Terahertz imaging of human skin pathologies using laser feedback interferometry with quantum cascade lasers.

Early detection of skin pathologies with current clinical diagnostic tools is challenging, particularly when there are no visible colour changes or morphological cues present on the skin. In this study, we present a terahertz (THz) imaging technology based on a narrow band quantum cascade laser (QCL) at 2.8 THz for human skin pathology detection with diffraction limited spatial resolution. THz imaging was conducted for three different groups of unstained human skin samples (benign naevus, dysplastic naevus, and melanoma) and compared to the corresponding traditional histopathologic stained images. The minimum thickness of dehydrated human skin that can provide THz contrast was determined to be 50 µm, which is approximately one half-wavelength of the THz wave used. The THz images from different types of 50 µm-thick skin samples were well correlated with the histological findings. The per-sample locations of pathology vs healthy skin can be separated from the density distribution of the corresponding pixels in the THz amplitude-phase map. The possible THz contrast mechanisms relating to the origin of image contrast in addition to water content were analyzed from these dehydrated samples. Our findings suggest that THz imaging could provide a feasible imaging modality for skin cancer detection that is beyond the visible.

Ultrafast Pulse Generation from Quantum Cascade Lasers.

Quantum cascade lasers (QCLs) have broken the spectral barriers of semiconductor lasers and enabled a range of applications in the mid-infrared (MIR) and terahertz (THz) regimes. However, until recently, generating ultrashort and intense pulses from QCLs has been difficult. This would be useful to study ultrafast processes in MIR and THz using the targeted wavelength-by-design properties of QCLs. Since the first demonstration in 2009, mode-locking of QCLs has undergone considerable development in the past decade, which includes revealing the underlying mechanism of pulse formation, the development of an ultrafast THz detection technique, and the invention of novel pulse compression technology, etc. Here, we review the history and recent progress of ultrafast pulse generation from QCLs in both the THz and MIR regimes.

Feedback Regimes of LFI Sensors: Experimental Investigations.

In this article, we revisit the concept of optical feedback regimes in diode lasers and explore each regime experimentally from a somewhat unconventional point of view by relating the feedback regimes to the laser bias current and its optical feedback level. The results enable setting the operating conditions of the diode laser in different applications requiring operation in different feedback regimes. We experimentally explored and theoretically supported this relationship from the standard Lang and Kobayashi rate equation model for a laser diode under optical feedback. All five regimes were explored for two major types of laser diodes: inplane lasers and vertical-cavity surface emitting lasers. For both lasers, we mapped the self-mixing strength vs. drive current and feedback level, observed the differences in the shape of the self-mixing fringes between the two laser architectures and a general simulation, and monitored other parameters of the lasers with changing optical feedback.

Self-Pulsations in Terahertz Quantum Cascade Lasers under Strong Optical Feedback: The Effect of Multiple Reflections in the External Cavity.

We have recently reported the self-pulsation phenomenon under strong optical feedback in terahertz (THz) quantum cascade lasers (QCLs). One important issue, however, we left open: the effect of multiple round trips in the external cavity on the laser response to feedback. Our current analysis also casts additional light on the phenomenon of self-pulsations. Using only one external cavity round trip (ECRT) in the model has been the common approach following the seminal paper by Lang-Kobayashi in 1980. However, the conditions under which the Lang-Kobayashi model, in its original single-ECRT formulation, is applicable has been rarely explored. In this work, we investigate the self-pulsation phenomenon under multiple ECRTs. We found that the self-pulsation waveform changes when considering more than one ECRT. This we attribute to the combined effect of the extended external cavity length and the frequency modulation of the pulsation frequency by the optical feedback. Our findings add to the understanding of the optical feedback dynamics under multiple ECRTs and provide a pathway for selecting the appropriate numerical model to study the optical feedback dynamics in THz QCLs and semiconductor lasers in general.

Terahertz quantum cascade laser under optical feedback: effects of laser self-pulsations on self-mixing signals.

In this article, we explore the interplay between the self-pulsations (SPs) and self-mixing (SM) signals generated in terahertz (THz) quantum cascade lasers (QCLs) under optical feedback. We find that optical feedback dynamics in a THz QCL, namely, SPs, modulate the conventional SM interference fringes in a laser feedback interferometry system. The phenomenon of fringe loss in the SM signal - well known in interband diode lasers - was also observed along with pronounced SPs. With an increasing optical feedback strength, SM interference fringes transition from regular fringes at weak feedback (C ≤ 1) to fringes modulated by SPs under moderate feedback (1 < C ≤ 4.6), and then [under strong feedback (C > 4.6)] to a SM waveform with reduced number of fringes modulated by SP, until eventually (under even greater feedback) all the fringes are lost and only SPs are left visible. The transition route described above was identified in simulation when the SM fringes are created either by a moving target or a current modulation of the THz QCL. This SM signal transition route was successfully validated experimentally in a pulsed mode THz QCL with SM fringes created by current modulation during the pulse. The effects of SP dynamics in laser feedback interferometric system investigated in this work not only provides a further understanding of nonlinear dynamics in a THz QCL but also helps to understand the SM waveforms generated in a THz QCLs when they are used for various sensing and imaging applications.

