Adaptation of visual spectra and opsin genes in seabreams

AbstractThree species of seabreams, Acanthopagrus berda, Acanthopagrus schlegelii and Pagrus major, living at different depths, were chosen to investigate how visual spectra and opsin genes evolve in response to various photic environments. The λmax of photoreceptors and opsin genes were measured and cloned from these species. Eight to twelve nm spectral shifts in the rod and blue cone cells were observed between the deep-sea, P. major, and shallow-sea species, A. berda and A. schlegelii. Furthermore, the deep-sea P. major has lost its red light vision. Six opsin genes, Rh1, Rh2A, Rh2B, SWS1, SWS2 and LWS, were identified from all three seabream species, with the LWS genes of P. major having undergone pseudogenization. These data indicate that the photic environment of habitats select for the physiology of visual spectra and coding of opsin genes

Luminescent characteristics and mitochondrial COI barcodes of nine cohabitated Taiwanese fireflies

Background Over 50 Taiwanese firefly species have been discovered, but scientists lack information regarding most of their genetics, bioluminescent features, and cohabitating phenomena. In this study, we focus on morphological species identification and phylogeny reconstructed by COI barcoding, as well as luminescent characteristics of cohabited Taiwanese firefly species to determine the key factors that influenced how distinct bioluminescent species evolved to coexist and proliferate within the same habitat. Methods In this study, 366 specimens from nine species were collected in northern Taiwan from April to August, 2016–2019. First, the species and sex of the specimens were morphologically and genetically identified. Then, their luminescent spectra and intensities were recorded using a spectrometer and a power meter, respectively. The habitat temperature, relative humidity, and environmental light intensity were also measured. The cytochrome oxidase I (COI) gene sequence was used as a DNA barcode to reveal the phylogenetic relationships of cohabitated species. Results Nine species—eight adult species (Abscondita chinensis, Abscondita cerata, Aquatica ficta, Luciola curtithorax, Luciola kagiana, Luciola filiformis, Curtos sauteri, and Curtos costipennis) and one larval Pyrocoelia praetexta—were morphologically identified. The nine species could be found in April–August. Six of the eight adult species shared an overlap occurrence period in May. Luminescent spectra analysis revealed that the λmax of studied species ranged from 552–572 nm (yellow–green to orange–yellow). The average luminescent intensity range of these species was about 1.2–14 lux (182.1–2,048 nW/cm2) for males and 0.8–5.8 lux (122.8–850 nW/cm2) for females, and the maximum luminescent intensity of males was 1.01–7.26-fold higher than that of females. Compared with previous studies, this study demonstrates that different λmax, species-specific flash patterns, microhabitat choices, nocturnal activity time, and/or an isolated mating season are key factors that may lead to the species-specific courtship of cohabitated fireflies. Moreover, we estimated that the fireflies start flashing or flying when the environmental light intensity decreased to 6.49–28.1 lux. Thus, based on a rough theoretical calculation, the sensing distance between male and female fireflies might be 1.8–2.7 m apart in the dark. In addition, the mitochondrial COI barcode identified species with high resolution and suggested that most of the studied species have been placed correctly with congeners in previous phylogenies. Several cryptic species were revealed by the COI barcode with 3.27%–12.3% variation. This study renews the idea that fireflies’ luminescence color originated from the green color of a Lampyridae ancestor, then red-shifted to yellow-green in Luciolinae, and further changed to orange–yellow color in some derived species

Synthesis, Characterization and Photovoltaic Properties of Di-Anchoring Organic Dyes

Three new organic dyes comprising carbazole, iminodibenzyl and phenothiazine moieties, as electron donors and di-anchoring rhodanine rings as the electron acceptors, were synthesized and evaluated for use in dye-sensitized solar cells. A solar cell employing dye-containing phenothiazine as a hole-transporting unit and di-anchoring rhodanine rings as the electron acceptors exhibits a short circuit photocurrent density of 10.6 mA cm-2, an open-circuit voltage of 0.658 V and a fill factor of 0.7, corresponding to an overall conversion efficiency of 4.91% at standard AM 1.5 sunlight

Synthesis and Characterization of Organic Dyes Containing Various Donors and Acceptors

New organic dyes comprising carbazole, iminodibenzyl, or phenothiazine moieties, respectively, as the electron donors, and cyanoacetic acid or acrylic acid moieties as the electron acceptors/anchoring groups were synthesized and characterized. The influence of heteroatoms on carbazole, iminodibenzyl and phenothiazine donors, and cyano-substitution on the acid acceptor is evidenced by spectral, electrochemical, photovoltaic experiments, and density functional theory calculations. The phenothiazine dyes show solar-energy-to-electricity conversion efficiency (η) of 3.46–5.53%, whereas carbazole and iminodibenzyl dyes show η of 2.43% and 3.49%, respectively

A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples

A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. PyrosequencingTM has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The PyrosequencingTM pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences. Therefore, utilizing the pyrogram signals to identify de novo SNPs in DNA pools has never been undertook. Here, in this study we developed an algorithm to address this issue. With the sequence and pyrogram of the wild-type allele known in advance, we could use the pyrogram obtained from the pooled DNA sample to predict the sequence of the unknown mutant allele (de novo SNP) and estimate its allele frequency. Both computational simulation and experimental PyrosequencingTM test results suggested that our method performs well. The web interface of our method is available at http://life.nctu.edu.tw/∼yslin/PSM/

