Element values for low‐pass prototype circuit and geometrical parameters of third‐order band‐stop FSS filter.
\r\n\tEnhanced parasitism in crop pests results in parasitoids dispersal from these habitats to the crop and switch to the target pest. Plants can also affect the impact of parasitoids on herbivore populations directly, by providing the parasitoids with food and shelter or by influencing their searching processes or indirectly, by affecting host suitability.
",isbn:null,printIsbn:null,doi:null,price:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"54b905c17bdc16bc8ebb9e8516597c0f",bookSignature:"Dr. Muhammad Anjum Aqueel",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/6757.jpg",keywords:"Biological control, Hymenopteran Wasps, Parasitoids, IPM, Evolution of Wasps, Diversity of Wasps, Biology of Wasps, Social Life of Wasps, Impact on Household, Control of Wasps, Beneficial Wasps, Behavior of Solitary Wasps, Host Parasitoid Interactions, Functional Response, Foraging, Conservation of Predatory Wasps",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:0,numberOfDimensionsCitations:0,numberOfTotalCitations:0,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"January 15th 2018",dateEndSecondStepPublish:"February 5th 2018",dateEndThirdStepPublish:"April 6th 2018",dateEndFourthStepPublish:"June 25th 2018",dateEndFifthStepPublish:"August 24th 2018",remainingDaysToSecondStep:"a year",secondStepPassed:!0,currentStepOfPublishingProcess:5,editedByType:null,editors:[{id:"220401",title:"Dr.",name:"Muhammad Anjum",middleName:null,surname:"Aqueel",slug:"muhammad-anjum-aqueel",fullName:"Muhammad Anjum Aqueel",profilePictureURL:"https://mts.intechopen.com/storage/users/220401/images/6386_n.jpg",biography:"Dr. Muhammad Anjum Aqueel has a Ph.D. degree from a prestigious Imperial College London, UK. He has been working as Assistant Professor (Entomology) in department of Entomology, College of Agriculture, University of Sargodha, Pakistan since March 2011 up to present date. During his research, he worked on tritrophic interactions of nitrogen fertilizer on aphids and their natural enemies. His interest is ecology of insects and their biological control. He is also interested in predator-prey and parasitoid-host interactions. Furthermore, he is currently running an Apiculture project and maintaining few thirty honey bee colonies in entomology department. This setup provides a valuable opportunity for undergraduate students to perform their practical demonstrations and for postgraduate students to conduct their research. He is interested in control of wax moth and Varroa mites in bee colonies in an integrated manner. He is also studying higher trophic effects of plant applications on foraging activity of bees and honey quality.\n\nCurrently, dr. Aqueel is supervising a significant number of Masters and PhD scholars. He is an author of 28+ research papers in international reputed journals and 2 books. In his academic career he contributed 8+ oral talks in many reputed international conferences.",institutionString:null,position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"0",totalChapterViews:"0",totalEditedBooks:"0",institution:null}],coeditorOne:null,coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"909",title:"Parasitology",slug:"parasitology"}],chapters:null,productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},personalPublishingAssistant:{id:"225753",firstName:"Marina",lastName:"Dusevic",middleName:null,title:"Mrs.",imageUrl:"https://mts.intechopen.com/storage/users/225753/images/7224_n.png",email:"marina.d@intechopen.com",biography:"As an Author Service Manager my responsibilities include monitoring and facilitating all publishing activities for authors and editors. From chapter submission and review, to approval and revision, copyediting and design, until final publication, I work closely with authors and editors to ensure a simple and easy publishing process. I maintain constant and effective communication with authors, editors and reviewers, which allows for a level of personal support that enables contributors to fully commit and concentrate on the chapters they are writing, editing, or reviewing. I assist authors in the preparation of their full chapter submissions and track important deadlines and ensure they are met. I help to coordinate internal processes such as linguistic review, and monitor the technical aspects of the process. As an ASM I am also involved in the acquisition of editors. 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To introduce convenient and feasible methods based on new paradigms to guide, the structure design is eagerly demanded. In the radio or microwave frequency domains, lumped circuit elements, e.g. resistors (R), inductors (L) and capacitors (C), can be effectively and flexibly used as blocks for designing complicated micro‐electronic devices, and the conventional circuit theory is widely and successfully adopted. One question naturally arises: can such a circuit theory, along with its accompanying mathematical machinery, be extended and applied to the design of plasmonic nanostructures working at the optical domain?
\nWithin this context, in this chapter, a new methodology, ‘equivalent nanocircuit (EN) theory’ is briefly introduced, and its representative applications in designing plasmonic devices with peculiar characteristics in optical or infrared frequency domains are enumerated. First, to start with the short introduction of the basis of ‘metatronics\', the analogy between micro‐electronic lumped circuit elements (R, L, C) and optical nanocircuit elements (nanoparticles, nanoantennas, nanogratings and optical meta‐surfaces) is established. Second, the method describing how to use the above optical nanocircuit elements to construct a single‐layer or multiple‐layer complicated meta‐material structure is proposed and thus the ‘metatronics’ concept moves forward to the multi‐order circuit theory. Finally, three representative applications of multi‐order EN theory to design infrared window meta‐materials are demonstrated: (1) a synthesis procedure for designing a third‐order Butterworth filter is proposed; (2) a metal‐insulator‐metal (MIM) ultra‐broadband absorber is successfully designed in the infrared range; (3) with the transparent conductive oxides (TCOs) semiconductor materials as building blocks, a design‐simplified broadband super‐flat perfect infrared absorber is realized.
\nOptical meta‐material bridges the gap between the conventional optics and the nanoworld, which gives rise to a diversity of surprising and profound effects fully appreciated and technologically explored in recent years [1–3]. The electromagnetic property of meta‐materials is dependent on their specifically and smartly engineered artificial structures. To explore new design methodology is eagerly demanded. Historically, in electronics, basic functionalities are synthesized by ‘lumped’ circuit elements, such as resistors, inductors, capacitors and transistors, and more complicated operations can be realized by combining them into a complicated circuit in some specific serial or parallel ways. Now, great interests in pushing classic circuit operation to infrared or visible optical frequency range have boomed in order to achieve an optical analogy [4–7]. Generally, just simply reducing the basic unit size of circuit to the micrometre (µm) or nanometre (nm) level would be technically difficult to achieve the above goals.
\nThe first challenge arises in the state‐of‐the‐art nanoscale fabrication technique is its inevitable difficulty to achieve deeply sub‐wavelength dimension becoming serious. The second challenge lies in material dispersion which is sometimes vital. As we know that metals such as gold, silver, aluminium and copper are highly conductive materials at RF and microwaves, commonly used in conventional circuits. However, at optical frequency, these metals would behave differently, and they exhibit plasmonic resonance instead of the usual conductivity, i.e. the coupling of optical signals with collective oscillation of conductive electrons at these metal surfaces is dominant where the real part of permittivity is negative. In other words, at optical wavelengths, the conduction current is no longer the dominant current circulating through lumped optical elements. Therefore, the traditional circuit theory and the corresponding methodology for micro‐electronics lose their functionality in optical frequency domain.
\nIn 2007, Engheta et al. have made an important breakthrough and first proposed the concept of ‘metatronics’ [6] which bridges the gap between low frequency circuitry design and high frequency nanodevice design. In their opinions, it is possible to realize the performance of lumped‐circuit‐like elements at optical frequency just by properly designing and suitably arranging plasmonic or/and non‐plasmonic nanoparticles, as shown in Figure 1. The theoretical framework of ‘metatronics’ is very simple and is based on one Maxwell equation \n
Analogy between sub‐wavelength nanoparticles and conventional lumped nanocircuit elements at optical frequency domain. Here, one nanoparticle can take a different role when the sign of its complex permittivity \n\nε\n\n is different. If combined in a specific way, different nanoparticles can possess some defined functionalities (adapted from Ref. [6], Figure 1).
