Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in Upland cotton (Gossypium hirsutum L.)

MIC-3 is a recently identified gene family shown to exhibit increased root-specific expression following nematode infection of cotton plants that are resistant to root-knot nematode. Here, we cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species to reveal sequence differences at the molecular level and identify chromosomal locations of MIC-3 genes in Gossypium species. Detailed sequence analysis and phylogenetic clustering of MIC-3 genes indicated the presence of multiple MIC-3 gene members in Gossypium species. Haplotypes of a MIC-3 gene family member were discovered by comparative analysis among consensus sequences across genotypes within an individual clade in the phylogram to overcome the problem of duplicated loci in the tetraploid cotton. Deficiency tests of the SNPs delimited six A_t-genome members of the MIC-3 family clustered to chromosome arm 4sh, and one D_t-genome member to chromosome 19. Clustering was confirmed by long-PCR amplification of the intergenic regions using A_t-genome-specific MIC-3 primer pairs. The clustered distribution may have been favored by selection for responsiveness to evolving disease and/or pest pressures, because large variants of the MIC-3 gene family may have been recovered from small physical areas by recombination. This could give a buffer against selection pressure from a broad range of pest and pathogens in the future. To our knowledge, these are the first results on the evolution of clustering and genome-specific haplotype members of a unique cotton gene family associated with resistant response against a major pathogen.     

Tunable Plasmonic Absorber Based on TiN-Nanosphere Liquid Crystal Hybrid in Visible and Near-Infrared Regions

In this paper, a tunable plasmonic absorber based on TiN-nanosphere/liquid crystal (LC) nanocomposite in visible and near-infrared regions is proposed. TiN-nanosphere/LC nanocomposite is a combination of titanium nitride (TiN) nanospheres dispersed in a host of LC and plays the main role in post fabrication tunability. The proposed absorber has three more than 90% absorption peaks and the absorption tunability of about 76 nm. It is shown that TiN-nanospheres are able to support localized surface plasmon resonance (LSPR). The Maxwell-Garnett theory is utilized to approximate the permittivity of the composite structure. Also, the effect of geometric parameters on the absorption is studied. Moreover, a single sheet of graphene is utilized to compensate the decrement of the absorption caused by the geometric parameters.     

Evaluation of DNA/DNA and prime-boost vaccination using LPG3 against Leishmania major infection in susceptible BALB/c mice and its antigenic properties in human leishmaniasis

One of the main issues in vaccine development is implementation of new adjuvants to improve the antigen presentation and eliciting the protective immune response. Heat shock protein (HSP) molecules are known as natural adjuvants. They can stimulate the innate and adaptive immune response against infectious diseases and cancer. Lipophosphoglycan 3 (LPG3), the Leishmania homologous with GRP94 (glucose regulated protein 94), a member of HSP90 family, is involved in assembly of LPG as the most abundant macromolecule on the surface of Leishmania promastigotes. In the present study as a primary step, we tested LPG3 as a vaccine candidate in two regimens, DNA/DNA and prime-boost (DNA/Protein), against Leishmania major infection in BALB/c mice model. Our results showed that LPG3 and its fragment (rNT-LPG3) are highly immunogenic in BALB/c mice and can stimulate the production of both IgG1 and IgG2a. In prime-boost immunization strategy, the level of antibody response was higher compared with DNA/DNA immunization. The levels of IFN-γ in the supernatant of splenocytes from mice immunized with DNA/DNA and prime-boost regimens were significantly higher when compared to control groups. In fact, immunization with prime-boost vaccination has higher ratio of IFN-γ/IL-5, suggesting a shift towards a Th1 response.In addition, sera reactivity against LPG3 in visceral leishmaniasis (VL) patients was significantly higher in comparison with cutaneous leishmaniasis (CL) patients. Therefore, we recommend further investigations on the usage of LPG3 co-delivery with candidate antigens for vaccine development against leishmaniasis.     

