Interband Regions Research Articles

Plasmon modes in double-layer gapped graphene

Abstract We calculate plasmon frequencies and decay rates of plasma oscillations in double layer gapped graphene (DLGG) made of two parallel monolayer gapped graphene sheets, separated by a dielectric spacer. The results are compared to those in double layer gapless graphene with the same parameters. Numerical calculations show that, as in other double-layer systems, two plasmon modes exist in DLGG, corresponding to in-phase and out-of-phase oscillations of carriers in two sheets of the system. The energy loss of acoustic plasmon mode in DLGG is remarkably different from that in DLG caused by a separation of intra- and inter-band single-particle excitation regions of DLGG. In addition, the increase in band gap leads to a significant decrease in DLGG plasmon frequencies. Finally, the temperature dependence of plasmon properties in DLGG differs remarkably from that in DLG, and the effect of the band gap on plasmon characters decreases notably with increasing temperature.

Polytene Chromosomes - A Portrait of Functional Organization of the Drosophila Genome.

This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures – bands and interbands. Generally, densely packed chromatin forms black bands, moderately condensed regions form grey loose bands, whereas decondensed regions of the genome appear as interbands. Recent progress in the annotation of the Drosophila genome and epigenome has made it possible to compare the banding pattern and the structural organization of genes, as well as their activity. This was greatly aided by our ability to establish the borders of bands and interbands on the physical map, which allowed to perform comprehensive side-by-side comparisons of cytology, genetic and epigenetic maps and to uncover the association between the morphological structures and the functional domains of the genome.These studies largely conclude that interbands 5’-ends of housekeeping genes that are active across all cell types. Interbands are enriched with proteins involved in transcription and nucleosome remodeling, as well as with active histone modifications. Notably, most of the replication origins map to interband regions. As for grey loose bands adjacent to interbands, they typically host the bodies of house-keeping genes. Thus, the bipartite structure composed of an interband and an adjacent grey band functions as a standalone genetic unit. Finally, black bands harbor tissue-specific genes with narrow temporal and tissue expression profiles. Thus, the uniform and permanent activity of interbands combined with the inactivity of genes in bands forms the basis of the universal banding pattern observed in various Drosophila tissues.

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.

Atomic-Force Microscopy Analyses on Dislocation in Extinction Bands of Poly(dodecamethylene terephthalate) Spherulites Solely Packed of Single-Crystal-Like Lamellae

This study, using atomic-force and polarized-optical light (AFM and POM) microscopies on the extinction banded spherulites of poly(dodecamethylene terephthalate) (P12T) at high Tc = 110 °C with a film thickness kept at 1–3 µm, has verified that banded spherulites can be composed of stacks of entirely single-crystal-like lamellae free of any twisting, flipping, or bending, and no branching of lamellae. Defects in the crystal packing of extinction bands are present in both intra-band and inter-band regions. The intra-band defects originate from the miss-match in spiral-circling into circular bands while the inter-band defects are in the interfaces between successive bands where single crystals in the ridge are jammed to deformation, then suddenly precipitate prior to initiating another cycle of banding. The fish-scale lamellae, at the initiation of a cycle, are orderly packed as terrace-like single crystals; conversely, near or on the defected regions, they are highly jammed or squeezed and deformed to beyond recognition of their original single-crystal nature.

Digitor/dASCIZ Has Multiple Roles in Drosophila Development.