Based on the above ‘metatronic’ concept, the optical impedance (an intrinsic parameter) of nanoparticles is similar to the electrical counterpart (Z=V/I) [8], which is independent of the surrounding environments. As sketched in Figure 2, two isolated sub‐wavelength nanospheres (radius R) with complex permittivity \n
Optical nanocircuit models for (a) dielectric or (b) plasmonic nanoparticles. E0 denotes the incident electric field, and thinner field lines together with the arrows represent the electric dipolar fringe field from nanospheres. (adapted from Ref. [8], Figure 1).
Here, as shown at the bottom of Figure 2, Iimp is the ‘impressed’ displacement current, Isph is displacement current circulating in nanospheres and Ifringe is displacement current for the fringe (dipolar) field. Such currents are all related to the polarization charges at the surface of nanospheres induced by light source and all can be intuitively interpreted as branch currents at nodes in a parallel circuit.
\nThe ‘average’ potential difference between the upper and lower hemi‐spherical surfaces of the sphere is given by
\nThus, after having obtained the ratio between the potential difference (Eq. 4) and the effective current evaluated from Eq. (2) or (3), one can, respectively, get the equivalent impedance for the ‘nanosphere’ or the ‘fringe’ branch of the circuit as
\nFrom Eq. (5), one can clearly see that the two parallel elements in the circuits (Figure 2) may behave differently, which is determined by the permittivity sign of the nanospheres as shown in Figure 1. For example, a non‐metallic (or dielectric) sphere can be thought as a capacitor (because of (\n
Instead, if such a sphere is made of plasmonic materials (e.g. Ag, Au), it behaves as an inductive element, since (\n
Naturally, one can implement a more complicated circuit by a series and parallel operations among different kinds of such lumped particles. If two nanoparticles share a common interface and electric field is tangential to the common interface, a parallel operation between them would be made effective (left‐column, Figure 3).
\nTwo conjoined two‐dimensional half‐spheres with different signs of permittivity, illuminated by a uniform electric field. Parallel (left) and series (right) configurations are, respectively, shown (adapted from Ref. [8], Figure 2).
In contrast, if the electric displacement vector locally is normal to that of common interface, the displacement current \n
In the above, just nanosphere is taken as an example particle. In fact, except for this, the basic ‘alphabets’ of metatronics can also be gratings, cylinder pillars, rectangle bricks and other antennas, and they have been widely applied to various wavelength regimes,for example in a series of theoretical analyses and numerical simulations [4, 7, 10–12].
\nThe recent experimental progresses [7, 13] have verified the validity and potentiality of the above optical nanocircuit paradigm introduced in Section 2.2, and also demonstrated the possibility of re‐configuring the circuit responses just by changing the orientation and polarization of illuminating field to induce a specific feature not available in conventional electric circuits. No doubt that this metatronics concept provides us an effective and practical tool to design optical nanodevices, such as designing and tuning of optical nanoantennas [14, 15] and meta‐surfaces [16].
\nOne representative example is shown in Figure 4 where a polarization‐selective optical filter making use of a simple sub‐wavelength grating is designed. Different incident illuminations and different effective optical connections between the nanoelements of this ‘stereo‐nanocircuit’ are chosen to conveniently control the light transmittance, i.e. to make the circuit functions either band‐stop or band‐pass. This scheme may be exploited for parallel processing of multiple flows of information through a single nanostructure.
\nSub‐wavelength grating with parallel plasmonic nanorods working as a two‐dimensional optical nanocircuit with a stereo‐functionality. (a) The E field is perpendicular to the nanorods and nanoinductors (including nanoresistors) and nanocapacitors form a series configuration (c). In contrast, if the E field is parallel to nanorods (b), a parallel configuration (d) of lumped circuit elements is formed instead (adapted from [10], Figure 1).
In detail, when electric field E is perpendicular to the nanorods (Figure 4a), the optical displacement current \n
In contrast, when E is parallel to the nanorods (Figure 4b), the optical displacement current \n
These equivalent impedances (series or parallel,in Eqs. (8) and (9)) finally determine the transmittance of the incident optical signal, and the latter is naturally derived as,
\nTo test this optical circuit approach, one can compare the results in Figure 5 calculated from Eq. (10) with those experimentally measured (10) or exactly numerical results with the help of a commercial software. As one expects, the grating with a ‘series’ configuration behaves as a band‐stop filter, however the same grating with a ‘parallel’ configuration as a band‐pass filter instead.
\nTransmittance spectra for five different samples from A to E. Experimentally measured data for (a) perpendicular or (b) parallel polarization of the incident wave impinging on the nanorod arrays. (c and d) Full‐wave simulation results and (e and f) calculation results from nanocircuit theory for polarization perpendicular (upper) or parallel (lower) to nanorods (adapted from Ref. [10], Figure 2).
Another representative example is related to the radio‐frequency (RF) antennas which have been widely investigated and applied in wireless telecommunication system in the last century. The functionality of RF antenna is information revolution. It is usually used with a radio transmitter or radio receiver. In transmission, a radio transmitter supplies an electric current oscillating at radio frequency (i.e. a high frequency alternating current (AC)) to the antenna’s terminals, and the antenna radiates the energy from the current as electromagnetic waves (radio waves). In analogy with their RF counterparts, optical antennas made of plasmonic nanoparticles are able to efficiently coupled localized sources or guided waves at the nanoscale level to far‐field radiation, and in turn, to convert the impinging radiation from the far‐field into sub‐wavelength localized or guided fields [17]. As the counterpart of RF antenna, an optical nanoantenna exhibits novice and interesting characteristics because of their plasmonic nature.
\nIn detail, as depicted in Figure 6a, a conventional linear RF antenna is loaded at its feeding gap with lumped circuit elements and changing the antenna input impedance allowance to operate at a given frequency or to achieve a good match for a specific feeding network. Analogously, an optical nanocircuit opens the same possibility for an optical nanoantenna (Figure 6b), and the complex optical input impedance can be interpreted as the parallel combination of the dipole intrinsic impedance Zdip and the gap impedance Zgap [11, 15]. The former impedance is assumed to be a fixed property of the nanoantenna geometry and surrounding environment, and the latter can be engineered to a large extent by loading the gap with different materials. Such as for a cylindrical gap with height of t, radius of a and excited by an incident electric field parallel to its axis, the gap impedance is given by,
\nOptical nanoantennas. RF dipole antenna (a) loaded with lumped circuit elements at its feeding gap, and analogously, a plasmonic dipole nanoantenna (b) loaded with optical nanocircuits (adapted from Ref. [15), Figure 1). The low inset shows the circuit model of antenna input impedance. (c) Tuning of nanoantenna resonance by ‘gap loading’ with different realistic materials (adapted from Ref. [15], Figure 3).
Thus, by filling the gap with different materials (or their proper series or parallel combination), the impedance of the gap can be tailored to a large degree. As a result, one can tune the frequency response (Figure 6c) or radiation pattern easily.
\nIn addition, except for the above sub‐wavelength grating and non‐antenna, meta‐surface represents another important type [18], the planar counterparts of meta‐materials that provide the unprecedented control of the amplitude, phase or polarization of light waves at the sub‐wavelength (nano) scale. For example, these two‐dimensional surfaces can alter the wave‐front of incident light for a widespread application in beam shaping [19–24], polarizers [25, 26] and flat lenses [27–29]. As proposed in [16], the fundamental building blocks are paired plasmonic or dielectric nanorods collectively working as an inductor–capacitor nanocircuit (Figure 7a, left), whose impedance depends directly on the filling ratio of plasmonic and dielectric materials. By suitably alternating these nanocircuit blocks on the transverse direction, one can synthesize a meta‐surface with the required inhomogeneous impedance profile. The configuration composed of a stack of three meta‐surfaces (Figure 7a, right), can fully control the nanoscale optical transmission, while simultaneously minimizing the reflection (impedance‐matching to free‐space), allowing, for example light deflection with an almost ideal efficiency as shown in Figure 7b.
\nMeta‐transmit‐array used for full control of nanoscale optical transmission. (a) Basic nanocircuit building block (left) and resulting meta‐screen (right) with transverse inhomogeneous profiles of surface impedance. (b) Full‐wave simulation of meta‐transmit‐array for light deflection with high efficiency and minimized reflection (adapted from Ref. [16]).
