we analyze the behavior of guided modes that depends on the size of the defect. Defects generated by decreasing or increasing the size of one of the holes produce donor or acceptor guided modes, respectively, in analogy with impurity levels in solid-state crystals. We conclude that the guiding mechanism for both donor and acceptor modes is produced by a unique phenomenon of multiple interference by a periodic structure.

Vector description of higher-order modes in photonic crystal fibers

We extensively study the propagation features of higher-order modes in a photonic crystal fiber (PCF). Our analysis is based on a full-vector modal technique specially adapted to accurately describe light propagation in PCF's. Unlike conventional fibers, PCF's exhibit a somewhat unusual mechanism for the generation of higher-order modes. Accordingly, PCF's are characterized by the constancy of the number of modes below a wavelength threshold. An explicit verification of this property is given through a complete analysis of the dispersion relations of higher-order modes in terms of the structural parameters of this kind of fiber. The transverse irradiance distributions for some of these higher-order modes are also presented, showing an excellent agreement with recent experimental measurements. In the same way, the full-vector nature of our approach allows us to analyze the rich polarization structure of the PCF mode spectrum.

Nearly zero ultraflattened dispersion in photonic crystal fibers

We present a procedure for achieving photonic crystal fibers with nearly zero ultraflattened group-velocity dispersion. Systematic knowledge of the special guiding properties of these fibers permits the achievement of qualitatively novel dispersion curves. Unlike the behavior of conventional fibers, this new type of dispersion behavior permits remarkably improved suppression of third-order dispersion, particularly in the low-dispersion domain.

Full-vector analysis of a realistic photonic crystal fiber

We analyze the guiding problem in a realistic photonic crystal fiber, using a novel full-vector modal technique. This is a biorthogonal modal method based on the non-self-adjoint character of the electromagnetic propagation in a fiber. Dispersion curves of guided modes for different fiber structural paremeters are calculated, along with the two-dimensional transverse intensity distribution of the fundamental mode. Our results match those achieved in recent experiments in which the feasibility of this type of fiber was shown.

Orientation-dependent and sequence-specific expansions of CTG/CAG trinucleotide repeats in Saccharomyces cerevisiae

A quantitative and selective genetic assay was developed to monitor expansions of trinucleotide repeats (TNRs) in yeast. A promoter containing 25 repeats allows expression of a URA3 reporter gene and yields sensitivity to the drug 5-fluoroorotic acid. Expansion of the TNR to 30 or more repeats turns off URA3 and provides drug resistance. When integrated at either of two chromosomal loci, expansion rates were 1 x 10(-5) to 4 x 10(-5) per generation if CTG repeats were replicated on the lagging daughter strand. PCR analysis indicated that 5-28 additional repeats were present in 95% of the expanded alleles. No significant changes in CTG expansion rates occurred in strains deficient in the mismatch repair gene MSH2 or the recombination gene RAD52. The frequent nature of CTG expansions suggests that the threshold number for this repeat is below 25 in this system. In contrast, expansions of the complementary repeat CAG occurred at 500- to 1,000-fold lower rates, similar to a randomized (C,A,G) control sequence. When the reporter plasmid was inverted within the chromosome, switching the leading and lagging strands of replication, frequent expansions were observed only when CTG repeats resided on the lagging daughter strand. Among the rare CAG expansions, the largest gain in tract size was 38 repeats. The control repeats CTA and TAG showed no detectable rate of expansions. The orientation-dependence and sequence-specificity data support the model that expansions of CTG and CAG tracts result from aberrant DNA replication via hairpin-containing Okazaki fragments.