In this study we provide evidence that the spindle matrix protein Skeletor in Drosophila interacts with the human ASCIZ (also known as ATMIN and ZNF822) ortholog, Digitor/dASCIZ. This interaction was first detected in a yeast two-hybrid screen and subsequently confirmed by pull-down assays. We also confirm a previously documented function of Digitor/dASCIZ as a regulator of Dynein light chain/Cut up expression. Using transgenic expression of a mCitrine-labeled Digitor construct, we show that Digitor/dASCIZ is a nuclear protein that is localized to interband and developmental puff chromosomal regions during interphase but redistributes to the spindle region during mitosis. Its mitotic localization and physical interaction with Skeletor suggest the possibility that Digitor/dASCIZ plays a direct role in mitotic progression as a member of the spindle matrix complex. Furthermore, we have characterized a P-element insertion that is likely to be a true null Digitor/dASCIZ allele resulting in complete pupal lethality when homozygous, indicating that Digitor/dASCIZ is an essential gene. Phenotypic analysis of the mutant provided evidence that Digitor/dASCIZ plays critical roles in regulation of metamorphosis and organogenesis as well as in the DNA damage response. In the Digitor/dASCIZ null mutant larvae there was greatly elevated levels of γH2Av, indicating accumulation of DNA double-strand breaks. Furthermore, reduced levels of Digitor/dASCIZ decreased the resistance to paraquat-induced oxidative stress resulting in increased mortality in a stress test paradigm. We show that an early developmental consequence of the absence of Digitor/dASCIZ is reduced third instar larval brain size although overall larval development appeared otherwise normal at this stage. While Digitor/dASCIZ mutant larvae initiate pupation, all mutant pupae failed to eclose and exhibited various defects in metamorphosis such as impaired differentiation, incomplete disc eversion, and faulty apoptosis. Altogether we provide evidence that Digitor/dASCIZ is a nuclear protein that performs multiple roles in Drosophila larval and pupal development.

Condensin II Regulates Interphase Chromatin Organization Through the Mrg-Binding Motif of Cap-H2.

The spatial organization of the genome within the eukaryotic nucleus is a dynamic process that plays a central role in cellular processes such as gene expression, DNA replication, and chromosome segregation. Condensins are conserved multi-subunit protein complexes that contribute to chromosome organization by regulating chromosome compaction and homolog pairing. Previous work in our laboratory has shown that the Cap-H2 subunit of condensin II physically and genetically interacts with the Drosophila homolog of human MORF4-related gene on chromosome 15 (MRG15). Like Cap-H2, Mrg15 is required for interphase chromosome compaction and homolog pairing. However, the mechanism by which Mrg15 and Cap-H2 cooperate to maintain interphase chromatin organization remains unclear. Here, we show that Cap-H2 localizes to interband regions on polytene chromosomes and co-localizes with Mrg15 at regions of active transcription across the genome. We show that co-localization of Cap-H2 on polytene chromosomes is partially dependent on Mrg15. We have identified a binding motif within Cap-H2 that is essential for its interaction with Mrg15, and have found that mutation of this motif results in loss of localization of Cap-H2 on polytene chromosomes and results in partial suppression of Cap-H2-mediated compaction and homolog unpairing. Our data are consistent with a model in which Mrg15 acts as a loading factor to facilitate Cap-H2 binding to chromatin and mediate changes in chromatin organization.

Histone H3S10 phosphorylation by the JIL-1 kinase in pericentric heterochromatin and on the fourth chromosome creates a composite H3S10phK9me2 epigenetic mark

The JIL-1 kinase mainly localizes to euchromatic interband regions of polytene chromosomes and is the kinase responsible for histone H3S10 phosphorylation at interphase in Drosophila. However, recent findings raised the possibility that the binding of some H3S10ph antibodies may be occluded by the H3K9me2 mark obscuring some H3S10 phosphorylation sites. Therefore, we have characterized an antibody to the epigenetic H3S10phK9me2 double mark as well as three commercially available H3S10ph antibodies. The results showed that for some H3S10ph antibodies their labeling indeed can be occluded by the concomitant presence of the H3K9me2 mark. Furthermore, we demonstrate that the double H3S10phK9me2 mark is present in pericentric heterochromatin as well as on the fourth chromosome of wild-type polytene chromosomes but not in preparations from JIL-1 or Su(var)3-9 null larvae. Su(var)3-9 is a methyltransferase mediating H3K9 dimethylation. Furthermore, the H3S10phK9me2 labeling overlapped with that of the non-occluded H3S10ph antibodies as well as with H3K9me2 antibody labeling. Interestingly, when a Lac-I-Su(var)3-9 transgene is overexpressed, it upregulates H3K9me2 dimethylation on the chromosome arms creating extensive ectopic H3S10phK9me2 marks suggesting that the H3K9 dimethylation occurred at euchromatic H3S10ph sites. This is further supported by the finding that under these conditions euchromatic H3S10ph labeling by the occluded antibodies was abolished. Thus, our findings indicate a novel role for the JIL-1 kinase in epigenetic regulation of heterochromatin in the context of the chromocenter and fourth chromosome by creating a composite H3S10phK9me2 mark together with the Su(var)3-9 methyltransferase.

