Description of markers used for the study of genetic variability of Pinus hartwegii.
\r\n\tAnimal food additives are products used in animal nutrition for purposes of improving the quality of feed or to improve the animal’s performance and health. Other additives can be used to enhance digestibility or even flavour of feed materials. In addition, feed additives are known which improve the quality of compound feed production; consequently e.g. they improve the quality of the granulated mixed diet.
\r\n\r\n\tGenerally feed additives could be divided into five groups:
\r\n\t1.Technological additives which influence the technological aspects of the diet to improve its handling or hygiene characteristics.
\r\n\t2. Sensory additives which improve the palatability of a diet by stimulating appetite, usually through the effect these products have on the flavour or colour.
\r\n\t3. Nutritional additives, such additives are specific nutrient(s) required by the animal for optimal production.
\r\n\t4.Zootechnical additives which improve the nutrient status of the animal, not by providing specific nutrients, but by enabling more efficient use of the nutrients present in the diet, in other words, it increases the efficiency of production.
\r\n\t5. In poultry nutrition: Coccidiostats and Histomonostats which widely used to control intestinal health of poultry through direct effects on the parasitic organism concerned.
\r\n\tThe aim of the book is to present the impact of the most important feed additives on the animal production, to demonstrate their mode of action, to show their effect on intermediate metabolism and heath status of livestock and to suggest how to use the different feed additives in animal nutrition to produce high quality and safety animal origin foodstuffs for human consumer.
",isbn:"978-1-83969-404-2",printIsbn:"978-1-83969-403-5",pdfIsbn:"978-1-83969-405-9",doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"8ffe43a82ac48b309abc3632bbf3efd0",bookSignature:"Prof. László Babinszky",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/10496.jpg",keywords:"Technological Feed Additives, Feed Industry, Quality of Compound Feed, Non-Antibiotic Growth Promoter, Product Quality, Additive Enzymes, Digestibility of Nutrients, NSP Enzymes, Farm Animals, Livestock, Immunity, Microbiome",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:null,numberOfDimensionsCitations:null,numberOfTotalCitations:null,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"November 24th 2020",dateEndSecondStepPublish:"December 22nd 2020",dateEndThirdStepPublish:"February 20th 2021",dateEndFourthStepPublish:"May 11th 2021",dateEndFifthStepPublish:"July 10th 2021",remainingDaysToSecondStep:"2 months",secondStepPassed:!0,currentStepOfPublishingProcess:4,editedByType:null,kuFlag:!1,biosketch:"Professor Emeritus from the University of Debrecen, Hungary who authored 297 publications (papers, book chapters) and edited 3 books. Member of various committees and chairman of the World Conference of Innovative Animal Nutrition and Feeding (WIANF).",coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"53998",title:"Prof.",name:"László",middleName:null,surname:"Babinszky",slug:"laszlo-babinszky",fullName:"László Babinszky",profilePictureURL:"https://mts.intechopen.com/storage/users/53998/images/system/53998.jpg",biography:"László Babinszky is Professor Emeritus of animal nutrition at the University of Debrecen, Hungary. From 1984 to 1985 he worked at the Agricultural University in Wageningen and in the Institute for Livestock Feeding and Nutrition in Lelystad (the Netherlands). He also worked at the Agricultural University of Vienna in the Institute for Animal Breeding and Nutrition (Austria) and in the Oscar Kellner Research Institute in Rostock (Germany). From 1988 to 1992, he worked in the Department of Animal Nutrition (Agricultural University in Wageningen). In 1992 he obtained a PhD degree in animal nutrition from the University of Wageningen.He has authored 297 publications (papers, book chapters). He edited 3 books and 14 international conference proceedings. His total number of citation is 407. \r\nHe is member of various committees e.g.: American Society of Animal Science (ASAS, USA); the editorial board of the Acta Agriculturae Scandinavica, Section A- Animal Science (Norway); KRMIVA, Journal of Animal Nutrition (Croatia), Austin Food Sciences (NJ, USA), E-Cronicon Nutrition (UK), SciTz Nutrition and Food Science (DE, USA), Journal of Medical Chemistry and Toxicology (NJ, USA), Current Research in Food Technology and Nutritional Sciences (USA). From 2015 he has been appointed chairman of World Conference of Innovative Animal Nutrition and Feeding (WIANF).\r\nHis main research areas are related to pig and poultry nutrition: elimination of harmful effects of heat stress by nutrition tools, energy- amino acid metabolism in livestock, relationship between animal nutrition and quality of animal food products (meat).",institutionString:"University of Debrecen",position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"1",totalChapterViews:"0",totalEditedBooks:"0",institution:{name:"University of Debrecen",institutionURL:null,country:{name:"Hungary"}}}],coeditorOne:null,coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"25",title:"Veterinary Medicine and Science",slug:"veterinary-medicine-and-science"}],chapters:null,productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},personalPublishingAssistant:{id:"185543",firstName:"Maja",lastName:"Bozicevic",middleName:null,title:"Ms.",imageUrl:"https://mts.intechopen.com/storage/users/185543/images/4748_n.jpeg",email:"maja.b@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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Venkateswarlu",coverURL:"https://cdn.intechopen.com/books/images_new/371.jpg",editedByType:"Edited by",editors:[{id:"58592",title:"Dr.",name:"Arun",surname:"Shanker",slug:"arun-shanker",fullName:"Arun Shanker"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"878",title:"Phytochemicals",subtitle:"A Global Perspective of Their Role in Nutrition and Health",isOpenForSubmission:!1,hash:"ec77671f63975ef2d16192897deb6835",slug:"phytochemicals-a-global-perspective-of-their-role-in-nutrition-and-health",bookSignature:"Venketeshwer Rao",coverURL:"https://cdn.intechopen.com/books/images_new/878.jpg",editedByType:"Edited by",editors:[{id:"82663",title:"Dr.",name:"Venketeshwer",surname:"Rao",slug:"venketeshwer-rao",fullName:"Venketeshwer Rao"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"4816",title:"Face Recognition",subtitle:null,isOpenForSubmission:!1,hash:"146063b5359146b7718ea86bad47c8eb",slug:"face_recognition",bookSignature:"Kresimir Delac and Mislav Grgic",coverURL:"https://cdn.intechopen.com/books/images_new/4816.jpg",editedByType:"Edited by",editors:[{id:"528",title:"Dr.",name:"Kresimir",surname:"Delac",slug:"kresimir-delac",fullName:"Kresimir Delac"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}}]},chapter:{item:{type:"chapter",id:"42037",title:"Silicon Nitride Photonic Crystal Free-Standing Membranes: A Flexible Platform for Visible Spectral Range Devices",doi:"10.5772/54846",slug:"silicon-nitride-photonic-crystal-free-standing-membranes-a-flexible-platform-for-visible-spectral-ra",body:'Two-dimensional (2D) photonic crystal (PhC) technology is well established at telecommunication bands, and materials such as Silicon (Si), Gallium Arsenide (GaAs) or Indium Phospide (InP) represent a common solution for applications at these wavelengths [1-5]. However, the interest of scientific community on structures operating in other spectral regions, such as the visible one, is growing up for both linear and non- linear applications [6-8]. Indeed, 2D-PhC resonant cavities in the visible spectral range are considered a promising tool to boost photonic devices performance in several fields, such as biosensing, integrated optics, quantum communications, solar energy, etc. As a consequence of this wide area of interest, a photonic platform able to answer to the needs of all these fields would be attractive for scientific and technical communities.