Laser feedback interferometry in multi-mode terahertz quantum cascade lasers.

The typical modal characteristics arising during laser feedback interferometry (LFI) in multi-mode terahertz (THz) quantum cascade lasers (QCLs) are investigated in this work. To this end, a set of multi-mode reduced rate equations with gain saturation for a general Fabry-Pérot multi-mode THz QCL under optical feedback is developed. Depending on gain bandwidth of the laser and optical feedback level, three different operating regimes are identified, namely a single-mode regime, a multi-mode regime, and a tuneable-mode regime. When the laser operates in the single-mode and multi-mode regimes, the self-mixing signal amplitude (peak to peak value of the self-mixing fringes) is proportional to the feedback coupling rate at each mode frequency. However, this rule no longer holds when the laser enters into the tuneable-mode regime, in which the feedback level becomes sufficiently strong (the boundary value of the feedback level depends on the gain bandwidth). The mapping of the identified feedback regimes of the multi-mode THz QCL in the space of the gain bandwidth and feedback level is investigated. In addition, the dependence of the aforementioned mapping of these three regimes on the linewidth enhancement factor of the laser is also explored, which provides a systematic picture of the potential of LFI in multi-mode THz QCLs for spectroscopic sensing applications.

Author Correction: Ultrafast switch-on dynamics of frequency-tuneable semiconductor lasers.

The original version of this Article contained an error in the Acknowledgements, which incorrectly omitted the following: 'We also acknowledge support from the Australian Research Council's Discovery Projects Funding Scheme (Grant DP 160 103910).' This has been corrected in both the PDF and HTML versions of the Article.

Ultrafast switch-on dynamics of frequency-tuneable semiconductor lasers.

Single-mode frequency-tuneable semiconductor lasers based on monolithic integration of multiple cavity sections are important components, widely used in optical communications, photonic integrated circuits and other optical technologies. To date, investigations of the ultrafast switching processes in such lasers, essential to reduce frequency cross-talk, have been restricted to the observation of intensity switching over nanosecond-timescales. Here, we report coherent measurements of the ultrafast switch-on dynamics, mode competition and frequency selection in a monolithic frequency-tuneable laser using coherent time-domain sampling of the laser emission. This approach allows us to observe hopping between lasing modes on picosecond-timescales and the temporal evolution of transient multi-mode emission into steady-state single mode emission. The underlying physics is explained through a full multi-mode, temperature-dependent carrier and photon transport model. Our results show that the fundamental limit on the timescales of frequency-switching between competing modes varies with the underlying Vernier alignment of the laser cavity.

Multi-spectral terahertz sensing: proposal for a coupled-cavity quantum cascade laser based optical feedback interferometer.

We propose a laser feedback interferometer operating at multiple terahertz (THz) frequency bands by using a pulsed coupled-cavity THz quantum cascade laser (QCL) under optical feedback. A theoretical model that contains multi-mode reduced rate equations and thermal equations is presented, which captures the interplay between electro-optical, thermal, and feedback effects. By using the self-heating effect in both active and passive cavities, self-mixing signal responses at three different THz frequency bands are predicted. A multi-spectral laser feedback interferometry system based on such a coupled-cavity THz QCL will permit ultra-high-speed sensing and spectroscopic applications including material identification.

Optical sorting and cultivation of denitrifying anaerobic methane oxidation archaea.

Denitrifying anaerobic methane oxidizing (DAMO) microorganisms play an important role in the global carbon and nitrogen cycles as they are able to mediate methane oxidation using nitrite/nitrate under anoxic conditions. However, the physiological properties of DAMO microorganisms remain poorly understood, partially since the organisms are difficult to isolate or cultivate in pure culture and partially because of their long cultivation time. In this study, DAMO cell sorting has been conducted by integrating optical tweezers within enclosed microfluidic chips. This integrated cell sorting method has high purity, low infection rates, and causes no discernable harm to cell viability. The purity of the sorted cells was controlled by the microfluidic chip structure design and operation, while the cell viability was verified by imaging the cultured DAMO archaea after 420 days.

Fluorescence plasmonic enhancement of FITC labeled PS nanoparticles coupled to silver island films.