Domain Requirements of the JIL-1 Tandem Kinase for Histone H3 Serine 10 Phosphorylation and Chromatin Remodeling in Vivo

The JIL-1 kinase localizes to Drosophila polytene chromosome interbands and phosphorylates histone H3 at interphase, counteracting histone H3 lysine 9 dimethylation and gene silencing. JIL-1 can be divided into four main domains, including an NH2-terminal domain, two separate kinase domains, and a COOH-terminal domain. In this study, we characterize the domain requirements of the JIL-1 kinase for histone H3 serine 10 (H3S10) phosphorylation and chromatin remodeling in vivo. We show that a JIL-1 construct without the NH2-terminal domain is without H3S10 phosphorylation activity despite the fact that it localizes properly to polytene interband regions and that it contains both kinase domains. JIL-1 is a double kinase, and we demonstrate that both kinase domains of JIL-1 are required to be catalytically active for H3S10 phosphorylation to occur. Furthermore, we provide evidence that JIL-1 is phosphorylated at serine 424 and that this phosphorylation is necessary for JIL-1 H3S10 phosphorylation activity. Thus, these data are compatible with a model where the NH2-terminal domain of JIL-1 is required for chromatin complex interactions that position the kinase domain(s) for catalytic activity in the context of the state of higher order nucleosome packaging and chromatin structure and where catalytic H3S10 phosphorylation activity mediated by the first kinase domain is dependent on autophosphorylation of serine 424 by the second kinase domain. Furthermore, using a lacO repeat tethering system to target mutated JIL-1 constructs with or without catalytic activity, we show that the epigenetic H3S10 phosphorylation mark itself functions as a causative regulator of chromatin structure independently of any structural contributions from the JIL-1 protein.

The Potassium Channel Interacting Protein 3 (DREAM/KChIP3) Heterodimerizes with and Regulates Calmodulin Function

Downstream regulatory element antagonistic modulator (DREAM/KChIP3), a neuronal EF-hand protein, modulates pain, potassium channel activity, and binds presenilin 1. Using affinity capture of neuronal proteins by immobilized DREAM/KChIP3 in the presence and absence of calcium (Ca(2+)) followed by mass spectroscopic identification of interacting proteins, we demonstrate that in the presence of Ca(2+), DREAM/KChIP3 interacts with the EF-hand protein, calmodulin (CaM). The interaction of DREAM/KChIP3 with CaM does not occur in the absence of Ca(2+). In the absence of Ca(2+), DREAM/KChIP3 binds the EF-hand protein, calcineurin subunit-B. Ca(2+)-bound DREAM/KChIP3 binds CaM with a dissociation constant of ∼3 μM as assessed by changes in DREAM/KChIP3 intrinsic protein fluorescence in the presence of CaM. Two-dimensional (1)H,(15)N heteronuclear single quantum coherence spectra reveal changes in chemical shifts and line broadening upon the addition of CaM to (15)N DREAM/KChIP3. The amino-terminal portion of DREAM/KChIP3 is required for its binding to CaM because a construct of DREAM/KChIP3 lacking the first 94 amino-terminal residues fails to bind CaM as assessed by fluorescence spectroscopy. The addition of Ca(2+)-bound DREAM/KChIP3 increases the activation of calcineurin (CN) by calcium CaM. A DREAM/KChIP3 mutant incapable of binding Ca(2+) also stimulates calmodulin-dependent CN activity. The shortened form of DREAM/KChIP3 lacking the NH(2)-terminal amino acids fails to activate CN in the presence of calcium CaM. Our data demonstrate the interaction of DREAM/KChIP3 with the important EF-hand protein, CaM, and show that the interaction alters CN activity.