In this Section, the ‘design stack’ is moved upward, from the ‘physical layer’ of optical lumped elements (pure nanoparticles, nanogratings, nanoantennas, etc.) to more complex functional devices, including: (1) infrared third‐order Butterworth filters; (2) metal‐insulator‐metal (MIM) ultra‐broadband absorbers; (3) simplified broadband super‐flat perfect infrared absorbers only composed of single transparent conductive oxides (TCOs). Among these design procedures for multi‐layer nanostructures in our research group, the suitability of the equivalent nanocircuit theory is confirmed once more which in turn enriches and expands the application of equivalent nanocircuit theory.
\nFrequency selective surfaces (FSSs) have been the subject of investigations by many researchers for decades. An FSS is a periodic structure usually composed of an assembly of identical elements arranged in one‐ or two‐dimensional lattice. These structures are used in a variety of important applications ranging from microwave systems and antennas to radar and satellite communications. The simplest FSS device is a filter. By means of circuit elements (e.g. resistors (R), inductors (L) and capacitors (C)) FSSs can be effectively and flexibly designed to functionalize a low‐pass, high‐pass, band‐pass or band‐stop responses in the microwave or RF domain [30, 31]. The great interests in FSS\'s application in higher frequency range to achieve high‐density and high‐speed optical analogues [5, 10] have been pushed and the goals have been synthesized as realistic nanostructures at optical frequency, thanks to the optical nanocircuit theory which proves once more to be an essential design tool to construct optical FSSs or filters.
\nDifferent from those basic ‘alphabets’ mentioned in the previous section (nanogratings, nanoantennas, etc.), here, nanobricks are chosen as the building blocks. One reason is that they are widely used as the atoms of meta‐material and plasmonic structure, and the second is that the brick\'s planar profile makes us easily calculate the equivalent impedance.
\nAs a demonstration, one layer of periodic nanosquare array based on indium‐tin‐oxide (ITO) used for an infrared FSS filer is presented (Figure 8). The reason why ITO material is chosen for making up of FSS filter cells is just that, it possesses low electrical resistance and high transmittance in the visible range and widely used as an electrode for displays [33]. Especially, in the infrared spectral range, ITO material can demonstrate a metallic performance and this makes it to become a counterpart of noble metal. In addition, in the practical calculations, the permittivity ITO is usually modelled by the Drude dispersion relation.
\nSchematic diagrams of (a) periodic nanosquare array (as for its unit cell, the width and height, as well as the gap distance between two adjacent unit cells are denoted as w, h and g), (b) equivalent lumped circuit elements and (c) whole equivalent circuit used for designing single‐layer FSS filter (adapted from Ref. [32], Figure 1).
When such a nanosquare array is illuminated vertically (along z‐direction) by an optical signal from the bottom side with electric field E polarized parallel to the x‐direction, the optical displacement current \n
Thus, the input impedance of a single layer is given by,
\nSubsequently, the equivalent circuit model of this whole FSS system (Figure 8c), where \n
Obviously, in order to achieve different optical responses, the impedances of nanocircuit elements can be changed, by tuning the structural size (w, h or g), the constituent material property (\n
The transmittances of the FSS filters composed of samples from A to D, shown in Figure 9a, are obtained through Eq. (14). In addition, one can employ a full‐wave FDTD simulation to check the validity of such an equivalent nanocircuit theoretical model, and the corresponding transmittance spectra are shown in Figure 9b for comparison. The comparison result indicates that they are consistent well with each other.
\n(a) Theoretical and (b) numerical transmittance spectra based on equivalent circuit theory and FDTD simulation for samples from A to D, respectively. (c) The resonance wavelength and transmittance dip as a function of w/g. (d) The representative electric field distribution for sample B at resonance wavelength (adapted from Ref. [32], Figure 2).
As investigated in Figure 9c, the band‐stop behaviour of the FSS filters is dependent on their geometric size. With the increment of w/g, the band‐stop centre has a red‐shift which can be well interpreted by the optical circuit theory [15]: the larger the width of the nanosquare unit cell, the bigger the inductor L induced between the two adjacent air gaps, hence leading to a higher resonant wavelength. In contrast, with the increment of w/g, the band‐stop depth decreases and this behaviour is a result of the fact that the larger the width of nanosquare unit cell the stronger the guidance of light. From the electric field distribution for one representative sample at the resonance frequency, one can see that the unit cell structure works as an antenna and the incident light is localized at the regions between two adjacent metal unit cells, resulting in significant resonant enhancement of localized field and a guidance of most light through the air gap [35, 36].
\nAs for a more practical and wide application, a flatter and broader band‐stop filtering response curve with a fast roll‐off would be much advantageous [37]. To gain this aim, as the general FSS‐based filter design scheme does [38, 39], a third‐order Butterworth band‐stop filter is realized by cascading triple‐layer of nanosquare unit cells with a specific separation distance D between the consecutive layers (Figure 10a). The corresponding equivalent circuit is modelled in Figure 10b. Then, the whole structure is separated into four regions along the propagation direction (Figure 10c). Finally, along the similar procedure, the transmittance T after the third layer can be obtained step by step.
\nSchematic diagrams of (a) triple‐layer FSS filter, (b) equivalent circuit and (c) S‐parameters (adapted from Ref. [32], Figure 3).
(1) As for the first layer, the theoretical S‐parameters are
\nHere, the impedance of the surrounding medium above or between the neighbouring layers is \n
(2) The reflected power PiR and transmitted power PiF from each layer are evaluated as follows,
\nFor simplicity, the absorption loss caused by the surrounding medium is assumed negligible.
\n(3) The total transmittance after the third layer is then written as
\nAs for any specific third‐order Butterworth filter with desired central band‐stop frequency and band‐stop width, one can easily get the suitable choice of geometrical parameters for design. For example, if the band‐stop edge frequencies are \n
Here, Gi is the normalized prototype element values and n is the order of the Butterworth filter, that is the number of resonators. As for a third‐order (n = odd) band‐stop filter (G1 = 1, G2 = 2, G3 = 1) with the height of nanosquare cells at each layer \n
As for this triple‐layer third‐order filter, if adopting parameters listed in Table 1, the theoretical and numerical transmittance spectra can be directly obtained (Figure 11a) based on Eq. (17) from an equivalent circuit theory and FDTD simulation, respectively. The comparison between single‐layer and triple layer filters indicates that, for a triple‐layer filter, its band‐stop width and depth both become larger, and moreover, its band‐stop bottom is much flatter. In addition, the transmittance is nearly zero, indicated by the electric field distribution in Figure 11b.
\n(a) Theoretical and numerical transmittance spectra for single‐layer (first‐order) or triple‐layer (third‐order) filter. (b) One representative electrical field distribution for a third‐order filter at a wavelength of 2000 nm (adapted from Ref. [32], Figure 4).
i | \nGi | \nZi | \nw/g (nm) | \nhi (nm) | \n
---|---|---|---|---|
1 | \n1 | \nZ | \n120/60 | \n150 | \n
2 | \n2 | \nZ/2 | \n120/60 | \n300 | \n
3 | \n1 | \nZ | \n120/60 | \n150 | \n
Element values for low‐pass prototype circuit and geometrical parameters of third‐order band‐stop FSS filter.
It is necessary to point out that the corresponding FDTD calculation results show a good agreement with for single‐layer case, but more obvious deviation from the equivalent circuit theoretical calculation. The reason for deviation arises from the simple assumption that the triple‐layer of nanosquare array is independent of each other. If the layer‐layer coupling is considered the deviation maybe reduced. However, anyway, the proposed synthesis procedure is confirmed helpful to design a Butterworth band‐stop filter.
\nMeta‐material absorbers are used broadly in thermal detectors [40], imaging [41], security detection [42] and stealth devices [43]. In 2008, Landy et al. first proposed a thin perfect meta‐material absorber simultaneously exciting electric and magnetic resonances (MRs) to realize the impedance match with the surrounding medium and thus eliminating any reflection and perfectly absorbing the incident waves at microwave bands [44]. Since then, applications to various wavelength regimes have been demonstrated widely by numerical simulations and experiments [45, 46]. However, the application of these perfect absorbers is limited for their narrowband and simple resonant behaviours.