Instability of CAG and CTG trinucleotide repeats in Saccharomyces cerevisiae

A quantitative genetic assay was developed to monitor alterations in tract lengths of trinucleotide repeat sequences in Saccharomyces cerevisiae. Insertion of (CAG)50 or (CTG)50 repeats into a promoter that drives expression of the reporter gene ADE8 results in loss of expression and white colony color. Contractions within the trinucleotide sequences to repeat lengths of 8 to 38 restore functional expression of the reporter, leading to red colony color. Reporter constructs including (CAG)50 or (CTG)50 repeat sequences were integrated into the yeast genome, and the rate of red colony formation was measured. Both orientations yielded high rates of instability (4 x 10(-4) to 18 x 10(-4) per cell generation). Instability depended on repeat sequences, as a control harboring a randomized (C,A,G)50 sequence was at least 100-fold more stable. PCR analysis of the trinucleotide repeat region indicated an excellent correlation between change in color phenotype and reduction in length of the repeat tracts. No preferential product sizes were observed. Strains containing disruptions of the mismatch repair gene MSH2, MSH3, or PMS1 or the recombination gene RAD52 showed little or no difference in rates of instability or distributions of products, suggesting that neither mismatch repair nor recombination plays an important role in large contractions of trinucleotide repeats in yeast.

Genetic and biochemical analysis of Msh2p-Msh6p: role of ATP hydrolysis and Msh2p-Msh6p subunit interactions in mismatch base pair recognition

Recent studies have shown that Saccharomyces cerevisiae Msh2p and Msh6p form a complex that specifically binds to DNA containing base pair mismatches. In this study, we performed a genetic and biochemical analysis of the Msh2p-Msh6p complex by introducing point mutations in the ATP binding and putative helix-turn-helix domains of MSH2. The effects of these mutations were analyzed genetically by measuring mutation frequency and biochemically by measuring the stability, mismatch binding activity, and ATPase activity of msh2p (mutant msh2p)-Msh6p complexes. A mutation in the ATP binding domain of MSH2 did not affect the mismatch binding specificity of the msh2p-Msh6p complex; however, this mutation conferred a dominant negative phenotype when the mutant gene was overexpressed in a wild-type strain, and the mutant protein displayed biochemical defects consistent with defects in mismatch repair downstream of mismatch recognition. Helix-turn-helix domain mutant proteins displayed two different properties. One class of mutant proteins was defective in forming complexes with Msh6p and also failed to recognize base pair mismatches. A second class of mutant proteins displayed properties similar to those observed for the ATP binding domain mutant protein. Taken together, these data suggested that the proposed helix-turn-helix domain of Msh2p was unlikely to be involved in mismatch recognition. We propose that the MSH2 helix-turn-helix domain mediates changes in Msh2p-Msh6p interactions that are induced by ATP hydrolysis; the net result of these changes is a modulation of mismatch recognition.

Recognition of DNA insertion/deletion mismatches by an activity in Saccharomyces cerevisiae

An activity in nuclear extracts of S.cerevisiae binds specifically to heteroduplexes containing four to nine extra bases in one strand. The specificity of this activity (IMR, for insertion mismatch recognition) in band shift assays was confirmed by competition experiments. IMR is biochemically and genetically distinct from the MSH2 dependent, single base mismatch binding activity. The two activities migrate differently during electrophoresis, they are differentially competable and their spectra of mispair binding are distinct. Furthermore, IMR activity is observed in extracts from an msh2- msh3- msh4- strain. IMR exhibits specificity for insertion mispairs in two different sequence contexts. Binding is influenced by the structure of the mismatch since an insertion with a hairpin configuration is not recognized by this activity. IMR does not result from single-strand binding because single-stranded probes to not yield IMR complex and single-stranded competitors are unable to displace insertion heteroduplexes from the complex. Similar results with intrinsically bent duplexes make it unlikely that recognition is conferred by a bend alone. Heteroduplexes bound by IMR do not contain any obvious damage. These findings are consistent with the idea that yeast contains a distinct recognition factor, IMR that is specific for insertion/deletion mismatches.

