Epigenetic inheritance of a phenotypically plastic epimutation

Organisms constantly have to adapt to changing environments in order to survive, thrive and successfully multiply. Phenotypic changes can be acquired by alterations of the deoxyribonucleic acid (DNA)sequence. If beneficial under natural selection, the DNA variation can become fixed permanently in a population and thereby drive its evolution. In addition to DNA sequence changes, a concept emerged that a soft, reversible layer could also potentially contribute to heritable adaptation. Epigenetic changes were shown to affect the development and complex phenotypic traits of almost isogenic organisms. Such changes can be inherited over many generations by strong self-reinforcing feedback loops without the initial trigger. Evidence for such a ‘soft’ inheritance is only just emerging and whether such phenomena are of physiological relevance in heritable adaptation though remains to be unraveled. Gene expression is regulated through several mechanisms. DNA does not exist as bare molecule, but is packaged into a highly complex structure called chromatin. Besides serving structural functions, chromatin also impacts gene expression. Chromatin can be broadly divided into transcriptionally active, gene-rich euchromatin and gene-poor, condensed heterochromatin, which serves as repressive structure for repetitive elements, such as transposons, and makes up most of the euchromatic genome. In some organisms, nuclear small ribonucleic acid (RNA) pathways are essential to initiate and maintain constitutive heterochromatin. The centerpiece of such pathways is a small RNA-bound Argonaute protein, which binds by complementary base-pairing to nascent transcripts and subsequently recruits effector complexes that mediate silencing. Given the appropriate small RNA, this pathway can theoretically target any expressed locus, thereby making it a versatile silencing strategy. In nematodes, small RNAs were shown to induce stable silencing of some protein coding genes that can be epigenetically maintained over tens of generations. During my PhD, I studied RNA interference (RNAi)-mediated epigenetic phenomena in the fission yeast Schizosaccharomyces pombe (S. pombe). In S. pombe, RNAi-mediated silencing is under strong negative control and can only be initiated in the presence of an enabling mutation, such as in genes encoding subunits of the RNA polymerase-associated factor 1 complex (Paf1C). On one hand, such mutations can have a detrimental effect on viability. On the other hand, the silencing phenotype observed in Paf1C mutants cannot be inherited to wild-type cells, suggesting that also all marks of the silencing event were erased. If RNAi-mediated epigenetic phenomena also exist in wild-type cells was not known. My main achievement during PhD was to discover that wild-type S. pombe cells remember a parental silencing event through acquiring a phenotypically neutral epimutation. I could show that such epimutation does not cause gene silencing when inherited by wild type cells. Yet, upon repeated mutation of Paf1C, the silencing phenotype was reinstated in subsequent generations. I could further show that the phenotypically neutral epimutation entails high levels of small interfering RNA (siRNA) and histone 3 lysine 9 tri-methylation (H3K9me3), and that its transgenerational inheritance depends on RNAi and H3K9 methylation. This finding is astounding, because H3K9me3 has commonly been associated with gene repression. That we have not observed silencing, despite high enrichments of this mark, was therefore highly unexpected. Based on my findings, I conclude that H3K9me3 is not repressive per se, but rather functions as stable epigenetic mark that can retain information of a previous gene-silencing event. Upon deposition of H3K9me3, the silencing phenotype is dependent on the modulation of Paf1C function. The discovery of this distinct form of epigenetic memory lets me speculate that it may have evolved to allow population adaptation to dynamic environments

Photothermal excitation of microcantilevers in liquid: effect of the excitation laser position on temperature and vibrational amplitude

Demands to improve the sensitivity and measurement speed of dynamic scanning force microscopy and cantilever sensing applications necessitate the development of smaller cantilever sensors. As a result, methods to directly drive cantilevers, such as photothermal or magnetic excitation, are gaining in importance. Presented is a report on the effect of photothermal excitation of microcantilevers on the increase in steady-state temperature and the dynamics of higher mode vibrations. First, the local temperature increase upon continuous irradiation with laser light at different positions along the cantilever was measured and compared with finite element analysis data. The temperature increase was highest when the heating laser was positioned at the free end of the cantilever. Next, the laser intensity was modulated to drive higher flexural modes to resonance. The dependence of the cantilever dynamics on the excitation laser position was assessed and was in good agreement with the analytical expressions. An optimal position to simultaneously excite all flexural modes of vibration with negligible heating was found at the clamped end of the cantilever. The reports findings are essential for optimisation of the excitation efficiency to minimise the rise in temperature and avoid damaging delicate samples or functionalisation layers

Angle Robust Reflection/Transmission Plasmonic Filters Using Ultrathin Metal Patch Array

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135614/1/adom201600397.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135614/2/adom201600397_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135614/3/adom201600397-sup-0001-S1.pd

Enhanced photodynamic leishmanicidal activity of hydrophobic zinc phthalocyanine within archaeolipids containing liposomes