\nThe most widely used scheme [47–49] instead is to slow down the incident wave or totally absorb them by a gradually changed pyramid‐shaped metal‐insulator‐metal (MIM) topology (Figure 12a). In fact, an absorber can also be thought as a filter, by operating the frequency response of the absorptance with A = 1 – T – R. Furthermore, each layer of the multi‐layer MIM absorber projecting to the bottom plane is a nanosquare structure (Figure 12b), same as basic building blocks for third‐order Butterworth filter (Section 3.1). Thus, naturally, the equivalent nanocircuit procedure can be directly transplanted to the design of MIM multi‐layer absorber.
\nSchematic diagrams of (a) MIM absorber, (b) equivalent lumped circuit elements and (c) whole equivalent circuit. Here, only single nanosquare patch layer is considered (adapted from Ref. [50], Figure 1).
The first step is to evaluate the impedance Z (Figure 12c) of each layer, following the same procedure in Section 3.1 which can be obtained as,
\nThe second step is to cascade the impedance of each layer into a whole circuit, for example that of a triple‐layer structure. Each layer is separated by one quarter of central wavelength of the incident light (Figure 12a). The corresponding equivalent circuit can be modelled as in Figure 12b, where \n
Then, the reflectance of this pyramid triple layer structure is given by,
\nBeyond the reflectance, one needs to calculate the transmittance through the bottom substrate. As shown in Figure 13a, based on the three different NS layers, the whole structure is separated into four independent regions from left to right. Then, the S‐parameters (S11, S21, …) for each layer are obtained as follows,
\nSchematic diagrams of (a) S‐parameters used for theoretical calculation and (b) equivalent nanocircuit model for the truncated pyramid triple‐layer absorber (adapted from Ref. [50], Figure 3).
For the convenience of calculation, the dielectric loss for light through SiO2 material is neglected as long as the gap distance between two adjacent layers is large enough. Under this simplification, the reflected power PiR and transmitted power PiF from each NS layer are evaluated as follows,
\nSolving Eqs. (22) and (23) simultaneously, the total transmittance T is finally expressed as,
\nNaturally, the absorptance A can be evaluated as,
\nThe absorption (A), reflection (R) and transmission (T) spectra calculated by above equations and corresponding FDTD simulations, shown in Figure 14a, show a good agreement between the two existing methods which further prove the feasibility of our equivalent circuit theory. The replacement of single‐layer absorber by a triple‐layer makes the absorptance bandwidth to become obviously wider and also the efficiency is significantly enhanced. The enhanced electric field (Figure 14b) concentrates at both the lateral edges of NS and air gaps between two adjacent unit cells that couples efficiently to the incident light and dissipate the energy within the metals via Ohmic loss [51]. After the third layer, nearly no light can be transmitted from the absorber.
\n(a) Comparison between theoretical results from equivalent nanocircuit theory and numerical calculations from FDTD simulation. (b) Electric field distribution at a wavelength of 2500 nm. Each nanosquare S patch has a varying width w of 300, 250 and 200 nm from bottom to top (adapted from Ref. [50], Figure 4).
In Section 3.2, a triple‐layer MIM absorber design has been successfully demonstrated based on the equivalent nanocircuit theory. The proposed synthesis circuit procedure is confirmed to be feasible enough to provide us a way to predict the responses of such absorbers. It need to be emphasized that, it is in principle possible to get a perfect absorber with a 100% absorption efficiency just by adding more NS layers beyond three layers. However, with the increase of NS layer number, the equation number contained in Eqs. (22) and (23) will be added. Correspondingly, solving the multi‐variable linear equations becomes more and more complicated and also time consuming which would be a big problem.
\nThus, in this section, an improved equivalent nanocircuit matrix algorithm emerges as the times requires [52] which can predict the complex frequency response of multi‐layer (with arbitrary layer numbers) nanostructures easily, without solving the multi‐variable linear equations. One can believe that it may provide inspiring advancements in future meta‐material designs.
\nThe construction of this equivalent nanocircuit matrix algorithm derives from the design of a simplified broadband super‐flat perfect absorber made of single transparent conductive oxides (TCOs) material [52]. In such an absorber design [53], in order to pursue a broadband flat response, until now, no matter how many layers, the multi‐layer MIM absorber or planar multiplexed pattern absorber still cannot achieve broadband flat perfect absorption as one expects. Furthermore, there has another challenge for these kinds of broadband absorber design which is related to the fabrication process. It is hard to scale down to higher frequency mainly because of the fabrication difficulty, including lithography and alignment between neighbouring layers or resonators. Within this context, one should explore new paradigms for broadband absorber design.
\nFortunately, we note that the transparent conductive oxides (TCOs), such as Al:ZnO (AZO), Ga:ZnO (GZO) and indium‐tin‐oxide (ITO), can play a fascinating role in the designing of broadband perfect absorber for its unique transmission or conductive property in near‐infrared (NIR) region [33, 53]. As shown in Figure 15a, periodic arrays of truncated pyramid structure made of TCOs could work as a broadband absorber in NIR frequency, furthermore such absorbers at broadband wavelengths have continuous flat responses with near‐unit light absorption. Comparing with the traditional multi‐layer metal‐insulator‐metal (MIM) absorber, TCOs absorbers using only one single material can greatly reduce the fabrication difficulty, one do not need to consider the perfect alignment to match the relative position of each pattern in different layers.
\nThe designed absorber unit consists of two TCOs elements (Figure 15): a truncated pyramid shaped resonator and a ground plane. The material used for the two elements can be only TCOs, i.e. materials for resonator and substrate are ITO. To establish the equivalent nanocircuit model for this absorber, one can hypothetically cut the whole pattern into n pieces along k(z)‐direction (Figure 15b).
\nSchematic diagrams of (a) the super‐flat absorber with atop span of ta = 0.1 μm, bottom span of tb = 1 μm, and ground plane thickness of t = 0.2 μm. (b) Side view of unit cell with H = 1.6 μm and (c) corresponding equivalent lumped circuit elements (adapted from Ref. [52], Figure 1).
The first step is to extract the equivalent reactance of a single piece (same as those in Sections 3.1 and 3.2). The local impedances of ITO patch (ZITO), air gaps (Zc1, Zc2) and total effective impedance (Zeff) can be calculated as,
\nWhen taking the single piece into the transmission line (TL) model, it can be modelled as a shunt admittance \n
Transmission‐line models of the truncated pyramid structure with (a) only a single piece and (b) a stack of n pieces (adapted from Ref. [52], Figure 2).
The second step is to connect each impedance into a complete TL circuit model. Series configuration of Zi alongside with parallel configurations \n
For the whole structure with n pieces, it can be thought as an n‐order filter along the transmission line, so the ABCD‐matrix is expressed as,
\nand the S matrix can be calculated as,
\nObviously, the transmission, reflection and absorption can be obtained from the S matrix as,
\nIn optical metatronic circuit, in order to have a parallel element between the two ports, ideally one needs to have a constant electric field across the nanoelement. Thus, each piece should be a thin slab with sub‐wavelength thickness in the z‐direction. Considering the present design, for a truncated pyramid structure with height H = 1.6 μm sketched in Figure 15, one can choose the thickness as 100 nm (cut number n =16) to get accurate results, smaller than wavelength (1–3 μm). By solving the transmission model in Figure 16b, the theoretical result is within a wavelength range of 1–3 μm (Figure 17a). It indicates that the absorption bandwidth becomes obviously wider and the efficiency is almost larger than 90%. The corresponding FDTD result (Figure 17a) indicates the feasibility of such a rigorous solution of TL model to describe the mechanism of this absorber. A good agreement between simulated and theoretical absorption at the wavelength larger than 1.5 μm, and only a slight deviation at the top absorption efficiency is observed. Furthermore, the simulation result shows that it has a flat response with absorption near unit between 1.4 and 2.6 μm.