Trying to develop such technological platform, the first problem one should face is the material choice. In principle it should be transparent in the whole visible spectral range with a relatively high refractive index (n), economical, compatible with silicon based technologies, robust, biocompatible and suited for easy functionalization with several biological species.
In past years several materials have been proposed with this purpose; among them, of remarkable interest are Gallium Nitride (GaN) [9], Gallium Phospide (GaP) [10], polymers [11] and Silicon Dioxide (SiO2) [12, 13]. Another appealing material is Silicon Nitride (Si3N4), which answers to most of the above-mentioned requirements. Indeed, stoichiometric silicon nitride is transparent in the visible spectral range with a refractive index n ∼ 1.9 (@ λ = 600nm), it can be grown on Si with low-cost and widely diffused growth facilities such as Plasma Enhanced Chemical Vapor Deposition (PECVD) [14], it is compatible with Si based electronics (it is used as insulator in MOSFET gates [15,16]), it is biocompatible and can be functionalized with several kinds of proteins [17–19].
Several Si3N4 2D-PhC cavities have been already proposed in past years [6,20,21], showing a maximum experimental quality factor (Q) of ∼ 5000 in the case of a double heterostructure nanocavity [21]. Moreover, recent advances in the development of nanobeam cavities have led to extremely high quality factors also in the visible range, with a maximum Q of ∼ 55000 [22–24].
This chapter is devoted to the use of Si3N4 PhC resonators as a flexible platform to realize photonic devices based on the engineering of nanoemitters spontaneous emission in the visible spectral range. First of all, the nanocavity design based on the closed band-gap principle will be presented and discussed. The chapter will then be focused on the nanotechnological procedures developed in recent years to realize high quality Si3N4 PhC cavities and the coupling of these structures with organic and inorganic nanoemitters. The versatility of the examined approaches will be also reviewed, showing how it is possible to couple several types of quantum light emitters to the two photonic states allowed in a closed band-gap single point defect nanocavity [25,26]. At the end of the chapter, a case of study on PhC-based biosensors [27] will be used to make the reader conscious of the possibility to realize advanced photonic devices in the visible spectral range exploiting the Si3N4 PhC technology. In the conclusions, we will discuss how improvements in modeling and processing of PhC structures in Silicon Nitride, which are highly compatible with both biological materials and inorganic quantum emitters, can further boost device performance, envisioning a broader application of two-dimensional PhC nanocavities in the visible spectral range.
A system composed by a quantum light emitter coupled to a resonant optical mode can be modeled as two interacting oscillators. The strength of this interaction can lead to two different coupling regimes known as strong and weak coupling. In weak coupling regime, the free-space spontaneous emission rate (Γ0) is modified by the so-called Purcell effect: the coupled system emits with a rate ΓC=FΓ0, where F = 3/(4π2)Q/V (λ/n)3 is called Purcell Factor (Q and V are the quality factor and the modal volume of the photonic mode, respectively). When the system is instead in the strong coupling regime, the confined excitons and photons coherently exchange energy with a coupling strength, g, inversely proportional to V, i.e. g ∝ 1/ √ V. Thus the properties of the photonic mode and, in particular, the electromagnetic field confinement in both time and spatial domains strongly affect the dynamic of the coupled system.
At visible wavelengths, these phenomena have been observed by means of several optically confined systems [28,29], but 2D-PhCs represent the most promising structures, since they give the best control on the optical properties of the resonators. To date, PhC cavities for visible spectral range are based on various geometries [6,11,21] and on higher-order modes of the widely studied H1 defect [30] (sketched in Fig. 1(a), inset). This resonator consists of a missed hole in a triangular PhC lattice, and it allows two orthogonally polarized resonant modes in the photonic band gap (hereafter referred to as x- and z-pole modes, on the base of the orientation of the wave vector).
The cross polarization of x- and z-pole modes and the absence of higher-order states represent non-negligible advances for applications in quantum optics [31,34]. Moreover, the H1 cavity presents the lowest V among PhC point defects, thus enhancing quantum electrodynamic (QED) phenomena in both strongly and weakly coupled systems. However, obtaining small V at visible wavelengths is a challenging goal, because of the low refractive index of transparent materials in this spectral range, which reduces the effectiveness in localizing the optical modes. Nevertheless, the aforementioned advantages, together with the increasing interest toward the realization of efficient emitting devices in the visible spectral range, foster theoretical and experimental studies to find alternative routes to improve light confinement in low-index H1 systems.
In the following, we consider a resonator consisting of a point defect H1 in a triangular lattice of air holes (period a, radius r) realized in a silicon nitride slab having refractive index n=1.93 and a thickness t. Plane-Wave Expansion (PWE) and 3D Finite Difference Time Domain (FDTD) algorithms [32] were used to investigate the electromagnetic response of such structure. All the calculations were restricted to modes with non-negligible components of the electric field along x and z and a non-negligible component of the magnetic field along y (hereafter referred to as TE- like modes).
One way to realize ultrasmall-volume PhC cavities while keeping high Q- factors in the visible range and preserving the dipole-like shape of the modes is the so-called closing band-gap technique [33], involving PhC slab thickness (t) optimization. As shown in Fig.1(a), the x-pole mode Q-factor has a maximum for t = 1.55a, while it is almost constant for t < 1.2a. The Photonic Band-Gap (PBG) existing for t = 0.7a disappears when t is increased to 1.55a (see Figs. 1(b) and 1(c)). In agreement with the closing band-gap principle [33], this effect is assigned to a new nature of the electromagnetic confinement in the xz plane: it is not still due to the PBG, but it has to be assigned to the momentum space mismatch between the cavity mode and the second guided mode in the PhC slab. The increased thickness of the slab leads to slight variations of the x- and z-pole modal profiles along y, thus leading to a wider modal volume, as shown in Fig. 1(a). However, these variations of V are negligible with respect to the increase in Q, since the modal extension in the xz plane is preserved. Indeed the Purcell factor [Fig. 1(d)] follows the Q-factor behavior: for t = 1.55a, F is maximized to F ∼ 78 with V ∼ 0.68 (λ/n)3 and Q ∼ 700. A similar trend has been found for the z-pole mode.
(a) Dependence of modal volume and Q factor on the thickness of the slab t. Inset, photonic crystal H1 cavity. (b), (c) Photonic band structure of the structure for t = 0.7a and t = 1.55a, respectively. (d) Dependence of the Purcell factor on t (for S = 0). (e) Modification of the resonant frequencies and of the Q factor of the degenerated modes when two cavity neighboring holes are moved, as shown in the inset. The holes are moved closer to (farther from) the center for S < 0 (S > 0). (f) Ez for the x-pole mode in an unmodified H1 cavity. (g) Ex for the z-pole mode in an unmodified H1 cavity. (h) Ez for the x-pole mode in a H1 cavity with S=0.2a. (i) Ex for the z-pole mode in a H1 cavity with S = 0.2a. (l) Definition of S.
