Bryum billardieri Schwaegr. against EV71 infection: in vitro and in vivo antiviral effects, identification of molecular mechanisms and active monomers.

Enterovirus 71 (EV71) commonly causes symptoms such as hand, foot, and mouth disease (HFMD) in infants and children and may lead to neurological disease and even death in severe cases. Appropriate vaccines for the prevention of HFMD are available in the clinic; however, they present different and serious adverse effects that cannot guarantee compliance and efficacy. The purpose of this study was to analyze the potential mechanism of Bryum billardieri Schwaegr. (BBS) against EV71 and analyze its potential active components. A previous in vitro antiviral assay was used to determine the best extraction method for the active site of BBS against EV71, and the results showed that the antiviral activity of BBS was more pronounced in the fraction that was extracted by aqueous extraction and alcoholic precipitation and then obtained by purification on a silica gel column (dichloromethane:methanol = 0:100). In addition, the therapeutic effects of BBS on EV71-infected mice were further investigated by in vivo pharmacological experiments. BBS reduced the lung index, viral titer, and degree of EV71-induced lung, brain, and skeletal muscle damage. The mechanism of anti-EV71 activity of BBS was also investigated by using ELISA and qRT-PCR, and it was found that BBS exerted its action mainly by regulating the expression of TLR3, TLR4, TNF-α, IL-2, and IFN-γ by modulating the activation of NF-κB and JAK2/STAT1 signaling pathways. Finally, the chemical structures of the active monomers in BBS were determined by using UPLC-MS and NMR techniques. The study revealed that one of the monomers on which BBS exerts its antiviral activity is saponarin. In conclusion, the results of this study suggest that BBS is considered a natural anti-EV71 product with enormous potential, and saponarin would be its non-negligible active monomer.

Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa.

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

Comparing three quantification methods on N/Si ratio analysis using electron energy loss spectroscopy (EELS).

Precision elemental analysis by EELS at a nano-meter scale is a desirable goal for industrial application, as well as basic scientific research on advanced material analysis. However, sample thickness variation leads to a systematic error in element quantification due to electron plural scattering events and prevents it to be a useful quantitative analytic method. In this paper, we compared three methods to minimize thickness effect: Fourier-log deconvolution, Jump ratio, and Si K-edge by quantifying the N/Si ratio versus different thickness on a standard Si3N4 crystal sample. The results indicated that Jump ratio method exceeded other two methods owing to its higher accuracy, short data acquisition time as well as minimum requirement for spectroscopy instrument. The jump ratio method was applied to calculate N/Si ratio in storage nitride layer of 3D NAND trench wafer and blanket wafer, both illustrated that the jump ratio method successfully corrected the thickness effect on EELS composition quantification and largely reduced the relative error compared with the non-corrected result.

Chamomile: A Review of Its Traditional Uses, Chemical Constituents, Pharmacological Activities and Quality Control Studies.

Matricaria chamomilla L. (MC) and Chamaemelum nobile (L.) All. (CN) are two varieties of Chamomile. These herbs have been used for thousands of years in Greece, Rome and ancient Egypt. Chamomile has been used for the treatment of stomach problems, cramps, dermatitis, and minor infections. The purpose of this study was to introduce the botanical characteristics and geographical distribution, traditional uses, chemical constituents, pharmacological activities, toxicity studies and quality control studies, and lay a theoretical foundation for the rational development and utilization of chamomile. This review powered that chemical constituents include flavonoids, coumarins, volatile oils, terpenes, organic acids, polysaccharides, and others. These compounds possess anticancer, anti-infective, anti-inflammatory, antithrombotic, antioxidant, hypolipidaemic, hypoglycaemic, antihypertensive, antidepressant, neuroprotective activities, among others. Chamomile is a widely used herb in traditional medicine. It brings great economic value due to its numerous pharmacological effects and traditional uses. However, more toxicity tests should be carried out to confirm its safety. There is need for further research to provide concrete scientific evidence and validate its medicinal properties.

Salvia plebeia R. Br. polysaccharides (SPP) against RSV (respiratory syncytial virus) infection: Antiviral effect and mechanisms of action.

OBJECTIVE: To investigate the antiviral effect of Salvia plebeia R. Br. polysaccharides (SPP) against RSV and underlying mechanisms. METHODS: SPP was extracted via alcohol-precipitation method and extract was separated into various fractions using ultrafiltration method. The polysaccharide content was determined using UV-Vis. Antiviral effect of SPP and fractions was measured using MTT method and Reed-Muench method. Sixty Balb/c mice were randomly divided into 6 groups, and received either Ribavirin or SPP. Their body weight and food intake were recorded every day throughout the experiment period. The lung index inhibition ratio and pulmonary virus titer were determined followed by the histological analysis of lungs. Furthermore, time-of-addition and effective stage analysis were carried out to determine the mechanism of action. The TLR-3 and TLR-4 levels in the lungs were determined using qRT-PCR. The levels of IFN-γ, IL-2 and TNF-α in serum were determined using ELISA. RESULTS: The SPP content is 4.396%. SPP has shown a good anti-RSV effect both in vitro (TI = 123.041) and in vivo models. The antiviral activity of fractions with molecular weight ≥ 10,000 is found to possess more potent antiviral activity than other fractions. SPP inhibits the RSV proliferation and reduces the lung lesions induced by RSV. The mechanism of action involves the inhibition of TLR-3 and TLR-4 in lungs, up-regulation of IFN-γ and IL-2, and down-regulation of TNF-α in serum. It is also shown to improve the body's immune function. CONCLUSION: SPP has a potential to treat diseases caused by RSV.

A method of using Si L-edge for O/Si and N/Si quantitative ratio analysis by electron energy loss spectroscopy (EELS).