\n(a) Comparison between theoretical result from equivalent nanocircuit theory and numerical calculation from FDTD simulation. (b) Absorption curves under four different geometric structures. Truncated pyramid (ta = 0.1 μm, tb = 1 μm); pyramid (ta = 0 μm, tb = 1 μm); truncated cone (top diameter dt = 0.1 μm, bottom diameter db = 1 μm); cone (top diameter dt = 0 μm, bottom diameter db = 1 μm), H = 1.6 μm and t = 0.2 μm for the four structures (adapted from Ref. [52], Figures 4 and 5).
Note that there is a slight deviation at the top absorption efficiency between simulation and theoretical prediction; we attribute this to the fact that there have deviations from extracted equivalent parameters. We employ the same full‐wave FDTD simulations, only change is the structure from truncated pyramid to full pyramid, the truncated cone and the full cone, respectively. The four absorption spectra are compared in Figure 17b. We can see that the absorption bandwidth changes slightly indicating that the geometry dependence of the absorption is relatively weak. The bandwidth decreasing from pyramid to cone shape is due to the decrease of corresponding response area, when square changes to circle with the same width (diameter). It should be pointed out here that each geometric parameters used in Figure 15 are not optimal. If we take the height, top width and bottom width altogether into account, much broader bandwidth could be expected.
\nAbove all, under the guidance of nanocircuit theory, one can realize a broadband super‐flat perfect infrared absorber in a single TCO material for its nice transmission and conductive properties. This simplified configuration without multi‐layered design might releases the fabrication and design difficulties and exhibits great potentials in the applications of infrared stealth system. Furthermore, this proposed equivalent circuit matrix algorithm is confirmed to be feasible enough to predict the complex frequency response of multi‐layer nanostructures, and it can relieve the calculation from solving the multi‐variable linear equations that can be easily extended to analyse other nanooptical devices.
\nIn summary, thanks to the concept of metatronics, which gives us the possibility to transplant traditional circuit operations into a high‐frequency nanodevice design. The equivalent nanocircuit (EN) theory is successfully confirmed to be feasible via the comparison with the numerical results from the rigorous FDTD calculation. With the toolbox of EN theory, an equivalent circuit matrix method can be used to conveniently predict the complicated frequency response of a complicated meta‐material structure. Although here, only three application examples were demonstrated, it can be naturally and easily extended to analyse other nanooptical devices. Anyway, the interests in combining optical guiding devices with classical circuits is always high because the EN theory provides inspiring advances for designing more complex circuit systems and other related applied fields, although the deviation between results from EN theory and rigorous FDTD simulation indicates that the NE theory is still on the way of further perfection.
\nThis work is supported by the National Natural Science Foundation of China (NNSF, Grants Nos. 11374318 and 11674312). C.L. thanks to the supports from the 100‐Talents Project of Chinese Academy of Sciences.
\nDevelopment is a complex process that involves a series of cell differentiation pathways starting from totipotent embryonic cells. According to Waddington’s concept of epigenetic landscape, a cell has to interact with surrounding stimuli and respond by giving a phenotype which defines its identity during development [1]. Each cell experiences different inter/intra-cellular signals and hence has its epigenetic signature of cell identity, which in turn directs its own specific gene expression pattern without alteration of DNA sequences (with the exception of the immunoglobulin genes in B and T cells). It is now clear that the diversity of cell type specific gene expression pattern is mediated by means of epigenetic mechanisms, such as DNA methylation, covalent histone modifications and chromatin remodeling. Once a cell’s identity is set, it is difficult to convert it to other unrelated lineages, thus leading to stable and irreversible differentiated cell states. Nevertheless, there are a few exceptions of cell fate conversion during embryo development and adult tissue/organ regeneration, e.g. vascular endothelium to smooth muscle cells [2], which involve changing a cell’s epigenetic signature into another unrelated kind.
Apart from a few exceptions of natural cell fate conversion events, different strategies have been developed aiming to reprogram differentiated somatic cell fate to a pluripotent state (Figure 1). A historical strategy of reprogramming is by somatic cell nuclear transfer (SCNT) experiments. SCNT involves transplantation of a cell nucleus into an enucleated egg/oocyte in order to generate a “cloned” animal with an equivalent genetic composition as the donor individual. It is possible to derive embryonic stem (ES) cells from nuclear transplanted (NT) embryos (ntES cells), which shows indistinguishable pluripotent gene expression profiles when compared to the normal ES cells derived from fertilized embryos. Another strategy of reprogramming is achieved by fusion of a differentiated cell with a pluripotent cell in order to generate a pluripotent-like tetraploid hybrid cell [3, 4, 5]. It has been proposed that cellular components, such as transcription factors, in the pluripotent cell are able to reprogram the differentiated cell nucleus. This idea aligns with the use of cell extracts from pluripotent cell types to revert differentiated cells into a pluripotent-like state [6, 7]. Presumably the cytoplasmic “reprogramming factors” from the pluripotent cells can be isolated and concentrated to achieve a higher reprogramming efficacy. A third strategy involves ectopic expression of defined transcription factors in somatic differentiated cells to generate induced pluripotent stem (iPS) cells. Delivery of the ectopic transcription factors can be achieved by viral approaches, such as the use of retrovirus, lentivirus, adeno-associated virus or Sendai virus, or by using episomal vesicles, or by direct mRNA or protein transfection. This technique has been successfully applied to reprogram a vast number of differentiated somatic cell types. Importantly, iPS cells can also be generated by using combinations of microRNAs (miRNAs) or small chemical molecules without the needs of ectopic expression of reprogramming factors [8]. The three reprogramming strategies show different reprogramming kinetics and efficiencies, which can be associated with the distinct epigenetic mechanisms in the erasure of somatic cell epigenetic signature and re-establishment of the pluripotent one. In this review, we focus on the dynamic changes of epigenetics mediated by different reprogramming strategies and how the modulation of epigenetic status improves the reprogramming efficiency.
Strategies of reprogramming cell fate. Differentiated cells can be reprogrammed to pluripotent state by somatic cell nuclear transfer (SCNT), cell fusion, and ectopic expression of defined transcription factors. SCNT involves transplantation of a single differentiated cell nucleus into an enucleated egg/oocyte, which develops as a nuclear transplanted (NT) embryo. Cell fusion involves artificial fusion of a differentiated and a pluripotent cell to form a tetraploid pluripotent-like cell. Defined transcription factors (Oct4, Sox2, Klf4, c-Myc) can be ectopically expressed in differentiated cells and convert them to induced pluripotent stem (iPS) cells.
SCNT was first done by Briggs and Kings in 1952, who transplanted a blastula nucleus into an enucleated egg of the amphibian Rana pipiens [9]. Few years later, Gurdon et al. succeeded by using differentiated Xenopus intestinal epithelial donor nuclei for SCNT [10]. In 1997, the first cloned mammal, Dolly the sheep, was generated [11], and since then, more than 23 other mammalian species have now been successfully cloned [12]. Normal development of nuclear transplanted (NT) embryos requires recapitulation of the gene expression profile that supports the embryogenesis process by the differentiated donor nucleus. This involves re-activation of pluripotency genes, in particular Oct4, Nanog and Sox2, and repression of somatic lineage genes. In fact, the efficiency of reprogramming by SCNT is generally very low and less than 1% of NT embryos can develop into normal adults [13, 14, 15]. The cloned newborns often suffer from developmental abnormalities owing to incomplete reprogramming. It has been observed that Oct4 was aberrantly expressed in cloned mouse blastocysts derived from cumulus donor nuclei [16, 17]. Besides, continuous expression of other somatic donor marker genes was demonstrated in some Xenopus NT embryos [18]. Some imprinted genes in donor cells were found to be aberrantly expressed in cloned embryos, presumably owing to the incomplete epigenetic reprogramming of the regulatory regions of imprinting loci [19, 20, 21]. Dysregulation of imprinted genes, such as Igf2, Igf2r, H19, and Xist, in cloned embryos can lead to both fetal and placental overgrowth and result in embryonic lethality or an abnormal growth condition called “large offspring syndrome”, which is commonly found in cloned mammals [22, 23, 24]. Since the SCNT process does not increase the frequency of genetic alterations, it is suggested that the variable phenotypes observed in cloned embryos are associated with the reprogrammed epigenetic status of the donor nuclei [25]. This is supported by the findings that the developmental defects in cloned animals were not transmittable to the next offspring generation, indicating the presence of aberrant epigenetic reprogramming [26]. Aberrant DNA methylation patterns were indeed observed in NT embryos [27]. It was also demonstrated that the bovine NT blastocysts lack asymmetric patterns of both H3K9 methylation and acetylation between the inner cell mass and trophectoderm [28], which may account for abnormal cloned embryo development.