The x- and z-pole modes engineering would foster many applications based on H1 nanocavities operating at visible wavelengths. For instance, the degeneracy of x- and z-pole modes may be useful for entangled photon generation [34]. Other applications, such as single-photon sources or PhC-based optical read out of lab-on-chip devices [27], require well-defined and linearly polarized non-degenerate resonances. Several solutions have been reported in past years to break the energy degeneracy of the optical modes or to recover it [30,35-37]. A promising strategy to obtain a control on x- and z-pole modes is displayed in Fig. 1(e): by acting on two cavity neighboring holes, the resonant frequency of the x-pole mode (fx) can be significantly modified while keeping constant the z-pole mode one. This finding can be ascribed to the selective modification of the wavevector k = (kx, ky, kz) along a specific axis. Indeed x- and z-pole modes have the strongest component of k oriented along the x and z axes, respectively. If two holes are moved one toward each other along the x axis (S<0, see Fig. 1(l) for definition), kx is modified without affecting kz. As a consequence, fx increases while fz does not change. In the same way fx decreases for S > 0, while keeping fz constant. Figures 1(f-i) display x- and z-pole modal profiles for S = 0 and S = 0.2a: the electric field component along x (Ex) of the z-pole mode profile remains unchanged when the holes are moved far from the center [Figs.1(g) and 1(i)]. The shift instead results in the elongation of the x-pole modal function along x [Figs. 1(f) and 1(h)], thus modifying its resonant frequency.
It is important to notice that such alterations of field distributions modify the modal Q factors [Fig. 1(e)]: when S < 0, abrupt changes are introduced near the electric field maximum of the z-pole mode function, resulting in an increase in radiation losses and in a smaller Q factor (Q ∼ 557 for S = −0.057a) [38]. In contrast, if S > 0 these abrupt variations are avoided, the radiative energy in the light-cone minimized, and the Q-factor of the z-pole mode enhanced together with almost preserved V and fz. The optimized Q-factor turns out to be Q ∼ 810 for S = 0.075a, and the Purcell factor is assessed as F ∼ 90.
These findings are confirmed by the analysis in the z-pole momentum space, obtained by using a 2D Fourier Transform (2DFT), reported in Figs 2(a) and (b) for S = −0.1a and S = 0.2a, respectively. The white circle of Figs 2 (a) and (b) delimits the leaky region, defined by the light cone [38-40]: the stronger the components within this area, the higher the radiation losses along y. For S = −0.1a (Figs. 2(a) and (e)) a sharp peak is present at the center of the leaky region, affecting the value of Q; instead if S = 0.2a (Figs. 2(b) and (f)), the 2DFT is almost constant inside the light cone.
Ex field-distribution in momentum space for the z-pole mode. The white circle represents the light-cone. (a) |2DFT(Ex)| for S = −0.1a. (b) |2DFT(Ex)| for a S = 0.2a. (c) Zoom to a specific area of (a). (d) Zoom to a specific area of (b). (e) Momentum function extracted from (a) for kz = 0. (f) Momentum function extracted from (b) for kz = 0. (g) Cross section of the lobe for S = −0.1a shown in Fig. 2(c) (black circles) and of the lobe S = 0.2a displayed in Fig. 2(d) (green squares). Red continuous line represents a gaussian fit of the case S = 0.2a
As demonstrated in [38], the Q-factor depends also on the shape of the two peaks outside the light cone. A Gaussian shape typically leads to higher Q-factor, giving a direct measure of the energy not coupled with the radiation mode. Figs. 2(c) and (d) show a zoom of Figs. 2(a) and (b), respectively: the behavior for S = −0.1a is far from a 2D Gaussian function. For S = 0.2a (Fig. 2(d)), it is instead clear that by moving two holes far from the center, a 2D Gaussian function for these peaks is obtained, as also confirmed by the 1D gaussian fitting of the cross section of these lobes reported in Fig. 2(g). Therefore, by increasing the z-pole Q-factor, a positive S does not substantially affect the position, modal volume and resonant frequency of the z-pole electric field main lobe, leading to a straightforward increase of the Purcell factor of microresonators.
This therefore verifies that momentum space engineering, a strategy exploited to improve the confinement of defect states localized within the PBG [11,38,42], can also be efficient for cavity resonances without PBG.
The 2D-PhC nanocavities were fabricated into a 400-nm-thick Si3N4 layer deposited on a silicon substrate by means of Plasma Enhanced Chemical Vapor Deposition (PECVD) technique. Si3N4 refractive index was measured through spectrophotometric methods (performed with a Varian Cary 5000 spectrophotometer), giving a value of nSiN = 1.93@λ = 600 nm.
The PhC geometry was defined using a Raith150 e-beam lithography tool (equipped with a Gemini Column) operating at 30 kV. A thickness of 400 nm of ZEP520-A resist was chosen to ensure sufficient durability as a mask for pattern transfer into the underlying Si3N4 and, at the same time, to ensure a good resolution of the e-beam writing. The key issue in the fabrication process is to achieve PhC devices with well-controlled patterns size.
A preliminary dose-test was performed to define the optimum layout since the actual size of the pattern is influenced by the electron dose. A proximity error correction (PEC) was also applied to accomplish this target and the final dose was determined through Scanning Electron Microscope (SEM) inspections at 10 kV. Moreover, in order to achieve smoother and circular holes and faster exposure, the EBL system was used in “circular mode”. In this mode, every circular hole is exposed by the deflection of the beam along concentric circles.
The patterns defined in the ZEP were then transferred into the Si3N4 layer using inductive coupled plasma reactive ion etching (ICP-RIE) in fluorine chemistry until the silicon substrate surface was reached. The membrane structure was released by wet etching of the underlying Si substrate in a TetraMethylAmmonium Hydroxide (TMAH) solution. Each sample consisted of an array of H1 nanocavities, whose dimensions were scaled according to the lattice period a (in the range a = 257 nm – 277 nm) thus allowing spectral shifting of the resonant wavelength. Fig. 3(a) shows a Scanning Electron Microscope (SEM) image of the realized resonators.
a) Top and bird’s eyes view of the realized nanocavities acquired by SEM. (b) Resonances obtained by drop casting colloidal nanocrystals on the structure for three different values of a and r = 0.308a. The inset shows the Lorentzian fitting of the resonant peak for a = 265 nm. (c)-(f) Resonance of x- and z-pole modes for different values of the hole shift and a = 270 nm. (g) Resonant frequencies of x- and z-pole modes as a function of the hole shift.
The theoretical findings described in section 2 have been experimentally demonstrated by coupling to the nanocavities both cyanine 3 (Cy3) fluorophore and core/shell CdSe/CdS colloidal dot-in-rod (DR) nanocrystals. Room temperature microphotoluminescence (μPL) characterization was therefore performed to investigate the properties of the coupled system.
A micromolar solution (10−6mol/l) of DRs in toluene was prepared by using the synthesis procedure described in [43] by L. Carbone and co-workers and drop-casted on the realized microcavities. Figure 3(b) displays three resonances for three different values of a. The resonant peaks are well fitted by a Lorentzian function [Fig. 3(b), inset] and result in a maximum Q ∼ 620 for an unmodified H1 cavity (a ∼ 265 nm).