The Golgi guanosine diphosphatase is required for transport of GDP-mannose into the lumen of Saccharomyces cerevisiae Golgi vesicles

The Saccharomyces cerevisiae Golgi lumenal guanosine diphosphatase is hypothesized to generate GMP which in turn allows entry of GDP-mannose into the lumen to serve as substrate for mannosylation of proteins and lipids. We have recently shown in studies in vivo that this GDPase is required for protein and sphingolipid mannosylation in the Golgi lumen of S. cerevisiae. We have now isolated Golgi-vesicles from wild type and gda1 null mutants (GDPase defective) and have found that the initial rate of GDP-mannose entry into mutant vesicles was 5-fold lower than into those of wild type. Because the concentration of GDP within vesicles is insufficient to inhibit Golgi lumenal mannosyltransferases and the null mutant vesicles are impaired in synthesis of Golgi mannoproteins, the above results demonstrate that the reduced availability of GDP-mannose in the null mutants is the cause for altered Golgi mannosylation of macromolecules.

Characterization of a DNA mismatch-binding activity in yeast extracts

An activity present in nuclear extracts of the yeast Saccharomyces cerevisiae binds specifically to oligonucleotides containing DNA mismatches, as judged by a band shift assay. The specificity of this activity for mismatched DNA was confirmed by competition experiments; binding to radiolabeled heteroduplexes was abolished in the presence of excess unlabeled heteroduplex but not when excess unlabeled homoduplex was added. Both T/G and T/- (single base deletion) mispairs were recognized in each of two sequence contexts. Binding was also observed with G/G, G/A, A/C, and T/C mismatches, but recognition of a C/C mispair was very weak. Competition studies with the various mismatches were consistent with the idea that a single activity recognizes all mispairs tested. Extracts from strains mutant in either or both of two putative mismatch recognition functions, MSH2 and MSH3, were also tested. Mismatch-binding activity was present in extracts of msh3- strains but completely absent in msh2- strains. The molecular weight of the major binding protein was estimated by UV cross-linking experiments to be approximately 110 kDa, in good agreement with the size predicted for Msh2 protein (Reenan, R. A. and Kolodner, R. D. (1992) Genetics 132, 963-973).

Polyamines and cell wall organization in Saccharomyces cerevisiae

Cells of Saccharomyces cerevisiae 179-5, an ornithine decarboxylase mutant (spe-1), showed several ultrastructural abnormalities when cultivated in the absence of polyamines. Besides the appearance of microvacuole-like spaces in the cytoplasm and of deformed nuclei, the most important alterations seemed to be located in the cell wall, which was thicker and of heterogeneous texture, and in the cell membrane, of irregular contour. These modifications could not be evoked by general stress conditions elicited by lack of nutrients. The relative levels of cell wall polysaccharides were altered in polyamine-deprived organisms, giving an envelope with increased mannan and decreased glucan content; this cell wall was incompletely attacked by the lytic enzyme zymolyase. Polyamine depletion led also to some abnormalities in the budding pattern. The above observations suggest the involvement of polyamines in the correct structure and organization of the yeast cell.

Altered heat-shock response in polyamine-depleted bacteria

A polyamine-auxotrophic mutant of E. coli was cultivated in the presence or absence of putrescine and submitted to heat shock over 3 different ranges of temperature. In all cases, protein synthetic capacity measured in comparison to that of cultures at the preshift temperature was much higher in polyamine-depleted bacteria under thermic stress. Addition of putrescine only before the shift-up was able to restore gradually normal control of the relative protein synthetic capacity.

Effect of alpha-difluoromethylornithine in lung metastases before and after surgery of primary adenocarcinoma tumors in mice

The depletion of polyamines by alpha-difluoromethylornithine (DFMO) treatment of mice after subcutaneous inoculation of adenocarcinoma M3 cells caused a remarkable inhibition in the growth rate of primary tumors as well as in the occurrence and number of lung metastases with a concomitant increase in survival time. Tumor-bearing mice submitted to the surgical removal of primary tumors and then treated with alpha-difluoromethylornithine also showed a significant reduction of lung metastases. In addition, a lower number of lung metastatic nodules correlated with decreased levels of polyamines in the same tissue. The described approach provides a useful experimental model for studies in human cancer therapy.