Although the rate of successful SCNT is very low, the reprogramming ability of factors in the egg/oocyte is highly efficient as the transplanted nuclei take less than 1 day to initiate cell division and trigger the “normal” developmental program. The donor cell epigenetic status has to be reprogrammed in order to support the embryonic program of development. In fact, genome-wide demethylation was observed in the cloned blastocysts [29]. It has been shown that the Oct4 promoter of somatic cells undergoes DNA demethylation after nuclear transplantation into the germinal vesicle of Xenopus oocytes [30]. This demethylation of the Oct4 promoter was found to be mediated by Tet3 in a mouse SCNT study [31], which is essential for the reactivation of Oct4 expression for successful SCNT. In addition, chromatin remodeling factors, such as ISWI and BRG1, are documented in facilitating the reprogramming of cell fate. It has been shown that ISWI, which is a chromatin remodeling ATPase, is able to dissociate TATA binding protein in somatic nuclei after incubation in the Xenopus egg extract, suggesting that ISWI-containing complexes are facilitating epigenetic reprogramming in an egg environment [32]. Besides, Xenopus egg extract depleted of BRG1 protein showed an abolishment of the reprogramming ability and hence failed to induce Oct4 expression in the somatic nuclei [33]. Therefore, chromatin structure remodeling is believed to be one of the reprogramming mechanisms. In addition, the maternal-derived histone H3 variant H3.3 in the enucleated egg was found to replace the canonical histone H3 in the donor nuclei after SCNT, leading to the reactivation of key pluripotent genes that are originally associated with repressive histone marks [34]. Histone H2A variant, macroH2A, also plays an important role in the reactivation of female donor cell’s inactive X chromosome during reprogramming. It was shown that knockdown of macroH2A facilitates X-reactivation and the expression of pluripotent genes in cloned Xenopus embryos [35]. More recently, it has been demonstrated that the H3K9 tri-methylation (H3K9me3) of the donor cell genome is a major epigenetic barrier to SCNT. Ectopic expression of H3K9 demethylases Kdm4b or Kdm4d in the mouse donor cells de-repressed the genomic regions that are resistant to reprogramming and thus significantly improving SCNT efficiency [36, 37]. Similarly, removal of H3K9me3 by ectopic expression of other H3K9 demethylases also demonstrated improved reprogramming efficiency in human and bovine SCNT experiments [38, 39].
Interestingly, it has been shown that the epigenetic state of a differentiated cell is directly correlated with its reprogrammability [40]. SCNT with ES cell nuclei demonstrated a much higher efficiency of generation of NT blastocysts than using other somatic cell types [41]. This could be associated with a more relaxed chromatin configuration in ES cells that may render their epigenome more susceptible for reprogramming [42]. Alternatively, it has been demonstrated that the cloning efficiency can be significantly improved by pre-treating the more differentiated and condensed chromatin state of somatic nuclei with epigenetic modifying agents, e.g. 5-aza-deoxycytidine and trichostatin A (TSA), that facilitate chromatin relaxation [43, 44, 45]. Interestingly, the effect of TSA treatment in improving SCNT is associated with the reactivation of a subset of genes that are repressed by H3K9me3 in the somatic cells [46], presumably through introducing histone hyper-acetylation at their promoters. Altogether, SCNT provides a quick route of epigenetic reprogramming for a differentiated cell to a pluripotent state. Identification of the responsible reprogramming factors in the egg and oocyte cytoplasm will be one of the key future directions to improve the efficiency of SCNT and therapeutic cloning.
Cell fusion is a natural event that is crucial for fertilization and in various organs such as placenta, skeletal muscles and bones [47]. It has been proposed that the fusion of bone marrow-derived stem cells and tissue cells, e.g. hepatocytes, is one of the mechanisms of tissue repair [48, 49]. Cell fusion experiments using pluripotent cells, e.g. an ES or embryonic germ (EG) cell, were shown to be able to reprogram a differentiated cell type [3, 4, 5]. Both ES and EG cells possess reprogramming ability and are able to reactivate pluripotent genes and silence differentiation genes in the somatic cell nucleus within a tetraploid hybrid cell after cell fusion. It is indeed the case that the new transcription profile of a hybrid cell is partly contributed by the reprogrammed somatic nucleus to a pluripotent-like state. Moreover, injection of hybrid cells into normal diploid blastocysts demonstrated their contribution to all three germ layers in the chimeras [4, 50], indicating the pluripotent nature of hybrid cells. Similar to the SCNT, different somatic cell types show different kinetics of reprogramming by the cell fusion approach, which could be associated with the somatic chromatin accessibility status [51, 52].
Cell fusion with a pluripotent cell can trigger extensive epigenetic reprogramming in the differentiated cell nucleus. It has been shown that reactivation of Oct4 from the somatic nucleus occurs before DNA replication after cell fusion [53], suggesting the involvement of active demethylation process [54]. This was further supported by the functional roles of Tet1 and Tet2 in the demethylation of Oct4 and imprinted control regions by fusing somatic cells with EG cells [55]. Besides, in a cell fusion experiment using thymocytes and ES cells from two different mouse strains, it was observed that the epigenetic profile of the somatic cell nucleus was reprogrammed to a similar pattern to that of the ES cell. Global histone H3 and H4 acetylation and H3K4 di- and tri-methylation were increased in the hybrid cell to a level comparable to ES cells, whereas these modifications are weak in the parental somatic thymocytes. Examination of gene specific loci showed that the Oct4 promoter was enriched with H3 acetylation and the promoter of the thymocyte marker Thy-1 was enriched with H3K27 tri-methylation in both ES cell and hybrid cell chromatin, whereas these epigenetic modifications are missing in the thymocyte [56]. Hence, the somatic genome has undergone epigenetic reprogramming triggered by fusion with the ES cell, suggesting that the process of cell fusion mediates a transcription activation-permissive chromatin state in the hybrid genome. In addition, silencing the somatic differentiation genes was shown to be associated with polycomb repressive complexes in the cell fusion experiment using ES cells [57].
Reprogramming to pluripotency by cell fusion approach requires lengthy selection of the successfully reprogrammed hybrid cells. The reprogramming efficiency of cell fusion is usually less than 0.001%, depending on the somatic cell types [50, 58]. The low reprogramming efficiency in hybrid cells can be largely enhanced by manipulation of key pluripotency-associated genes like Nanog [58, 59] and Sall4 [60], or by activation of the Wnt signaling pathway [61], emphasizing the importance of these factors in cell fusion reprogramming. Overexpression of Nanog or Sall4 in ES cells demonstrated a several hundred-fold increase in reprogramming efficiency after cell fusion. Similarly, treatment of ES cells with Wnt3a for 24–48 hours enhanced the reprogramming of somatic cells by 20-fold. However, owing to the low reprogramming efficiency and the tetraploid genome of the resulting hybrid cells, reprogramming by the cell fusion approach becomes less promising in regenerative medicine.