To explore the mode shifting over a wide spectral range, an organic fluorophore (Cy3) with broad emission spectrum was immobilized on the device. The μPL spectra for different values of S reported in Figures 3(c-f) show that the z-pole mode is almost unaffected by holes shifting, while x-pole resonant wavelength can be broadly tuned by means of S. Polarization-resolved measurements were carried out to identify the two modes, and their resonant wavelengths (λx and λz) as a function of S are displayed in Fig. 3(g). In agreement with the theoretical results of Fig. 3(e), the x-pole mode is tunable over a range ∆λx ∼ 40 nm. Small discrepancies between experimental results and theoretical calculations have been observed in terms of slight variations of λz and weak nonlinearity of λx; since these variations do not show a clear dependence on S, they could be reasonably attributed to unavoidable fabrication imperfections. The theoretical findings about the influence of the holes position on the z-pole Q-factor have been confirmed by the experiments. For S = 15 nm Q ∼ 750 has been measured, while for S = −20 nm the z-pole Q-factor falls down to a value of ∼ 200.
It is well known that in 2D-PhC slabs the in-plane confinement (xz) is due to the photonic band gap produced by the PhC periodicity, while in the out-of-plane direction (y) the confinement is due to the total internal reflection. As already mentioned, in the xz plane the electromagnetic field is localized in the center of the cavity (see figures 1(f-i)); FDTD simulations show also that along y the main lobe of the confined radiation is in the center of the slab (see Fig. 4).
Cross view of the electric field x-component with the superposition of the slab cross-section at z = 0.
The coupling reported in section 4.1 is thus not optimized, as the nanocrystals and the organic molecules are deposited on top of the cavities.
A viable strategy to approach the maximum allowed Purcell factor is to localize the nanoemitters in the center of the slab. This has been done with colloidal dot-in-rod nanocrystals using the same fabrication process described in section 3 and splitting the growth procedure of the Si3N4 slab in two steps. Figure 5(a) shows a sketch of the fabrication procedure. First of all, a 200 nm thick Si3N4 slab was grown on a Si substrate. A thin layer of colloidal DRs, with a molar concentration of ∼ 10−6mol/l was then spin-coated on it with a rotating speed of 500 rpm, thus obtaining a thickness lower than 10 nm as assessed by SEM inspection. After solvent evaporation, a second 200 nm thick layer of Si3N4 was grown on top of the sample. We verified the uniformity of the deposited layer by exploiting both the morphological characterization and the photoluminescence maps collected by a confocal microscope. A SEM cross-section of the resulting sandwiched structure is shown in Fig. 5(b). The nanocavities were then realized through electron beam lithography and dry and wet etching processes by following exactly the fabrication procedure reported in paragraph 3 (Fig. 5(c)).
a) Sketch of the fabrication process, (b) cross-section SEM image of the un-patterned sample; (c) bird’s eye view of the fabricated Si3N4 2D-PhC H1 nanocavity membrane and (d) photoluminescence spectra collected from the 2D-PhC H1 nanocavities with different lattice constants a.
Also in this case, the optical measurements of the nanocavities were carried out by the OLYMPUS FluoView 1000 confocal laser scanning microscope, with a spatial resolution of 200 nm. A CW laser diode emitting at wavelength λex = 405 nm was used as excitation source. In Fig. 5(d) are reported the photoluminescence spectra collected from the 2D-PhC H1 nanocavities with different lattice constants a. Superimposed to the broad emission spectrum (FWHM ∼ 30 nm) of NCs uncoupled to the cavity, sharp peaks with a quality factor of about 600 are clearly detected, assessing the modulating effects of the PhC nanocavity on the emission of NCs coupled to the optical mode localized in the defect. Moreover, the normalized frequency a/λ of the experimental results was found to be about a/λ ∼ 0.46 against the expected value of a/λ of ∼ 0.431. As already suggested in case of the modal selective tuning, this slight difference can be mainly attributed to the effects of fabrication imperfections, inducing unavoidable uncontrolled variations in the optical properties of the PhC nanocavities [45].
The efficient coupling between the semiconductor nanocrystals layer and the dielectric cavity is due to the fact that the nanocrystals layer can be precisely positioned in the maximum of the confined electric field in the vertical direction. Indeed, in this case the Purcell effect results optimized [46] and the spontaneous emission rate strongly increased, leading to the possibility to measure a better Q-factor [47]. At the same time it is noteworthy to point out how the introduction of a guest material, embedded in two Si3N4 layers, does not affect the optical properties of the nanocavity as shown by the good match of the calculated and measured Q-factors (equal to 680 and 600, respectively).
Recently the light molding properties of PhC have been profitably exploited to boost the performance of optical sensors and transducers for biochemical analyses [48-50]. This paragraph proposes the idea of exploiting the sharp resonances of PhC nanocavities to assign unique spectral features to fluorophore-labeled bioanalytes, thus allowing their identification through wavelength-resolved light detection. Spectral tagging of organic dyes through photonic crystal nanocavities is experimentally proved to bring important benefits to cutting edge devices for biodiagnostics, such as DNA and protein biochips, in terms of improved sensitivity, efficiency and multiplexing capability.
PhC nanocavities can be embedded in a two-dimensional array, to realize an improved optical detection system of a miniaturized assay for genomic and proteomic analyses, (DNA or protein microarray). Fig. 6(a) is a three-dimensional sketch of the biochip architecture including different nanocavities, each having a different resonant wavelength. Moreover, a one-to-one correspondence is also preserved between a cavity and a group of specific bio-molecules (probes) immobilized on the surface (as shown in the expanded view of Fig. 6(a)). The as-realized chip can be exposed to a biological solution containing unknown target species, or analytes; conjugation between the analytes and their complementary probes takes place on the device surface [51]. Since the target analytes are typically labeled with fluorescent markers, the binding events can be revealed through optical inspection of the biochip readout area, thus allowing a complete compositional analysis of the assay [52].
Sketch of the proposed strategy for PhC-NC biochip. (a) Schematic of the array of PhC nanocavities patterned on the readout area. Inset: Detail showing examples of PhC nanocavities. The cavities are functionalized with different probes molecules, that specifically interact with complementary target analytes labeled with fluorescent markers. The signal is collected from this area and spectrally discriminated in order to identify the different spectral tags univocally associated to each nanocavity and thus to each bioprobe. (b) Example of a possible luminescence detected from the whole readout area (black line) as compared to the unmodified broad marker luminescence (red dotted line). The presence of each peak in the spectrum reveals the presence of the corresponding analyte in the investigated assay.
The recourse to a microarray configuration already allows the simultaneous analysis of a certain number of analytes thanks to spatial discrimination [52,53]. Here we upgrade the allowed degree of parallelization by assigning a peculiar spectral signature, given by the resonating behavior of each cavity, to each bioprobe immobilized on the surface. This gives the possibility to distinguish the spectral response of each target analyte bound to the corresponding probe, albeit a single common fluorophore is used for the labeling of the whole unknown solution. Fig. 6(b) exemplifies a possible spectral scan of the signal collected from the whole readout area. Different peaks can be observed on the emission spectrum of the fluorescent marker, each revealing the presence of a specific target analyte in the investigated assay. Besides the spatial discrimination implemented in microarray configurations, in this case the spectral distinction contributes substantially to the parallelization of the device. We also expect a beneficial effect given by Purcell effect, which increases the radiative emission rate of emitting materials interacting with quantum confined systems [54, 55]. Hence, a significant increase in the luminescence intensity of the markers coupled to the PhC cavities is envisioned, leading to a significant improvement of the signal-to-noise ratio and of the overall sensitivity of the biochip detection.