Optical properties of a fluorescence molecule can be drastically changed by surface plasmons excited in neighboring metallic nanostructures. Here we investigated the fluorescence enhancement behavior of fluorescein isothiocyanate (FITC) labeled polystyrene nanoparticles coupled to silver island films (SIFs) via a 15 nm polymethyl methacrylate separation layer theoretically and experimentally. Up to 24-fold fluorescence enhancement was experimentally achieved when the annealing time of the 25 nm Ag films was 50 min, which is in good agreement with the theoretical simulation result based on the finite-difference time-domain method. Furthermore, significant fluorescence spectral distortion on SIFs was also observed compared with samples on glass slides, which is sufficiently related to the scattering properties of SIFs and the lifetimes of FITC.

Comparison of T-matrix calculation methods for scattering by cylinders in optical tweezers.

The T-matrix method, or the T-matrix formulation of scattering, is a framework for mathematically describing the scattering properties of an object as a linear relationship between expansion coefficients of the incident and scattering fields in a basis of vector spherical wave functions (VSWFs). A variety of methods can be used to calculate the T-matrix. We explore the applicability of the extended boundary condition method (EBCM) and point matching (PM) method to calculate the T-matrix for scattering by cylinders in optical tweezers and hence the optical force acting on them. We compare both methods with the discrete-dipole approximation (DDA) to measure their accuracy for different sizes and aspect ratios (ARs) for Rayleigh and wavelength-size cylinders. We determine range of sizes and ARs giving errors below 1% and 10%. These results can help researchers choose the most efficient method to calculate the T-matrix for nonspherical particles with acceptable accuracy.

Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.

Maternal inheritance of mitochondrial genomes and complex inheritance of chloroplast genomes in Actinidia Lind.: evidences from interspecific crosses.

The inheritance pattern of chloroplast and mitochondria is a critical determinant in studying plant phylogenetics, biogeography and hybridization. To better understand chloroplast and mitochondrial inheritance patterns in Actinidia (traditionally called kiwifruit), we performed 11 artificial interspecific crosses and studied the ploidy levels, morphology, and sequence polymorphisms of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) of parents and progenies. Sequence analysis showed that the mtDNA haplotypes of F1 hybrids entirely matched those of the female parents, indicating strictly maternal inheritance of Actinidia mtDNA. However, the cpDNA haplotypes of F1 hybrids, which were predominantly derived from the male parent (9 crosses), could also originate from the mother (1 cross) or both parents (1 cross), demonstrating paternal, maternal, and biparental inheritance of Actinidia cpDNA. The inheritance patterns of the cpDNA in Actinidia hybrids differed according to the species and genotypes chosen to be the parents, rather than the ploidy levels of the parent selected. The multiple inheritance modes of Actinidia cpDNA contradicted the strictly paternal inheritance patterns observed in previous studies, and provided new insights into the use of cpDNA markers in studies of phylogenetics, biogeography and introgression in Actinidia and other angiosperms.

Development and characterization of 59 polymorphic cDNA-SSR markers for the edible oil crop Sesamum indicum (Pedaliaceae).

PREMISE OF THE STUDY: Polymorphic simple sequence repeat markers from transcript sequences (cDNA-simple sequence repeat [SSR]) were developed for the edible oil crop Sesamum indicum to facilitate the genetic study of this species. • METHODS AND RESULTS: We found 7702 SSR loci in the 60960 unigenes, and 1550 primer pairs were designed and synthesized. In total, 59 primer pairs showed polymorphism within 36 individuals; the number of alleles per locus ranged from two to four, and the expected and observed heterozygosity ranged from 0.05 to 0.74 and 0 to 0.30, respectively. • CONCLUSIONS: These polymorphic markers will greatly facilitate studies of the genetic structure of S. indicum populations as well as the identification and conservation of the species.

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.

BACKGROUND: Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development. RESULTS: Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 Arabidopsis genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions. CONCLUSIONS: This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.

[Phylogenetic analysis and detection of selective pressure on the CVNH domains].

Cyanovirin-N (CV-N) is a novel protein with broad-spectrum antiviral activity. Its homologs constitute a protein family known as CVNH (Cyanovirin-N homology), which possess the evolutionarily conserved anti-HIV (Human immunodeficiency virus) domain. In this study, more details about the patchy organism distribution of CVNH domain were explored by reconstructing gene trees. Duplicated CVNH sequences were also identified in a wide range of species including Aspergillus niger, Neosartorya fischeri NRRL 181, Penicillium chrysogenum Wisconsin 54-1255, Neurospora crassa, Cyanothece sp. PCC, and Ceratopteris richardii. Besides these findings, both the mechanistic and mechanistic-empirical combination (MEC) models were used to analyze the adaptive evolution of amino acid sites in the CVNH domain. Our results showed that: (1) neither model reveals significant sites undergoing positive selection; (2) purifying selection has played a dominant role during CVNH evolution; and (3) the MEC model better fits the CVNH data set. Furthermore, the ancestral branch leading to Cyanothece sp. PCC 7822 and 7424 were examined using "branch-specific" and "branch-site" models. Six positively selected sites (34L, 63L, 13H, 76C, 78K, and 80I) were identified on the branch.