In a groundbreaking discovery, Yamanaka et al. demonstrated that somatic cell state can be reprogrammed to a pluripotent state by the introduction of only four transcription factors; Oct4, Sox2, Klf4 and c-Myc, which are now also known as the Yamanaka factors. The first generation of iPS cells was obtained using a Fbx15-driven selection construct (Fbx15-iPS) and displayed a gene expression pattern very similar to that of normal pluripotent ES cells. However, the somatic epigenetic signature was only partially reprogrammed; the Oct4 promoter, for example, retained some DNA methylation and no germline transmission was observed for these cells in chimeric mice. Hence these first-generation iPS cells were not fully pluripotent in nature [62]. Given the potential reprogramming capacity of these four factors, the second generation of iPS cells was generated by selection with a Nanog reporter construct (Nanog-iPS) [63, 64]. During the reprogramming process, the virally delivered transgenes were silenced, but on the contrary, the endogenous Oct4 and Sox2 loci were re-activated for the maintenance of pluripotency in iPS cells. In contrast to the Fbx15-iPS cells, these Nanog-iPS cells were able to undergo germline transmission in chimeric mice, and thus share this crucial feature of pluripotency with normal ES cells. These landmark studies that pioneered the derivation of mouse iPS cells led to the possibility of using the same strategy to generate human iPS cells. An initial study was performed by Thomas et al. in which a different combination of factors, OCT4, SOX2, NANOG and LIN28, was used to reprogram human fibroblasts into iPS cells [65]. Thereafter, Yamanaka and other groups succeeded in generating human iPS cells by using the same 4 Yamanaka factors as in the mouse iPS systems [66, 67]. To date, a number of different somatic cell types have been successfully reprogrammed into iPS cells, e.g. neural stem cells, keratinocytes, hepatocytes, gastric epithelia cells, pancreatic β cells, terminally differentiated B and T cells [8].
By using the defined transcription factor approach to reprogram cell fate, about 0.1–3% of the somatic starting cell population can be converted into iPS cells in around 2–3 weeks. The reprogramming efficiency is believed to be correlated with the differentiation state of the starting somatic cells. It has been shown that hematopoietic stem and progenitor cells can be reprogrammed to iPS cells 300 times more efficient than the terminally differentiated B and T cells [68]. Interestingly, partially de-differentiating mature B cells by either knockdown of Pax5 or forced expression of C/EBPα resulted in efficient reprogramming by the Yamanaka factors [69], suggesting that the epigenetic status of differentiated cells is crucial in successful reprogramming. The dynamics of transcription profile and epigenetic patterns during the reprogramming process from somatic to iPS cells were studied in details. The reprogramming of somatic cell fate is a sequential stochastic event which involves a gradual silencing of the somatic lineage genes and the viral transgenes, and a sequential expression of alkaline phosphatase and SSEA1 in partially reprogrammed cells, whereas endogenous Oct4 and Nanog are only activated in fully reprogrammed iPS cells. Induction of the four Yamanaka factors results in an immediate cellular response of inactivation of thousands of somatic lineage distal enhancers and, to a smaller extent, the H3K4me3-enriched somatic gene promoters [70, 71], leading to down-regulation of somatic identity genes. This initial phase of reprogramming is also accompanied by a global reduction of H3K27me3 resulting in loss of heterochromatin [72]. Meanwhile, mesenchymal transcription factors, such as Snail1/2, Zeb1/2, are repressed [70, 73, 74], whereas epithelial transcription factors, such as Cdh1, Epcam, are activated [75, 76], resulting in mesenchymal-epithelial transition (MET). This is associated with an increase in H3K4me2 at epithelial genes, but a decrease in H3K4me2 and H3K79me2 at mesenchymal genes [71, 77]. Despite an increase in global H3K36me2/3 level, loss of H3K36me2/3 was observed at the Ink4-Arf locus, leading to enhanced cell proliferation during reprogramming [78]. The following phase of reprogramming is marked by upregulation of endogenous pluripotency genes to establish transcriptional program, which is independent of transgene expression [73, 79]. The final phase of reprogramming involves elongation of telomeres, X-reactivation in female iPS cells, and upregulation of DNA methylation genes [79]. This coincides with loss of DNA methylation and downregulation of Xist expression in the somatic inactive X chromosome [80, 81].
A number of epigenetic remodeling factors are involved in the reprogramming events. Both polycomb (PcG) and trithorax (TrxG) group proteins were found to be crucial in the derivation of iPS cell colonies. Upon knockdown of Wdr5, which is a core component of TrxG protein complex, cells failed to establish H3K4me3 at the pluripotent genes, like Oct4 and Nanog, for their reactivation [82]; whereas inhibition of the core components of the polycomb repressive complex 1 and 2 reduced reprogramming efficiency [83], partly because of the dysregulation of genes involved in the MET process [84]. This is similar to the findings that inhibition of H3K79 methyltransferase DOT1L facilitates the loss of H3K79me2 mark at the mesenchymal genes to promote MET during reprogramming [83]. The H3K27 demethylase Kdm6a (also known as Utx) can directly interact with Oct4/Sox2/Klf4 to remove the repressive H3K27me3 mark from the early pluripotent genes in somatic cells for their reactivation [85]. This is in agreement with the findings that depletion of histone H2A variant, macroH2A, enhances reprogramming, owing to its co-occupancy with H3K27me3 to repress pluripotent genes [86, 87]. Besides, the H3K36 demethylase Kdm2b (also known as Jhdm1b) enhances the activation of early responsive genes (Cdh1, Epcam, Dsg2, Dsp, Irf6) during reprogramming through the removal of H3K36me2 at their promoters [88]. Interestingly, H3K9me3 was also found to be one of the major epigenetic barriers in the generation of iPS cells [89], similar to the findings in SCNT experiments. Depletion of the H3K9 methyltransferases SUV39H1/H2, Ehmt1/2 and Setdb1 or inhibition of Cbx3, a protein that recognizes H3K9 methylation, enhances reprogramming by de-repressing Nanog and abolishing the cellular responses to BMP signaling [89, 90, 91]. Although Dnmt3a/b were found to be dispensable [92], DNA demethylation of key pluripotency loci mediated by Tet proteins is required for efficient reprogramming [93, 94, 95].
Previous studies demonstrated that the partially reprogrammed iPS cells contained significantly fewer genes marked by the bivalent chromatin signature (co-existence of both H3K4 and H3K27 methylation) and an enrichment of DNA hyper-methylated loci when compared to the wild-type ES cells and the fully reprogrammed iPS cells [70]. Therefore, it is proposed that completion of the epigenetic reprogramming process is pre-requisite for the acquisition of pluripotency. This is supported by the observation that treatment of partially reprogrammed iPS cells with the DNA methyltransferase inhibitor 5-aza-cytidine was able to promote their transition into the fully reprogrammed pluripotent state [70]. Besides, inhibition of H3K27 methyltransferase Ezh2 by small molecule, GSK-126, reduced reprogramming efficiency [84], whereas inhibition of DOT1L by small molecule, EPZ004777, showed enhancement of reprogramming [83]. Various histone deacetylase inhibitors (HDACi) were also shown to improve reprogramming [96, 97, 98, 99, 100]. In combination with HDACi valproic acid, human iPS cells can be generated only with Oct4 and Sox2 with a comparable reprogramming efficiency by the four Yamanaka factors [101]. Interestingly, it was found that vitamin C can increase reprogramming efficiency by promoting the transition of pre-iPS cells to fully reprogrammed cells [102], potentially through acting as a cofactor of Kdm2b to induce H3K36me2/3 demethylation [78], activation of H3K9 demethylases (Kdm3a, 3b, 4c and 4d) to remove H3K9me3 [89], and promoting Tet-mediated DNA demethylation [103]. With the aid of small chemical molecules, the iPS cell reprogramming efficiency and duration could be further improved.
“Epigenetic memory” refers to the persistent expression of parental genes in the daughter cells through the inheritance of distinctive epigenetic marks. Consequently, the epigenetic profile of a parent cell is faithfully passed on to its daughter cells such that the gene expression pattern is memorized and maintained throughout cell generations. In the situation of reprogramming cell fate, the persistent somatic cell epigenetic signature and the expression of lineage genes in the reprogrammed cells is thus regarded as an example of epigenetic memory.