PhC nanocavities resonating in the visible spectral range were fabricated in Si3N4 membranes on a Si substrate, exploiting the modified single defect H1 nanocavity described in section 2 [33,43,47,57]. Several chips were fabricated, each containing an array of optimized H1 resonators with variable lattice constant a, thus tuning the corresponding resonant wavelengths. We tested the proposed architecture both with single-stranded DNA (ss-DNA) and antibody probes immobilized on the Si3N4 surface of two different devices. Complementary DNA targets or specific secondary antibodies, labeled with cyanine 3 (Cy3) and rodhamine (TRITC) fluorophores, respectively, were then allowed to recognize the immobilized probes, thus obtaining a uniform fluorescent monolayer of the biomolecular species.
The effects of fluorescence enhancement and peak sharpening in resonant conditions are clearly observed in the emission spectra reported in Fig. 7(a) for PhC nanocavities treated with TRITC-labeled proteins and in Fig. 7(b) for DNA-functionalized nanocavities (five uppermost lines, compared to the lowest spectrum corresponding to the emission of Cy3- DNA strands without photonic resonators). In both cases it is evident that the change of the lattice period a of the photonic crystal resonator leads to the modification of the spectral response coming from target analytes conjugated by the same broad emitting organic dye: a specific spectral feature is thus attributed to the target analytes captured on different cavities. The best measured Q-factor obtained in the PhC-nanocavities DNA-chip prototype is ∼ 725, corresponding to a full-width at half maximum of ∼ 0.9 nm. Taking into account the spectral resolution limits, a conservative estimate suggests the possibility to distinguish up to 150 different resonant peaks within the 150nm bandwidth of the Cy3 emission spectrum. This means that up to 150 parallel analyses can be simultaneously performed with one single spectral scan of the readout area of the biochip, thus drastically decreasing the time required for a complete compositional identification.
By confocal microscopy it is also possible to visualize the effects of emission enhancement in resonant conditions, as reported in the photoluminescence maps reported in Fig. 7(c). In this array of five different nanocavities, functionalized with ss-DNA and hybridized with Cy3-labeled complementary DNA sequences we have performed a spectral scanning of the acquisition wavelength with a resolution of 2 nm. When the detection wavelength matches one of the five resonating wavelengths of the nanocavities, marked from λ1 to λ5 in Fig. 7(b), it is possible to distinguish a bright spot in the center of each nanocavity.
a) PL spectra collected from TRITC-labeled proteins captured onto the PhC nanocavities; (b) PL spectra collected from Cy3–labeled DNA (colored lines) onto the PhC nanocavities as compared to Cy3 emission spectrum collected on a PhC pattern (black line); (c) PL maps of an array of five Cye-labeled DNA-PhC nanocavities, collected at different wavelengths [also indicated in (b)]. For each spectrum and PL map, the reported a value indicates the lattice period of the measured PhC nanocavity.
In order to quantify the enhancement effect of each photonic crystal pattern, in Fig. 8 it is reported a three-dimensional intensity profile collected on a Cy3-labeled DNA functionalized nanocavity in resonant conditions. The central bright spot corresponding to the H1 defect cavity reveals a signal improvement as high as 160 as compared to the luminescence coming from unpatterned Si3N4 surface. A major role of the Purcell effect [54,55] can be envisioned, by virtue of the strong optical quantum confinement performed by the H1-shifted nanocavities.
Noteworthy, the photonic crystal pattern itself causes an improvement of fluorescence emission as compared to the surrounding unpatterned Si3N4 layer, although the immobilization and hybridization processes have been homogeneously performed on the whole sample surface. In this case, an enhancement of ~ 20 times is achieved. This behavior may be ascribed to the combination of two effects. First, the free-standing membrane layer makes available a larger surface area to the probes immobilization (about a factor of 4 more than the unpatterned layer), resulting in a higher number of immobilized Cy3-labeled analytes in the PhC regions. Second, in 2D-PhC patterns an efficient transfer channel between externally radiated light and energy trapped in the membrane is represented by the so-called leaky modes [48,57,58]. The coupling of such modes with the absorption or emission bands of neighboring emitters may lead to a significant increase of their luminescence. Although the photonic crystal pattern has not been specifically optimized to maximize such effect, the role of leaky modes localized on the PhC pattern for the further increase of the luminescence experimentally observed is not negligible.
Three-dimensional intensity profile of photoluminescence collected from Cy3- labeled DNA captured by a functionalized nanocavity. Emission outside the PhC pattern has been normalized to unit. A 20-fold luminescence enhancement due to the PhC pattern, as compared to the unpatterned Si3N4 surface, has been measured. The cavity confinement further enhances Cy3 emission up to 160-fold.
The insertion of PhC cavities in classical biochip architectures leads, therefore, to a huge increase of the emission intensity of fluorescent markers, thus providing higher sensitivity, and allowing detection of very small amounts of target biomolecules in the investigated solution. In addition, the nanocavities attribute peculiar spectral features to the target analytes captured by their surface, so that the presence of specific species in the solution can be inferred by a simple spectral analysis of the optical response of the read-out region. This enables parallel detection of multiple elements, thus accelerating the analysis time.
This chapter details the use of Si3N4 2D-PhC nanocavities as flexible platform to realize photonic devices based on the engineering of spontaneous emission of nanoemitters in the visible spectral range. The versatility of the approach is demonstrated by coupling several types of emitters to the two photonic states allowed in a closed band gap single point defect nanocavity. In particular, DNA strands and antibodies marked with Cy3 and TRITC organic dyes have been immobilized on top of the nanocavities, while colloidal quantum dots emitting in the visible spectral range have been dropcasted on the devices and also positioned in the resonators at the maximum of the localized photonic mode. The optical measurements, carried out by μPL confocal microscopy, revealed maximum quality factors close to the theoretical estimations for all the emitters. Improvements in modeling and processing of PhC structures in Silicon Nitride, which is highly compatible with both biological materials and inorganic quantum emiters, let us envision a broader application of two-dimensional PhC nanocavities also in the visible spectral range. In particular, the coupling of a single colloidal dot-in-rod nanocrystal with a photonic crystal cavity would be an important milestone to reach in next years, and would allow further improvements of single photon rate and stability.
Forests of the Trans-Mexican Volcanic Belt (TMVB) physiographic region are among the most threatened areas in Mexico. The TMVB region encloses a large number of natural protected areas (NPA), the Protection of Flora and Fauna Area Nevado de Toluca (PFFANT) is one of them. The closeness of this NPA to large cities entails environmental pressures that includes the presence of human settlements, illegal logging, introduction of exotic species and the growing incidence of forest parasites like bark beetles and dwarf mistletoes [1, 2, 3].
\nPFFANT is formed by conifer forests, with the genera Pinus and Abies being the most representative of this zone [4, 5]. Pinus hartwegii Lindl. is forming large forest stands and is the pine species which grows at the highest altitudes in the PFFANT [6], unfortunately is affected by dwarf mistletoes (Arceuthobium spp.) and bark beetles (Dendroctonus spp.). The incidence of these parasites is growing, probably because of climate change and deforestation [1, 7, 8, 9].