Biosynthesis of NiFe2O4@Ag Nanocomposite and Assessment of Its Effect on Expression of norA Gene in Staphylococcus aureus

Activity of norA efflux pump has been known as a resistance mechanism to antibiotics like ciprofloxacin in Staphylococcus aureus. This study was carried out to assess the effect of biosynthesized NiFe₂O₄@Ag nanocomposite on expression of norA gene in Staphylococcus aureus. In this experimental study, 30 clinical samples were collected from patients hospitalized at different hospitals in Guilan Province, Iran. Then, clinical isolates of S. aureus were identified by standard microbiological tests. Antimicrobial susceptibility tests of clinical and standard strains of S. aureus were done by disk diffusion method according to CLSI guideline. Fourier transform infrared spectroscopy (FT‐IR) was used to analyze the various functional groups present in the biosynthesized NiFe₂O₄@Ag nanocomposite. This analysis confirmed the formation of alga proteins coated on magnetite nanocomposite. X‐ray diffraction (XRD) verified the crystalline structure of NiFe₂O₄@Ag and the deposition of silver on the surface of NiFe₂O₄. Energy dispersive X‐ray mapping (EDX‐map) analysis confirmed the existence of Ag, Ni, Fe and O in the final product. Scanning electron microscopy (SEM) confirmed that the nanocomposites were spherical in shape and Transmission electron microscopy (TEM) results revealed that the NiFe₂O₄@Ag had the particle size about 100 nm. Antibacterial activity of NiFe₂O₄@Ag alone and combined with ciprofloxacin was evaluated using the disk assay method, and minimum inhibitory concentration (MIC) by broth dilution method. Afterwards, the expression of norA efflux pump gene with and without of NiFe₂O₄@Ag nanocomposite and ciprofloxacin was evaluated by Real‐Time PCR. Real‐Time PCR results demonstrated that the expression of norA gene in the strains exposed to both NiFe₂O₄@Ag nanocomposite (1/4 MIC) and ciprofloxacin (1/8 MIC) significantly reduced in comparison to untreated strains. This study reveals that, when NiFe₂O₄@Ag nanocomposite is combined with ciprofloxacin, the inhibitory effect of ciprofloxacin increases against growth of S. aureus. Therefore, NiFe₂O₄@Ag nanocomposite can be considered as an effective factor to decrease the growth of S. aureus along with ciprofloxacin.     

The role of induced mutation in conversion of photoperiod dependence in cotton

Wild cotton germplasm resources are largely underutilized because of photoperiod-dependent flowering of "exotic" cottons. The objectives of this work were to explore the genome-wide effect of induced mutation in photoperiod-converted induced cotton mutants, estimating the genetic change between mutant and wild-type cottons using simple sequence repeats (SSRs) as well as understand the pattern of SSR mutation in induced mutagenesis. Three groups of photoperiod-converted radiomutants ((32)P) including their wild-type parental lines, A- and D-genome diploids, and typically grown cotton cultivars were screened with 250 cotton SSR primer pairs. Forty SSRs revealed the same SSR mutation profile in, at least, 2 independent mutant lines that were different from the original wild types. Induced mutagenesis both increased and decreased the allele sizes of SSRs in mutants with the higher mutation rate in SSRs containing dinucleotide motifs. Genetic distance obtained based on 141 informative SSR alleles ranged from 0.09 to 0.60 in all studied cotton genotypes. Genetic distance within all photoperiod-converted induced mutants was in a 0.09-0.25 range. The genetic distance among photoperiod-converted mutants and their originals ranged from 0.28 to 0.50, revealing significant modification of mutants from their original wild types. Typical Gossypium hirsutum cultivar, Namangan-77, revealed mutational pattern similar to induced radiomutants in 40 mutated SSR loci, implying possible pressure to these SSR loci not only in radiomutagenesis but also during common breeding process. Outcomes of the research should be useful in understanding the photoperiod-related mutations, and markers might help in mapping photoperiodic flowering genes in cotton.     

Wideband Graphene-Based Fractal Absorber and its Applications as Switch and Inverter

In this paper, the idea of square fractal geometry has been utilized to introduce a tunable wideband graphene-based perfect plasmonic absorber in the near-infrared region. It consists of a MgF₂ layer and an array of gold squares fractal loaded on a graphene layer. In the designed absorber a single layer of graphene has been used instead of multilayered graphene structures. The structure is polarization-insensitive under normal incidence due to the geometric symmetry. The absorption and bandwidth of the structure are almost insensitive to the incident angle up to 15° and 45° for TE and TM polarizations, respectively. Moreover, by choosing appropriate structural parameters, the resonance wavelength of the desired plasmonic absorber can be controlled. The absorption of the introduced structure can be tuned by changing the chemical potential of the graphene. Therefore, the proposed fractal absorber can act as switch and inverter at λ = 1995 nm. Furthermore, the equivalent circuit model of the absorber has been derived to confirm the validity of the simulation results. The superiorities of our fractal absorber are wide full-width at half-maximum of 406 nm, multi-applicant, perfect absorption, and fabrication feasibility due to the simple structure with the maximum absorption tolerance error of 5.12%.