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

<p>Abstract</p> <p>Background</p> <p><it>Neocallimastix patriciarum</it> is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (<it>GHs</it>) produced by this anaerobic fungus.</p> <p>Results</p> <p>We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to <it>N. patriciarum </it>to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative <it>GH </it>contigs and classified them into 25 <it>GH</it> families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the <it>GH1</it>, <it>GH3</it>, <it>GH5</it>, <it>GH6</it>, <it>GH9</it>, <it>GH18</it>, <it>GH43 </it>and <it>GH48 </it>gene families, which were highly expressed in <it>N. patriciarum </it>cultures grown on different feedstocks.</p> <p>Conclusions</p> <p>These <it>GH </it>genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.</p

Physicochemical Properties of Glycine-Based Ionic Liquid [QuatGly-OEt][EtOSO3] (2-Ethoxy-1-ethyl-1,1-dimethyl-2-oxoethanaminium ethyl sulfate) and Its Binary Mixtures with Poly(ethylene glycol) (Mw = 200) at Various Temperatures

This work includes specific basic characterization of synthesized glycine-based Ionic Liquid (IL) [QuatGly-OEt][EtOSO3] by NMR, elementary analysis and water content. Thermophysical properties such as density, ρ, viscosity, η, refractive index, n, and conductivity, κ, for the binary mixture of [QuatGly-OEt][EtOSO3] with poly(ethylene glycol) (PEG) [Mw = 200] are measured over the whole composition range. The temperature dependence of density and dynamic viscosity for neat [QuatGly-OEt][EtOSO3] and its binary mixture can be described by an empirical polynomial equation and by the Vogel-Tammann-Fucher (VTF) equation, respectively. The thermal expansion coefficient of the ILs is ascertained using the experimental density results, and the excess volume expansivity is evaluated. The negative values of excess molar volume for the mixture indicate the ion-dipole interactions and packing between IL and PEG oligomer. The results of binary excess property (VmE ) and deviations (Δη, Δxn, ΔΨn, ΔxR, and ΔΨR) are discussed in terms of molecular interactions and molecular structures in the binary mixture

Conservation and Phylogeography of Taiwan Paradise Fish, Macropodus opercularis Linnaeus

The paradise fish (Macropodus opercularis) is naturally distributed in western Taiwan, but is rare now because of such factors as environment pollution & habitat loss. Conservation of this animal in Taiwan is becoming more urgent. Some closely related species, such as Chinese paradise fish (M. chinensis), are difficult to distinguish with morphological characters. We sequenced & compared the control region of mitochondrial DNA (mtDNA) to reveal the genetic distance & molecular phylogeny of paradise fish populations from different geographical regions: Taiwan, Singapore, & mainland China. The interspecific distance between M. opercularis (Taiwan, Singapore) & M. chinensis (Zhejiang, Jilin) is 0.1341 ±0.0124, much more highly divergent than the distance between the Taiwanese and Singaporean populations, or within the Chinese populations. Five haplotypes from 11 specimens of the Taiwanese native population have been identified from a 1034-bp-length of mtDNA. However, the lower haplotypic diversity (H = 0.68) indicates a decreasing population in Taiwan, in contrast with the M. chinensis (H = 0.89). In addition, the unique genotype in Miaoli & Taichung may imply their subdivision because of exotic input of fish from a different geographic region. Thus conservation work should focus on avoiding the random release of paradise fishes into the wild

Characterization of the complete mitochondrial genome of Abscondita cerata (Olivier, 1911) (Coleoptera: Lampyridae) and its phylogenetic implications

We sequenced and assembled the complete mitochondrial genome of Abscondita cerata from Nankang, Taipei City, Taiwan. The complete mitogenome of A. cerata is 16,964 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the A. cerata are A: 43.93%, T: 36.74%, C: 11.05%, and G: 8.28%. The AT and GC skewness of the mitogenome sequence are 0.0891 and −0.1434, showing the genome composition skewness toward adenine and cytosine. The clade including all Lampyridae species is well supported. The result indicates that Luciolinae is a monophyletic group but Lampyrinae is not a monophyletic group, as Lamprigera yunnana, which was originally classified into Lampyrinae, is sister to Luciolinae. The genus Lamprigera may share a unique phylogenetic position in Lampyridae. The genus Luciola is a polyphyletic group and the genus Abscondita is a monophyletic group. A. cerata is the sister species to A. chinensis in China. Mitogenomic data from this study will provide useful molecular markers for further studies on the population genetics, speciation, and conservation of endemic species A. cerata in Taiwan

Species-Specific Flash Patterns Track the Nocturnal Behavior of Sympatric Taiwanese Fireflies

It is highly challenging to evaluate the species’ content and behavior changes in wild fireflies, especially for a sympatric population. Here, the flash interval (FI) and flash duration (FD) of flying males from three sympatric species (Abscondita cerata, Luciola kagiana, and Luciola curtithorax) were investigated for their potentials in assessing species composition and nocturnal behaviors during the A. cerata mating season. Both FI and FD were quantified from the continuous flashes of adult fireflies (lasting 5–30 s) via spatiotemporal analyses of video recorded along the Genliao hiking trail in Taipei, Taiwan. Compared to FD patterns and flash colors, FI patterns exhibited the highest species specificity, making them a suitable reference for differentiating firefly species. Through the case study of a massive occurrence of A. cerata (21 April 2018), the species contents (~85% of the flying population) and active periods of a sympatric population comprising A. cerata and L. kagiana were successfully evaluated by FI pattern matching, as well as field specimen collections. Our study suggests that FI patterns may be a reliable species-specific luminous marker for monitoring the behavioral changes in a sympatric firefly population in the field, and has implication values for firefly conservation