\nMéxico ranks fourth in terms of deforestation, with approximately 670,000 ha/year causing losses in genetic diversity and changes in locally adapted populations for example giving place to an increase of parasites populations [10, 11, 12, 13]. Results of forest health diagnoses have suggested that bark beetles are a group of parasites that have affected large extension of forests in Mexico (40.5%), followed by parasitic plants (38.7%), both of them leaving negative consequences in the forest, like high mortality rates of trees affected [11, 14, 15].
\nBark beetles grow under the cortex and induce weakening of the tree, the construction of galleries and the inoculation of a staining fungi which is carried by female beetle results death [14]. In the PFFANT, Dendroctonus adjunctus is affecting P. hartwegii [6, 14]. Dwarf mistletoes are obligate heterotrophic plants that acquire all their water and nutrients from their host and can significantly inhibit its growth causing permanent deformation of the stem and crown. This parasite weakens trees in such a way that they become more susceptible to attack by insects, particularly bark beetles. In the PFFANT, P. hartwegii is the host of Arceuthobium vaginatum and A. globosum [6, 8, 15]. Bark beetles and dwarf mistletoes epidemics can lead to shifts in forest, forest successional trajectories and susceptibility to future disturbances [16, 17, 18].
\nForest trees are key drivers of terrestrial biodiversity because they function as a carbon sink, preserve the water quality and regulate climate [19, 20]; genetic variability studies are crucial to understand the basic biology of these organisms and to obtain insights on evolution, disease resistance and conservation genetics [21, 22, 23]. In conifer species for example, gene flow is mediated by three types of genomes with contrasting inheritance: nuclear (biparental), mitochondrial (maternal) and chloroplast (paternal) this particularity opens avenues to the study of conifer DNA polymorphism, the study of genetic variability with these three types of markers allow making inferences on the distribution of genetic resources and habitat connectivity [24].
\nIn this study, nuclear DNA (ncDNA), mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) were used to assess the genetic variability and population structure of P. hartwegii populations affected by bark beetles and dwarf mistletoes, expecting that genetic variability will be low in the parasitized populations. We want to contribute to the conservation of mountain pine populations of the PFFANT generating information which helps in the identification of populations genetically valuable.
\nSampling was carried out in the Protection of Flora and Fauna Area Nevado de Toluca, which forms part of the Trans-Mexican Volcanic Belt physiographic region. The geographical coordinates of the study zone are 18° 51′ 31″ and 19° 19′ 03″ N and 99° 38′ 54″ and 100° 09′ 58″ W; it is a priority region for conservation due to its diversity of ecosystems in which pine-fir forests and high mountain prairie dominate [1, 25].
\nWe sampled a total of 180 individuals of P. hartwegii. A distance of 50 m was between each tree sampled. Samples were classified into four groups (categories): trees with signs of attack by bark beetles (BB), trees with signs of attack by dwarf mistletoe (DM), trees with signs of attack of both parasites (BM), and trees with no signals of any parasite, which were considered as healthy trees (HT). Each sample consisted of young needle tissue. Immediately after collecting the needles, they were placed on ice for transport to a laboratory where they were maintained at −70°C.
\nCetyltrimethylammonium bromide (CTAB) method was implemented with a few modifications [26]. Needle tissue was ground to a fine powder with a chilled mortar and pestle, making two washes, the first with 100% ethanol (v/v) and the second with 75% ethanol (v/v). DNA was re-suspended in 70 μL TE and stored at −20°C until it was used.
\nPCRs were performed in a reaction volume of 10 μL, containing: ammonium buffer 15 mM, MgCl2 25 mM, dNTP mix 10 mM, primer 20 μM, DNA 10 ng/μL and 0.5 U of Taq polymerase (Sigma). To amplify nuclear (ncDNA), we used anchored microsatellites (ASSR) which proved to be genetically stables and heritable: ASSR-15 and ASSR-29 [27] and one operon: UBC 254 [28], one cytochrome oxidase sequence: cox3in, was used to amplify mitochondrial (mtDNA) [30] and one highly polymorphic microsatellite: 10FF/RR, to amplify chloroplast (cpDNA) [31] (Table 1).
\nPrimer name | \nMarker type | \nSequence (5′ → 3′) | \n
---|---|---|
UBC-254 | \nNuclear operon [28] | \n5′-CGCCCCCATT-3′ | \n
ASSR-15 | \nNuclear anchored microsatellite [29] | \n5′-(CT)7GCA-3′ | \n
ASSR-29 | \nNuclear anchored microsatellite [29] | \n5′-(CT)7GTA-3′ | \n
ASSR-20 | \nNuclear anchored microsatellite [29] | \n5′-(CT)7ATG-3′ | \n
COX3in | \nMitochondrial cytochrome oxidase III gene sequence [30] | \n5′-GTA GAT CCA AGT CCA TGG CCT-3′ 5′-GCA GCT GCT TCA AAG CC-3′ | \n
10 FF/RR | \nChloroplast microsatellite [31] | \n5′-CAGAAGCCCAAGCTTATGGC, 5′-CGGATTGATCCTAACCATAC | \n
Description of markers used for the study of genetic variability of Pinus hartwegii.
Amplifications were performed in a Master Cycler Gradient (Eppendorf) Thermal Cycler in all 40 cycles. For ncDNA primers: 1 min of denaturation at 94°C, 1 min of annealing at 48°C and 1 min of extension at 72°C. For mtDNA primers: 1 min of denaturation at 94°C, 1 min of annealing at 48–55°C and 1 min of extension at 72°C. For cpDNA: 1 min of denaturation at 94°C, 1 min of annealing at 58–60°C and 1 min of extension at 72°C; all samples with all primers were given a 7 min of pre-amplification denaturation at 94°C and a 5 min of post-amplification at 72°C.
\nThe amplification products were separated by electrophoresis in agarose gel (1.5%) at constant voltage (100 V and 90 mA). Gels were visualized by UV transilluminator (UVP) with ethidium bromide (10 mg/mL).
\nDNA patterns were inferred according to dominant nature of markers used, so each amplified product was scored for all genotypes for its presence or absence, we made a binary matrix in which band presence was assigned a value of one (1) and the absence of a band a value of zero (0). Co-migrating bands were assumed as the same locus and the same band when scoring.
\nWe used PopGene 32 [32], Genealex 6.5 [33] and TFPGA [34] to obtain genetic diversity parameters: mean number of alleles per locus (A), mean number of observed alleles (na), effective number of alleles (ne), Nei’s genetic diversity indices (He); as long as we sampled parasitized trees we used Graphpad Prima 7.0 to perform a chi square test and detect if there were differences in heterozygosis according to the categories considered in sampling. The number of polymorphic alleles (LP), percentage of polymorphic alleles (%LP), population structure fixation indices (GST), indicators of heterozygosis (HT: total genetic diversity of the locus, HS: genetic diversity within populations), gene flow (Nm) and Nei’s genetic distance (D) between the four categories we obtained BB, DM, BM, and HT [35].