H3S10 phosphorylation by the JIL-1 kinase regulates H3K9 dimethylation and gene expression at the white locus in Drosophila

The JIL-1 kinase is a multidomain protein that localizes specifically to euchromatin interband regions of polytene chromosomes and is the kinase responsible for histone H3S10 phosphorylation at interphase. Genetic interaction assays have suggested that the function of the epigenetic histone H3S10ph mark is to antagonize heterochromatization by participating in a dynamic balance between factors promoting repression and activation of gene expression as measured by position-effect variegation (PEV) assays. Interestingly, JIL-1 loss-of-function alleles can act either as an enhancer or indirectly as a suppressor of wm4 PEV depending on the precise levels of JIL-1 kinase activity. In this study, we have explored the relationship between PEV and the relative levels of the H3S10ph and H3K9me2 marks at the white gene in both wild-type and wm4 backgrounds by ChIP analysis. Our results indicate that H3K9me2 levels at the white gene directly correlate with its level of expression and that H3K9me2 levels in turn are regulated by H3S10 phosphorylation.

Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA‐binding protein occupancy

The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome-wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with "active" chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non-polytene chromosomes.

The epigenetic H3S10 phosphorylation mark is required for counteracting heterochromatic spreading and gene silencing inDrosophila melanogaster

The JIL-1 kinase localizes specifically to euchromatin interband regions of polytene chromosomes and is the kinase responsible for histone H3S10 phosphorylation at interphase. Genetic interaction assays with strong JIL-1 hypomorphic loss-of-function alleles have demonstrated that the JIL-1 protein can counterbalance the effect of the major heterochromatin components on position-effect variegation (PEV) and gene silencing. However, it is unclear whether this was a causative effect of the epigenetic H3S10 phosphorylation mark, or whether the effect of the JIL-1 protein on PEV was in fact caused by other functions or structural features of the protein. By transgenically expressing various truncated versions of JIL-1, with or without kinase activity, and assessing their effect on PEV and heterochromatic spreading, we show that the gross perturbation of polytene chromosome morphology observed in JIL-1 null mutants is unrelated to gene silencing in PEV and is likely to occur as a result of faulty polytene chromosome alignment and/or organization, separate from epigenetic regulation of chromatin structure. Furthermore, the findings provide evidence that the epigenetic H3S10 phosphorylation mark itself is necessary for preventing the observed heterochromatic spreading independently of any structural contributions from the JIL-1 protein.

Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster

BackgroundDespite many efforts, little is known about distribution and interactions of chromatin proteins which contribute to the specificity of chromomeric organization of interphase chromosomes. To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously.ResultsHere we demonstrate that in interphase chromosomes of Drosophila cell lines, the interband regions are enriched for a specific set of proteins generally characteristic of the "open" chromatin (RNA polymerase II, CHRIZ (CHRO), BEAF-32, BRE1, dMI-2, GAF, NURF301, WDS and TRX). These regions also display reduced nucleosome density, histone H1 depletion and pronounced enrichment for ORC2, a pre-replication complex component. Within the 13 interband regions analyzed, most were around 3-4 kb long, particularly those where many of said protein features were present. We estimate there are about 3500 regions with similar properties in chromosomes of D. melanogaster cell lines, which fits quite well the number of cytologically observed interbands in salivary gland polytene chromosomes.ConclusionsOur observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization.