Even though it has been shown that prolonged in vitro culture of mammalian embryos can lead to aberrant expression of imprinted and non-imprinted genes owing to associated epigenetic ‘errors’ [104, 105]. It has been shown that many cloned embryos demonstrate different degrees of resemblance with donor cell gene expression patterns. The aberrant epigenetic pattern in cloned embryos is thought to be the result of persistence of the epigenetic memory of the donor cells. Indeed, the resemblance of DNA and histone modification patterns of NT embryos to those of the donor cell types supports this conclusion [45, 46, 47]. For example, both global and gene-specific patterns of DNA methylation in cloned bovine and mouse embryos were shown to be similar to those of their respective donor somatic cell types [28, 106, 107]. The phenomenon of epigenetic memory is also highlighted by the X inactivation pattern in cloned embryos. In normal fertilized embryos, the paternal X chromosome is preferentially silenced in the trophectoderm and extraembryonic endoderm lineages, whereas random X inactivation occurs in the inner cell mass. However, in NT embryos generated from female donor nuclei, the inactive X chromosome of the donor cell is preferentially chosen for inactivation in the trophectoderm, which is in contrast to the random X inactivation in the embryo proper, demonstrating a certain extent of memory of the inactive X chromosome status [48]. Random X inactivation in the placenta was found in deceased cloned bovine embryos, which suggests that the persistence of this inactive X chromosome memory in the placenta may be crucial for fetal survival [49].
The epigenetic memory in NT embryos that maintains the donor expression gene states can be explained by the inheritance of DNA methylation patterns. Heritability of DNA methylation is mediated by the activity of the maintenance DNA methyltransferase Dnmt1 which preferentially targets hemi-methylated DNA. Thus, Dnmt1 restores the parental methylation status on the newly synthesized daughter DNA strand, thereby maintaining a silent gene state after cell division [108]. Methylated donor genes, such as pluripotency genes, remain inactivated after SCNT, apparently owing to the persistent donor-specific methylation pattern in the cloned embryos, possibility mediated by the residual somatic form of Dnmt in the donor nucleus. DNA methylation therefore provides a plausible mechanism for the propagation of a silent memory state in SCNT [109]. On the other hand, an active gene memory of the donor differentiation state is also observed in NT embryos. For example, both the donor endoderm and neurectoderm markers, Edd and Ncam, were found to be aberrantly expressed in Xenopus NT embryos derived from the respective donor cell types [18]. This active gene memory was further demonstrated to be associated with the incorporation of a histone H3 variant H3.3 at the active gene loci in Xenopus NT embryos [110]. Histone variant H3.3 is enriched in the regulatory region of active genes and is preferentially marked by modifications associated with an active chromatin state, such as H3K4 methylation, H3K9 acetylation and H3K79 methylation [111, 112]. Experiments using a mutant form of H3.3 demonstrated that the K4 residue on H3.3 plays a key role in the inheritance of active epigenetic memory [110], proposing a model in which H3.3 K4 methylation creates an “active histone environment” for the recovery of active chromatin configuration in daughter cells after chromosomal replication [113].
Early studies of iPS cells demonstrated that the Nanog-iPS cells displayed not only a highly similar transcriptome to wild-type ES cells, but also an ES cell histone modification profile. Genome-wide comparison of histone modifications (H3K4 and H3K27 tri-methylation) between ES cells, MEFs and MEF-derived iPS cells demonstrated that more than 94% of the ES- or MEF-signature genes in iPS cells have identical histone methylation marks as in ES cells. Only 0.7% of these signature genes retain the histone methylation status of the original MEFs [63]. However, other gene expression profile studies of iPS cells showed that a significant number of differentiation genes have a similar expression pattern to that in the somatic cell of origin, but not in ES cells [114, 115, 116, 117]. This transcriptional memory in iPS cells was found to be correlated with biased differentiation towards the original cell lineage, and with less competence in differentiation to other unrelated somatic lineages [115, 118, 119, 120, 121]. Importantly, the persistent expression of somatic genes in iPS cells was associated with the somatic DNA methylation pattern [117, 122, 123, 124], highlighting the crucial role of epigenetic regulation in the retention of memory. This is in fact similar to the observation that an incomplete removal of donor cell DNA methylation pattern was observed in some aberrantly developed NT embryos [125]. Strikingly, the addition of epigenetic modifying agents, such as DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC), can enhance the iPS cell reprogramming efficiency [70] and improve the differentiation competency to other unrelated somatic lineages [120]. Interestingly, it has been demonstrated that continuous passaging of iPS cells abrogates somatic DNA methylation patterns [115], which suggests a passive replication-dependent mechanism in loss of the parental memory in iPS cells. Nevertheless, a study showed that the epigenetic memory in some iPS cell lines cannot be removed even after extended passages [124]. Apart from DNA methylation, microRNA expression pattern was also shown to have a role in the retention of somatic memory in iPS cells derived from hematopoietic progenitors [126]. However, it should be emphasized that other profiling studies of iPS cells failed to find the gene expression and epigenetic differences when compared to ES cells [127, 128]. It thus proposes that the “somatic memory” in iPS cells could be an artifact of incomplete reprogramming resulting in variation between iPS cell lines [129]. It is also possible that there are individual iPS cell lines expressing gene signatures owing to culture conditions and laboratory practices [130], similar to the scenario that some ES cell lines exhibit preferential differentiation towards specific lineages [131, 132, 133]. In summary, the epigenetic memory in iPS cells remains a contentious issue.
Although the term “epigenetic landscape” was first introduced by Waddington in 1942 [1], our understanding of how the epigenome of a cell type is maintained and altered during differentiation is still far from complete. The reversal of the differentiated state of a cell has important implications for our understanding of normal development and for regenerative medicine. Epigenetic reprogramming provides heritable changes of cell identity, and thus is a key event for the complete and permanent conversion of cell fate (Figure 2). Although reprogramming of cell fate can be achieved by different strategies, the rate (reprogramming time) and efficiency (number of reprogrammed cells) are far from comparable to the natural event during fertilization/de-differentiation. Achieving a complete epigenetic reversion to generate reprogrammed cells or iPS cells with a comparable potency state of early embryos would imply that these cells can respond correctly to differentiation-promoting signals, and more importantly, decrease the tumorigenic potential owing to pre-disposing epimutations. Notably, the status of epigenetic memory in iPS cells can be regarded as a state of incomplete reprogramming. The biased differentiation owing to the persistent somatic epigenetic memory in iPS cells might be useful in efficient differentiation to the desired cell type of origin, which usually results in a heterogeneous cell population by using un-optimized differentiation protocols. On the contrary, it has been shown that in vitro culture condition can alter the epigenetic status of iPS cells [134]. With an optimized culture condition, a more homogeneous population of iPS cells can be obtained, which corresponds to the naïve state of pluripotency, and hence, further abrogate the somatic “epigenetic memory”. A more recent approach in reprogramming involves the use of a combination of small chemical molecules and epigenetic modifying agents, without any ectopic expression of transcription factors [135, 136]. This approach seems to induce pluripotent reprogramming process different from the transcription factor-mediated approach. Therefore, unlocking the secrets of epigenetic resetting mechanisms during cell differentiation can shed light on the development of more efficient and complete reprogramming approaches to further advance regenerative medicine.
Mechanisms of epigenetic reprogramming. Epigenetic patterns in differentiated cells need to be reprogrammed to those of pluripotent cells, which results in silencing of differentiated genes and reactivation of pluripotency genes. Epigenetic reprogramming can be achieved by modulation of DNA methylation and histone modifications by various epigenetic modifying enzymes, such as Dnmt, Tet, Kdm2b, Kdm4b, Utx, Ezh2 (PcG), histone variant replacement, and chromatin remodeling enzymes. Other epigenetic mechanisms may also be involved. It is believed that a collaborative contribution of different epigenetic mechanisms is required for complete reversal of the differentiated cell state.
This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region (SAR), China (Grant no. HKU775510M and HKU774712M).
The authors declare that they have no conflict of interest.
Authors are listed below with their open access chapters linked via author name:
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\\n\\nJim Van Os 2015-18
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\\n\\nFei Wei 2016-18
\\n\\nIoannis Xenarios 2017, 2018
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\\n\\nXin-She Yang 2017, 2018
\\n\\nYulong Yin 2015, 2017, 2018
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\n\n\n\n\n\n\n\n\n\nJocelyn Chanussot (chapter to be published soon...)
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