\nWe obtained electrophoretic patterns with high reproducibility and clear band resolution. UBC-254: 11 bands, ASSR-15: 7 bands, ASSR-29: 11 bands, Cox3in: 8 bands and 10FF/RR: 7 bands, combined in 139 band patterns, ranging from 200 to 2000 bp; additionally there were bands only present in HT trees.
\nThe number of alleles per locus (na) and the number effective alleles (ne) ranged from 1.3 to 2.0 indicating that the number of alleles transferred from one generation to the next is low; these low values of na and ne consequently act on heterozygosis (Nei’s genetic diversity: He), which also was low compared with other Pinus species (Table 2).
\n\n | ncDNA | \nmtDNA | \ncpDNA | \n|||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
BB | \nDM | \nBM | \nHT | \nBB | \nDM | \nBM | \nHT | \nBB | \nDM | \nBM | \nHT | \n|
n | \n35 | \n75 | \n35 | \n35 | \n75 | \n35 | \n35 | \n35 | \n75 | \n35 | \n35 | \n34 | \n
na | \n1.9 ± 0.3620 | \n2 | \n1.9 ± 0.3620 | \n1.7 ± 0.4237 | \n1.4 ± 0.5175 | \n1.8 ± 0.4629 | \n1.6 ± 0.5175 | \n1.5 ± 0.5345 | \n1.4 ± 0.5345 | \n2 | \n1.4 ± 0.5345 | \n1.6 ± 0.5345 | \n
ne | \n1.3 ± 0.2964 | \n1.3 ± 0.3067 | \n1.7 ± 0.2872 | \n1.3 ± 0.2666 | \n1.0 ± 0.1433 | \n1.1 ± 0.1859 | \n1.1 ± 0.2395 | \n1.0 ± 0.1047 | \n1.0 ± 0.0395 | \n1.1 ± 0.2033 | \n1.0 ± 0.1056 | \n1.1 ± 0.1661 | \n
He | \n0.1924 ± 0.1648 | \n0.1993 ± 0.1586 | \n0.1877 ± 0.1526 | \n0.1831 ± 0.1552 | \n0.0539 ± 0.1016 | \n0.0810 ± 0.1196 | \n0.0872 ± 0.1382 | \n0.0582 ± 0.0828 | \n0.0295 ± 0.0368 | \n0.1267 ± 0.1260 | \n0.0592 ± 0.0857 | \nND | \n
%LP | \n87.5 | \n87.5 | \n100 | \n75.86 | \n23.10 | \n75.86 | \n86.21 | \n33.33 | \n55.56 | \n33.33 | \n55.56 | \nND | \n
Genetic variability of Pinus hartwegii in attacked (by bark beetle and dwarf mistletoe) and nonattacked trees for nuclear DNA (ncDNA), mitochondrial DNA (mtDNA), and chloroplast DNA (cpDNA); bark beetle attacked tree (BB), dwarf mistletoe attacked tree (DM), bark beetle and dwarf mistletoe attacked tree (BM) and healthy tree (HT); sample size (n), number of alleles per locus, effective number of alleles per locus (ne), Nei’s genetic diversity, percentage of polymorphic loci (%LP), (ND) no data.
Among categories (BB, DM, BM and HT) we observed, in some cases, a tendency of BB, DM and BM to present higher values of He, for example with ncDNA BB and DM categories showed He values 0.1924 and 0.1993, respectably, higher than in HT trees which was 0.1831, with cpDNA DM trees presented high He compared with HT (Table 2). According to Chi square tests, the distribution of He showed statistically significant differences between the BB, DM, BM and HT categories (Table 3).
\nMarker | \nΧ2 | \nP | \n
---|---|---|
ASSR-15 | \n1.0614 | \n0.0001 | \n
ASSR-29 | \n1.8906 | \n0.0001 | \n
UBC254 | \n0.8028 | \n0.0001 | \n
10FF/RR | \n0.8732 | \n0.0001 | \n
COX3IN | \n0.5732 | \n0.0001 | \n
Comparison of genetic variability between groups (BB, DM, BM and HT) in Pinus hartwegii.
Estimated population structure based on GST (fixation index) was very low probably due to high levels of gene flow (Table 4). The rates of gene flow (Nm) derived from GST were very high with all markers, averaging 15.1 migrants per generation (Table 4). Based on these results (low-population differentiation/high gene flow), we assume that inbreeding rates are low.
\n\n | ncDNA | \nmtDNA | \ncpDNA | \n|||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Mean | \nSD | \nMAX | \nMIN | \nMean | \nSD | \nMAX | \nMIN | \nMean | \nSD | \nMAX | \nMIN | \n|
GST | \n0.0321 | \n39.8316 | \n0.1404 | \n0.0006 | \n0.0170 | \n0.0065 | \n0.0230 | \n0.0049 | \n0.0475 | \n0.0312 | \n0.0961 | \n0.0096 | \n
Nm | \n15.0849 | \n10.8853 | \n55.5996 | \n3.0604 | \n28.9288 | \n14.9747 | \n59.5707 | \n21.2152 | \n10.0279 | \n17.0230 | \n51.3333 | \n4.7046 | \n
HT | \n0.1946 | \n0.0203 | \n0.4906 | \n0.0302 | \n0.0713 | \n0.0122 | \n0.3294 | \n0.0064 | \n0.0832 | \n0.0064 | \n0.2076 | \n0.0064 | \n
HS | \n0.1884 | \n0.0194 | \n0.4850 | \n0.0120 | \n0.0700 | \n0.0116 | \n0.3218 | \n0.0063 | \n0.0792 | \n0.0058 | \n0.1955 | \n0.0063 | \n
Summary of Pinus hartwegii population differentiation (GST), genic flow (Nm), total genetic diversity of the locus (HT), average genetic diversity (HS), for nuclear (ncDNA), mitochondrial (ncDNA) and chloroplast DNA markers (cpDNA).
Genetic distances ranged from 0.003 between DM/BM with mtDNA and DNA cp markers to 0.014 between HT/DM and HT/BB with ncDNA and cpDNA markers; for all markers parasitized trees had the highest genetic distances between nonattacked trees (HT) and attacked trees (BB, DM and BM) (Table 5).
\n\n | \n | HT | \nBB | \nDM | \nDM | \n
---|---|---|---|---|---|
ncDNA | \nHT | \n__ | \n\n | \n | \n |
BB | \n0.006 | \n__ | \n\n | \n | |
DM | \n0.014 | \n0.007 | \n__ | \n\n | |
BM | \n0.012 | \n0.004 | \n0.007 | \n__ | \n|
mtDNA | \nHT | \n__ | \n\n | \n | \n |
BB | \n0.002 | \n__ | \n\n | \n | |
DM | \n0.010 | \n0.001 | \n__ | \n\n | |
BM | \n0.004 | \n0.001 | \n0.003 | \n__ | \n|
cpDNA | \nHT | \n__ | \n\n | \n | \n |
BB | \n0.014 | \n__ | \n\n | \n | |
DM | \n0.003 | \n0.013 | \n__ | \n\n | |
BM | \n0.005 | \n0.006 | \n0.001 | \n__ | \n
Matrix for genetic distance values for bark beetle attacked tree (BB), dwarf mistletoe attacked tree (DM), bark beetle and dwarf mistletoe attacked tree (BM) and healthy tree (HT) in Pinus hartwegii samples, evaluated with nuclear (ncDNA), mitochondrial (mtDNA) and chloroplast (cpDNA) markers.