Identification and molecular genetic characterization of the polytene chromosome interbands in Drosophila melanogaster

Being inserted into the polytene chromosome interbands, P transposable elements integrated in the genome of Drosophila produce new bands, enabling their use as markers of interband positions on the physical map. Molecular genetic analysis of 13 interbands marked as described showed that in most cases these regions were represented by intergenic spacers and by 5' noncoding regions of the genes. The interband regions consist of unique chromatin type whose decondensation is not obviously associated with transcription. In addition, interbands are enriched with the specific CHRIZ protein. Comparison of chromosomal protein sets and histone modifications in the polytene chromosome interband regions and in the corresponding sequences of the diploid cell chromosomes demonstrated their complete similarity relative these characteristics. In both cell types, interband regions contained open chromatin markers, including RNA polymerase II, ORC, GAF, TRX, and acetylated histones. At the same time, these regions appeared to be depleted of the repressed chromatin proteins, PC, E(Z), H3K9Me3, H3K27Me3, and some others. The similarity between interband chromosomal regions from different cell types is also manifested in the sets of DNAse I hypersensitive sites, which proved to be hot spots for transposon insertions. Our results suggest that band-interband structure is a fundamental principle of the interphase chromosome organization.

Functional analysis of Drosophila polytene chromosomes decompacted unit: the interband

Differential compaction of the interphase chromosomes is important for proper functioning of the eukaryotic genome. Such non-uniform compaction is most easily observed in Drosophila salivary gland polytene chromosomes as a reproducible banding pattern. Functional mechanisms underlying the establishment and maintenance of the banding pattern remain unclear but have been hypothesized to involve transcription and chromatin insulators. We tested functional properties of DNA fragments from several transcriptionally inert interband regions that behave as autonomous decompacted units of polytene chromosomes. Our results suggest that, in the absence of transcription, the decondensed state of interband regions does not depend on the presence of insulator elements but instead correlates with the presence of transcriptional enhancers.

Allocyclic regions and banding patterns in the chromosomes of Najas marina

Seven spontaneous allocyclic regions have been observed in the prophase and prometaphase chromosomes of the first pollen mitosis in race B of Najas marina. Morphologically the allocyclic regions were similar to the cold-induced H-segments observed in some organisms. C-bands were shown to correspond to the allocyclic regions. In addition, after use of the C-banding method there were paired dots in the centromeric regions of all the six chromosomes. With quinacrine mustard staining the allocyclic regions were not differentiated in any way. However, with phase contrast microscope these regions were sometimes visible as unstained gaps when acetic acid treated chromosomes were stained with Feulgen. There were no allocyclic regions in B chromosomes. After C-banding two dark dots were also visible in the centromeric region of the B chromosome. The rest of this chromosome was stained as pale as the interband regions in A chromosomes. In this respect, the B chromosomes behave like facultative heterochromatin. It was proposed that both the formation of allolyclic regions and C-bands depend on the presence of a special protein component in these chromosome regions.

Mapping mesoscale heterogeneity in the plastic deformation of a copper single crystal

Part of a ‘multiscale characterization’ study of heterogeneous deformation patterns in metals is reported. A copper single crystal was oriented for single slip in the (111)[] slip system and tested to ∼10% strain in roughly uniaxial compression. The macroscopic strain field was monitored during the test by optical ‘image correlation’. The strain field was measured on orthogonal surfaces, one of which (the x-face) was oriented perpendicular to [] and contained the [] direction of the preferred slip system. The macroscopic strain developed in an inhomogeneous pattern of broad, crossed shear bands in the x-face. One, the primary band, lay parallel to (111). The second, the ‘conjugate’ band, was oriented perpendicular to (111) with an overall () habit that contains no common slip plane of the fcc crystal. The mesoscopic deformation pattern was explored with selected area diffraction, using a focused synchrotron radiation polychromatic beam with a resolution of 1–3 µm. Areas within the primary, conjugate and mixed (primary + conjugate) strain regions of the x-face were identified and mapped for their orientation, excess defect density and shear stress. The mesoscopic defect structure was concentrated in broad, somewhat irregular primary bands that lay nominally parallel to (111) in an almost periodic distribution with a period of about 30 µm. These primary bands were dominant even in the region of conjugate strain. There were also broad conjugate defect bands, almost precisely perpendicular to the primary bands, which tended to bridge primary bands and terminate at them. The residual shear stresses were large (ranging to well above 500 MPa) and strongly correlated with the primary shear bands; interband stresses were small. The maximum resolved shear stresses within the primary bands were oriented out of the plane of the bands, and, hence, could not recover the dislocation structure in the bands. The maximum resolved shear stresses in the interband regions lay predominantly in {111} planes. The results are compared to the mesoscopic defect patterns found in Cu in etch pit studies done some decades ago, which also revealed a mesoscopic dislocation structure made up of orthogonal bands.