In this work, the in vitro anti-Leishmania activity of photodynamic liposomes made of soybean phosphatidylcholine, sodium cholate, total polar archaeolipids (TPAs) extracted from the hyperhalophile archaea Halorubrum tebenquichense and the photosensitizer zinc phthalocyanine (ZnPcAL) was compared to that of ultradeformable photodynamic liposomes lacking TPAs (ZnPcUDLs). We found that while ZnPcUDLs and ZnPcALs (130 nm mean diameter and ?35 mV zeta potential) were innocuous against promastigotes, a low concentration (0.01 µM ZnPc and 7.6 µM phospholipids) of ZnPcALs irradiated at a very low-energy density (0.2 J/cm2) eliminated L. braziliensis amastigotes from J774 macrophages, without reducing the viability of the host cells. In such conditions, ZnPcALs were harmless for J774 macrophages, HaCaT keratinocytes, and bone marrow-derived dendritic cells. Therefore, topical photodynamic treatment would not likely affect skin-associated lymphoid tissue. ZnPcALs were extensively captured by macrophages, but ZnPcUDLs were not, leading to 2.5-fold increased intracellular delivery of ZnPc than with ZnPcUDLs. Despite mediating low levels of reactive oxygen species, the higher delivery of ZnPc and the multiple (caveolin- and clathrin-dependent plus phagocytic) intracellular pathway followed by ZnPc would have been the reason for the higher antiamastigote activity of ZnPcALs. The leishmanicidal activity of photodynamic liposomal ZnPc was improved by TPA-containing liposomes.Fil: Perez, Ana Paula. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; ArgentinaFil: Casasco, Agustina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Servicio de Parasitología y Chagas; ArgentinaFil: Schilrreff, Priscila. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Defain Tesoriero, María Victoria. Instituto Nacional de Tecnología Industrial. Centro de Investigación y Desarrollo en Química; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; ArgentinaFil: Duempelmann, Luc. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; ArgentinaFil: Pappalardo, Juan Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Altube, María Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Higa, Leticia Herminia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Morilla, María José. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Petray, Patricia Beatriz. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Servicio de Parasitología y Chagas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Romero, Eder Lilia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología. Laboratorio de Diseño de Estrategias de Targeting de Drogas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Temporal Evolution of Multiday, Epileptic Functional Networks Prior to Seizure Occurrence

Epilepsy is one of the most common neurological disorders, characterized by the occurrence of repeated seizures. Given that epilepsy is considered a network disorder, tools derived from network neuroscience may confer the valuable ability to quantify the properties of epileptic brain networks. In this study, we use well-established brain network metrics (i.e., mean strength, variance of strength, eigenvector centrality, betweenness centrality) to characterize the temporal evolution of epileptic functional networks over several days prior to seizure occurrence. We infer the networks using long-term electroencephalographic recordings from 12 people with epilepsy. We found that brain network metrics are variable across days and show a circadian periodicity. In addition, we found that in 9 out of 12 patients the distribution of the variance of strength in the day (or even two last days) prior to seizure occurrence is significantly different compared to the corresponding distributions on all previous days. Our results suggest that brain network metrics computed fromelectroencephalographic recordings could potentially be used to characterize brain network changes that occur prior to seizures, and ultimately contribute to seizure warning systems

Plasmonic Metalens for Narrowband Dual-Focus Imaging

A new type of metalens with the capability to selectively focus narrowband light is reported at different focal planes depending on polarization. Two zone planes with two different focal lengths are spatially multiplexed and encoded in the subwavelength regime with arrays of orthogonal silver nanostructures, which are designed to exhibit strong wavelength- and polarization-dependent scattering profiles. Using this principle, imaging under white-light illumination with independent focal planes is experimentally demonstrated for each polarization at the narrowband resonant wavelength. Furthermore, each focal plane can be dynamically controlled with an output polarizer. In contrast to conventional refractive and diffractive optical elements, functional metalenses allow additional control over wavelength and polarization properties of light for a wide range of applications.This work was financially supported by the Engineering and Physical Sciences Research Council (EPSRC): Integrated Photonic and Electronic Systems (EP/L015455/1); Cambridge Overseas Trust and the Mexican National Council on Science and Technology (CONACyT)

Understanding 'non-genetic' inheritance : insights from molecular-evolutionary crosstalk

The idea for this paper was initially proposed by I.A.-K. and was further developed by all authors in a workshop generously funded by grant No 789240 from the European Research Council (ERC) to F.J.W. S.E.S. acknowledges support from Wesleyan University and The John Templeton Foundation.Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.Publisher PDFPeer reviewe

Plasmonic Color Filters for Industrial Applications

Light can strongly interact with metallic nanostructures, leading to resonant excitation of the confined electrons. This results in a strong near-field enhancement with subwavelength confinement. The resonance condition can be controlled by the material, shape and surrounding of the metal nanostructures. Thus, this so-called field of plasmonics holds great potential for applications in photonics. Besides biosensing, novel applications are scarce though, not only due to challenges in the up-scaling process, but also because of expense of material, design complexity and sensitivity of the structures in ambient conditions. Furthermore, intrinsic losses impede the implementation compared to competing alternatives. This thesis describes the development and realization of color filters based on plasmonic structures. The structures are tailored for intriguing applications and their large-scale manufacturing. Specifically the variability of plasmonic color filters is exploited and applied. This precisely controllable change of color appearance can be essential for applications such as optical security or imaging systems, for which first realizations are presented here. In particular, color filters are investigated, which strongly change their optical appearance with the angle of incidence. Additionally, a given color is only visible from one tilt direction. This unique feature makes these color filters highly attractive for optical security applications. Further, the high sensitivity to the surrounding material can be utilized; a position dependent modification of the color filters can be achieved by inkjet printing of transparent inks with different refractive indices. Additionally, a different set of plasmonic color filters are studied, which can be precisely controlled with the incident polarization while having almost angle-independent optical properties. This renders them ideal for camera filters, where a large-field-of-view is desired. By controlling the optical properties of the filters, a plasmonic multispectral imaging device is demonstrated. Overall, the used fabrication methods and materials are compatible with large-scale and cost-efficient manufacturing methods. Thus this thesis may help paving the way for everyday products based on plasmonics