We found low levels of genetic variability in mountain pine, but also that parasitized trees in some cases had highest levels of heterozygosity; this is not rare if we take into account that plants are subject to various abiotic and biotic stresses, especially those long-lived species like conifers; thus, slow-growing plants will invest heavily in defenses against parasites because of high cost of replacing tissue [9, 36]; substantial variation in susceptibility, damage and resistance are well documented in natural plant populations [21, 37, 38, 39].
\nLevels of heterozygosis in mountain pine were in general low, but in spite of this with ncDNA, we observed a tendency of parasitized trees (BB and DM) to have more genetic variability and this is relevant because in a population stressed by an increment of parasites, high genetic diversity individuals will have more chances to adapt themselves to changes in their environment and attack by parasites and pathogens.
\nSome theories propose that dwarf mistletoes performance is regulated by physiological (genetic) condition of the host and that infections are greater in sites with high stress, also long-term contact and evolutionary history between specific plant and parasites are expected to increase plant defenses, tree species have been co-evolving with mistletoes for 25 million years, so high genetic variability of parasitized organisms is an insight of co-evolution system [16, 40, 41]. The genetics of host resistance due to a co-evolutionary linkage has been reported in some pine species, such as P. edulis, P. lawsonii, P. montezumae and Fagus sylvatica with their associated bark beetles [9, 42], and for P. ponderosa and Douglas-fir (Pseudotsuga menziesii) to dwarf mistletoes [37, 40, 43, 44].
\nIn PFFANT, pine forests are under high abiotic stress like the presence of human settlements and logging which in turn could be causing biotic stress situations like incrementing incidence of parasites (e.g., because of the loss of trees, bark beetles move to sites where there were no infections and the infection spreads in trees which are predicted to have low defenses). The location of populations parasitized and with high genetic variability is a valuable data to be taken into account for conservation science.
\nP. hartwegii form dense forest stands in the PFFANT, and their associated parasites are also present with a patchy distribution. They are not present in all populations, indeed there are healthy trees in populations highly parasitized (also called “scape trees”) it could suggest that the parasites of mountain pine select their host based on genetic cues. There is a hypothesis called “gene by gene coevolution” which pose that host-parasite relationship had been kept polymorphisms in plants, these has been recognized in the existence of two cases: host-specificity, and variation in host preference [40, 45], we suggest that in view of the levels of He in parasitized trees, it is possible that a gene-by-gene coevolution case is present in the interaction of mountain pine with its parasites, although there is a need for more studies to probe it. It appears that we are facing a coevolution dynamics, where trees with higher genetic diversity are attacked due to its genes; parasites track specific host genotypes under natural conditions [46, 47, 48] not only to phenotypic characteristics. In other words, plant genetic diversity affects enemies and mutualists [49].
\nOrganelle genomes provide information about the relative capacity of dispersal of males and females; mtDNA is maternally inherited, and cpDNA is paternally inherited in pines, this shapes gene flow and genetic diversity within and among populations in a particular way [22, 50, 51], we found low levels of GST, in comparison with some other pine species at organelle genomes [24] and registered high levels of gene flow, these data could suggest that mountain pine subpopulations studied at PFFANT are poorly differentiated which in turn could mean that the population as a whole must be managed and conserved as genetically unique; also we registered the highest with mtDNA on this we can infer that P. hartwegii’s most important means of gene flow seems to be the seed (Table 4), but it is also probably due to the reforestation plans performed at PFFANT by government institutions, which in most of the cases is performed with pines from off-site seed carrying foreign DNA.
\nHigh levels of deforestation have been reported at PFFANT, mainly due to illegal logging leading to forest fragmentation, which in turn has devastating effects on forest trees, taking off the best conformed trees, which reduce levels of gene flow and allele diversity, promoting inbreeding and genetic drift [52]. Since conifers are wind pollinated and long lived organisms, effects of inbreeding and or genetic drift are not drastic yet (in view of our results) and the levels of genetic variability reported here may only reflect standing genetic variation, when a population passes through selective pressures it adapts mainly from standing genetic variation [53, 54].
\nGenetic distances differed according to marker type; there has been reported high polymorphism in Dendroctonus ponderosa related to geographic region [55]. Our results may be explained by differences in land use in which trees were sampled, which could impose different selection pressures in parasites and hosts in response to biogeographic discontinuities [42, 56]. We observed, for example that dwarf mistletoe infections response to altitude, at least Arceuthobium vaginatum and A. globossum (parasites of P. hartwegii) disappear above 3600 masl (personal observation at FFPANT). The lowest genetic distances we found were between DM and BB trees with the tree markers (Table 4), and these trees are genetically similar and have high levels of polymorphism, the differences between HT trees and DM, BB trees may consist in those which parasitized trees possess and make parasites choose them [40, 45], while markers we used are not specifically related with defense and resistance pathways in plants, we report a reliable difference which can serve as a first insight to conduce more studies on genetic resistance of conifers to bark beetles and dwarf mistletoes.
\nThe presence of probably immune trees (HT) and resistant trees (BM) must be taken into account to conserve mountain pine forests of the FFPANT, specially confronting an increase of infected areas by bark beetles and dwarf mistletoes; BM are trees whose seeds could be used in reforestation programs, especially in areas where infections are growing, and HT seeds could be used to create barriers which impede the spread of outbreaks.
\nPinus forests of the FFPANT are home and a potential distribution area of many species of plants and animals some of which also have high levels of genetic variability which in turn makes FFPANT an important place to conservation of species [4, 57, 58, 59, 60]. These forests provide water to urban areas, hence the importance of preserving this natural area should not be dismissed; there is an urgent need to protect these forests, as long as forest fragmentation is increasing.
\nIt has been reported that there are differences in susceptibility to parasites attack among tree species and even among individuals within a species; when different species interact, selective changes may occur as a result of the interaction; models of host–parasite interactions support the idea that variation in host resistance is, at least partially, genetic and assume the presence of genetic variation [23, 46, 48]. In conifers, some theories have been proposed to explain this variability, including variations in terpene or phenolic content [61], differences in constitutive defenses [62, 63] and differences in growing conditions [64, 65]. Population genetics theory predicts that under many selective regimes, fitness will increase the number of heterozygous loci [23]; many authors have reported that genetic variability of trees affected by parasites, in terms of heterozygosity, they report that heterozygous individuals were resistant and suggest that heterozygosity and plant resistance are positively correlated [61, 66, 67, 68, 69].
\nMore studies are needed in order to reaffirm the results reported here, may be with other kinds of molecular markers, and to continue the improvement of management and preservation of the FFPANT. Forests worldwide need to be protected in face of an imminent climate change.
\nThe authors wish to thank Consejo Nacional de Ciencia y Tecnología (CONACyT) and the Universidad Autónoma del Estado de México (UAEMéx) for financial support. Also, they thank the CIEAF students who helped in the laboratory and fieldwork.
\nSupporting women in scientific research and encouraging more women to pursue careers in STEM fields has been an issue on the global agenda for many years. But there is still much to be done. And IntechOpen wants to help.
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