Comparison of grouper infection with two different iridoviruses using transcriptome sequencing and multiple reference species selection.

Due to high-density aquafarming in Taiwan, groupers are commonly infected with two different iridoviruses: Megalocytivirus (grouper iridovirus of Taiwan, TGIV) and Ranavirus (grouper iridovirus, GIV). Iridoviral diseases cause mass mortality, and surviving fish retain these pathogens, which can then be horizontally transferred. These viruses have therefore become a major challenge for grouper aquaculture. In this study, comparisons of the biological responses of groupers to infection with these two different iridoviruses were performed. A novel approach for transcriptomic analysis was proposed to enhance the discovery of differentially expressed genes and associated biological pathways. In this method, suitable and available reference species are selected from the NCBI taxonomy tree and the Ensembl and KEGG databases instead of either choosing only one model species or adopting the NCBI non-redundant dataset as references. Our results show that selection of multiple appropriate model species as references increases the efficiency and performance of analyses compared to those of traditional approaches. Using this method, 17 shared pathways and 5 specific pathways were found to be significantly differentially expressed following infection with the two iridoviruses, among which 11 pathways were additionally identified based on the proposed method of multiple reference species selection. Among the pathways responsive to infection with a specific iridovirus, the spliceosomal pathway (ko03040; p-value = 0.0011) was exclusively associated with TGIV infection, while the glycolysis/gluconeogenesis pathway (ko00010; p-value = 0.0032) was associated with GIV infection. These findings and designed corresponding biological experiments may facilitate a deeper understanding of the mechanisms by which both TGIV and GIV cause fatal infections, as well as the ways in which they induce different pathologies and symptoms. We believe that the proposed novel mechanism for de novo transcriptomic analysis provides superior and comprehensive functional annotations and that the resulting shared and specific pathways identified may help immunologists develop specific vaccines against various types of iridovirus in the near future.

Antenna coupled photonic wire lasers.

Slope efficiency (SE) is an important performance metric for lasers. In conventional semiconductor lasers, SE can be optimized by careful designs of the facet (or the modulation for DFB lasers) dimension and surface. However, photonic wire lasers intrinsically suffer low SE due to their deep sub-wavelength emitting facets. Inspired by microwave engineering techniques, we show a novel method to extract power from wire lasers using monolithically integrated antennas. These integrated antennas significantly increase the effective radiation area, and consequently enhance the power extraction efficiency. When applied to wire lasers at THz frequency, we achieved the highest single-side slope efficiency (~450 mW/A) in pulsed mode for DFB lasers at 4 THz and a ~4x increase in output power at 3 THz compared with a similar structure without antennas. This work demonstrates the versatility of incorporating microwave engineering techniques into laser designs, enabling significant performance enhancements.

Effective mode selector for tunable terahertz wire lasers.

We demonstrate an effective mode selector design that enables a terahertz quantum cascade wire laser to have a robust single-mode operation at frequencies much lower than the gain peak. This is achieved by selectively guiding the undesired modes into a lossy session while keeping the desired lasing mode largely unperturbed. The large mode discrimination obtained by this mode selector is necessary to further extend the tuning range to the lower half of the gain curve. Additionally, the connectors of this mode selector conveniently provide electrical bias to the wire lasers without degrading the lasing performance.

Terahertz tomography using quantum-cascade lasers.

The interfaces of a dielectric sample are resolved in reflection geometry using light from a frequency agile array of terahertz quantum-cascade lasers. The terahertz source is a 10-element linear array of third-order distributed-feedback QCLs emitting at discrete frequencies from 2.08 to 2.4 THz. Emission from the array is collimated and sent through a Michelson interferometer, with the sample placed in one of the arms. Interference signals collected at each frequency are used to reconstruct an interferogram and detect the interfaces in the sample. Because of the long coherence length of the source, the interferometer arms need not be adjusted to the zero-path delay. A depth resolution of 360 µm in the dielectric is achieved with further potential improvement through improved frequency coverage of the array. The entire experiment footprint is <1 m × 1 m with the source operated in a compact, closed-cycle cryocooler.

Perfectly phase-matched third-order distributed feedback terahertz quantum-cascade lasers.

We report a novel laser cavity design in third-order distributed feedback (DFB) terahertz quantum-cascade lasers based on a perfectly phase-matching technique. This approach substantially increases the usable length of the third-order DFB laser and leads to narrow beam patterns. Single frequency emissions from 151 apertures (5.6 mm long device) are coherently added up to form a narrow beam with (FWHM≈6×11°) divergence. A similar device with 40 apertures shows more than 5 mW of optical power with slope efficiency ∼140 mW/A at 10 K pulsed operation.