     

Analytical Methods of Equivalent Circuit Model and Transmission Matrix for a Plasmonic Switch with Sensing Capability in Near-Infrared Region

In this paper, the simultaneous switching and sensing capabilities of a compact plasmonic structure based on a conventional rectangular hole in a silver film are proposed and investigated. The proposed structure has ultrahigh sensitivity up to 3000 nm/RIU and high figure of merit of 170 RIU⁻¹. Also, the simulation results show the potential of the presented refractive index sensor to detect malaria infection, cancer cells, bacillus bacteria, and solution of glucose in water. Simultaneously, by changing the incident lightwave polarization, the structure behaves like a plasmonic switch, which has high extinction ratios of 15.81, 31.20, and 25.03 dB at three telecommunication wavelengths of 850, 1310, and 1550 nm, respectively. The ultrafast response time of 20 fs is achieved for the wideband application of the switching capability at the wavelength range of 1056 to 1765 nm. Moreover, the equivalent circuit model and transmission (ABCD) matrix methods are derived to validate the simulated results. Simple design, good agreement between the numerical and analytical results, biomedical applications, ultrahigh sensitivity, and ultrafast performance of the proposed structure help this idea to open up paths for design and implementation of other multi-application plasmonic devices in near-infrared region. To the best of our knowledge, the mentioned analytical methods have not been studied former at near-infrared wavelengths. Therefore, the achievements could pave the way for verifying the simulation results of plasmonic nanostructures in future investigations.

     

Molecular evolution of the clustered <Emphasis Type="Italic">MIC</Emphasis>-<Emphasis Type="Italic">3</Emphasis> multigene family of <Emphasis Type="Italic">Gossypium</Emphasis> species

The Gossypium MIC-3 (Meloidogyne Induced Cotton-3) gene family is of great interest for molecular evolutionary studies because of its uniqueness to Gossypium species, multi-gene content, clustered localization, and root-knot nematode resistance-associated features. Molecular evolution of the MIC-3 gene family was studied in 15 tetraploid and diploid Gossypium genotypes that collectively represent seven phylogenetically distinct genomes. Synonymous (d_S) and non-synonymous (d_N) nucleotide substitution rates suggest that the second of the two exons of the MIC-3 genes has been under strong positive selection pressure, while the first exon has been under strong purifying selection to preserve function. Based on nucleotide substitution rates, we conclude that MIC-3 genes are evolving by a birth-and-death process and that a ‘gene amplification’ mechanism has helped to retain all duplicate copies, which best fits with the “bait and switch” model of R-gene evolution. The data indicate MIC-3 gene duplication events occurred at various rates, once per 1 million years (MY) in the allotetraploids, once per ~2 MY in the A/F genome clade, and once per ~8 MY in the D-genome clade. Variations in the MIC-3 gene family seem to reflect evolutionary selection for increased functional stability, while also expanding the capacity to develop novel “switch” pockets for responding to diverse pests and pathogens. Such evolutionary roles are congruent with the hypothesis that members of this unique resistance gene family provide fitness advantages in Gossypium.     

Effects of Toxoplasma gondii and Toxocara canis Antigens on WEHI-164 Fibrosarcoma Growth in a Mouse Model

Cancer is the main cause of death in developed countries. However, in underdeveloped countries infections and parasitic diseases are the main causes of death. There are raising scientific evidences indicating that parasitic infections induce antitumor activity against certain types of cancers. In this study, the effects of Toxoplasma gondii and Toxocara canis egg antigens in comparison with Bacillus Calmette Guerin (BCG) (known to have anticancer distinctive) on WEHI-164 fibosarcoma transplanted to BALB/c mice was investigated. Groups of 6 male BALB/c mice injected with T. gondii antigen, BCG, or T. canis egg antigen as case groups and alum alone as control groups. All mice were then challenged with WEHI-164 fibrosarcoma cells. The mice were examined for growth of the solid tumor and the tumor sizes were measured every other day up to 4 wk. The mean tumor area in T. gondii, BCG, or alum alone injected mice in 4 different days of measurements was 25 mm², 23 mm², and 186 mm² respectively. Also the mean tumor area in T. canis injected mice in 4 different days was 25.5 mm² compared to the control group (alum treated) which was 155 mm². T. gondii parasites and T. canis egg antigens induced inhibition of the tumor growth in the fibrosarcoma mouse model. We need further study to clarify the mechanisms of anti-cancer effects.