The COOH-terminal Domain of the JIL-1 Histone H3S10 Kinase Interacts with Histone H3 and Is Required for Correct Targeting to Chromatin

The JIL-1 histone H3S10 kinase in Drosophila localizes specifically to euchromatic interband regions of polytene chromosomes and is enriched 2-fold on the male X chromosome. JIL-1 can be divided into four main domains including an NH(2)-terminal domain, two separate kinase domains, and a COOH-terminal domain. Our results demonstrate that the COOH-terminal domain of JIL-1 is necessary and sufficient for correct chromosome targeting to autosomes but that both COOH- and NH(2)-terminal sequences are necessary for enrichment on the male X chromosome. We furthermore show that a small 53-amino acid region within the COOH-terminal domain can interact with the tail region of histone H3, suggesting that this interaction is necessary for the correct chromatin targeting of the JIL-1 kinase. Interestingly, our data indicate that the COOH-terminal domain alone is sufficient to rescue JIL-1 null mutant polytene chromosome defects including those of the male X chromosome. Nonetheless, we also found that a truncated JIL-1 protein which was without the COOH-terminal domain but retained histone H3S10 kinase activity was able to rescue autosome as well as partially rescue male X polytene chromosome morphology. Taken together these findings indicate that JIL-1 may participate in regulating chromatin structure by multiple and partially redundant mechanisms.

Giemsa C-banding of barley chromosomes

Giemsa C-banding was applied to somatic metaphase chromosomes of 70 reciprocal translocations of barley. Hordeum vulgare L. Based on changes in C-banding patterns in combination with changes in arm ratios, if necessary, breakpoints were localized precisely in 16, and to smaller or larger chromosome segments in 36 translocations. In 18 symmetrical translocations, chromosomes with interchanges could not be identified, because breakpoints were distal to marker bands. Especially with asymmetrical translocations the use of C-banding can assign breakpoints to chromosomes and chromosome arms sooner and often more precisely than currently used procedures. Breakpoints were equally distributed among short and long arms, but with a surplus at centromeres. Translocations with breakpoints in two short arms, a short and a long arm, and two long arms, respectively, were found in a 1:2:1-ratio indicating that arms combined at random. All breakpoints were located in interband regions. The karyotype of one translocation only had a semidicentric chromosome; in another, one chromosome had a persistent gap. Translocations used in cytogenetic studies had a high frequency of asymmetrical interchanges with more distal breakpoints than little-studied translocations. A possible translocation tester set with cytologically distal breakpoints is presented.

Dependence of the optical properties of UHV deposited silver thin films on the deposition parameters and their relation to the nanostructure of the films

Silver films were deposited on glass substrates under different deposition conditions, i.e. different film thicknesses, deposition rates and deposition angles. Their optical properties were measured by spectrophotometry in the spectral range of 185–3300 nm. The Kramers–Kronig method was used to analyze the reflectivity curves of the silver films to obtain their optical constants. The influence of substrate temperature on the microstructure of thin metallic films, the structure zone model (SZM), is well established, whereas there has been some previous work on the influence of film thickness and morphology, deposition rate and deposition angle on the microstructure and morphology of thin films. An effective medium approximation (EMA) analysis was used to establish the relationship between the atomic force microscopy results, SZM predictions and EMA results, and hence the optical properties of silver thin films. The predictions of the Drude free-electron theory are compared with experimental results for dielectric functions of Ag films produced under different deposition conditions. The real part of the dielectric constant increases with film thickness and decreases with increasing deposition rate and with increasing incidence angle, whereas the imaginary part of the dielectric constant decreases with increasing film thickness and deposition rate and with decreasing incidence angle over the whole energy range measured, including the interaband and interband regions.