In EELS core loss excitation, inverse jump ratio is defined as a ratio between intensity of a pre-core-loss-edge and a signal of the core loss excitation after background subtraction. A linear relationship between inverse jump ratio of Si L-edge and O/Si and N/Si intensity ratio is found for electron energy loss spectroscopy (EELS) analysis. This relationship is used to analyze O/Si and N/Si atomic ratio to quantify the elemental distribution in SiON films and the result is compared with XPS analysis on the same SiON films. The method is applied to blanket wafer elemental analysis and can be used for flash memory structure (3D NAND) to obtain atomic ratios of N/Si and O/Si for tunnel oxide at sub-nanometer scale.

Band gap measurement by nano-beam STEM with small off-axis angle transmission electron energy loss spectroscopy (TEELS).

An energy band gap measurement method based on nano-beam STEM with small off-axis angle valence band transmission electron energy loss spectroscopy (TEELS) is reported. The effect of multiple scattering event is removed by self-convolution method to obtain a single scattering loss function and a dielectric function is calculated from the single scattering valence band energy loss function through Kramers-Kronig (K-K) analysis. Optical band gaps are extracted from energy loss spectra and the imaginary part of the dielectric functions for crystalline and amorphous SiOx, SiNx, and SiON through linear fitting of on-set regions yielding results that are independent of sample thickness. The TEELS band gap data are consistent with those obtained from reflection electron energy loss spectroscopy (REELS) measurements.

DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria.

Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require both morphological diagnostics and molecular tools, such as DNA barcoding, for correct identification. In particular, the use of the subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding has proven useful in species identification for insects. However, to date, no studies have been carried out on the DNA barcoding of Nigerian butterflies. We evaluated the utility of DNA barcoding applied for the first time to 735 butterfly specimens from southern Nigeria. In total, 699 DNA barcodes, resulting in a record of 116 species belonging to 57 genera, were generated. Our study sample comprised 807 DNA barcodes based on sequences generated from our current study and 108 others retrieved from BOLD. Different molecular analyses, including genetic distance-based evaluation (Neighbor-Joining, Maximum Likelihood and Bayesian trees) and species delimitation tests (TaxonDNA, Automated Barcode Gap Discovery, General Mixed Yule-Coalescent, and Bayesian Poisson Tree Processes) were performed to accurately identify and delineate species. The genetic distance-based analyses resulted in 163 well-separated clusters consisting of 147 described and 16 unidentified species. Our findings indicate that about 90.20% of the butterfly species were explicitly discriminated using DNA barcodes. Also, our field collections reported the first country records of ten butterfly species-Acraea serena, Amauris cf. dannfelti, Aterica galena extensa, Axione tjoane rubescens, Charaxes galleyanus, Papilio lormieri lormeri, Pentila alba, Precis actia, Precis tugela, and Tagiades flesus. Further, DNA barcodes revealed a high mitochondrial intraspecific divergence of more than 3% in Bicyclus vulgaris vulgaris and Colotis evagore. Furthermore, our result revealed an overall high haplotype (gene) diversity (0.9764), suggesting that DNA barcoding can provide information at a population level for Nigerian butterflies. The present study confirms the efficiency of DNA barcoding for identifying butterflies from Nigeria. To gain a better understanding of regional variation in DNA barcodes of this biogeographically complex area, future work should expand the DNA barcode reference library to include all butterfly species from Nigeria as well as surrounding countries. Also, further studies, involving relevant genetic and eco-morphological datasets, are required to understand processes governing mitochondrial intraspecific divergences reported in some species complexes.

Are the Yellow and Red Marked Club-Tail Losaria coon the Same Species?

Losaria coon (Fabricius, 1793) is currently comprised of ten subspecies, which were originally described under two names, Papilio coon and P. doubledayi before 1909, when they were combined as one species. The main difference between them is the colour of abdomen and hindwing subterminal spots-yellow in coon and red in doubledayi. Wing morphology, male and female genitalia, and molecular evidence (DNA barcodes) were analysed for multiple subspecies of L. coon and three other Losaria species-rhodifer, neptunus, and palu. Our molecular data support the separation of L. coon and L. doubledayi stat. rev. as two distinct species, with L. rhodifer positioned between them in phylogenetic analyses. Wing morphology and genitalic structures also confirm the molecular conclusions. Our findings divide L. coon into two species occupying different geographic ranges: with L. coon restricted to southern Sumatra, Java, and Bawean Island, while L. doubledayi occurs widely in regions from North India to northern Sumatra, including Hainan and Nicobar Islands. Hence, future conservation efforts must reassess the status and threat factors of the two species to form updated strategies.

DNA Barcoding Silver Butter Catfish (Schilbe intermedius) Reveals Patterns of Mitochondrial Genetic Diversity Across African River Systems.

The silver butter catfish (Schilbe intermedius) is widely distributed across African river systems. To date, information on its mitochondrial genetic diversity, population structure, and historical demography are not well-established. Herein, we combined newly generated mitochondrial cytochrome c oxidase (COI) subunit I gene sequences with previously published COI sequences in the global databases to reconstruct its phylogeography, population genetic structure, and historical demography. Results from the mtDNA phylogeography and species delimitation tests (Cluster algorithm - Species Identifier, Automatic Barcode Gap Discovery and Poison Tree Process model) revealed that S. intermedius comprises at least seven geographically defined matrilines. Although the overall haplotype diversity of S. intermedius was high (h = 0.90), results showed that East (Kenya) and West (Nigeria) African populations had low levels of haplotype diversity (h = ~0.40). In addition, population genetic polymorphism and historical demographics showed that S. intermedius populations in both East and West Africa underwent severe contractions as a result of biogeographic influences. The patterns of genetic diversity and population structure were consistent with adaptive responses to historical biogeographic factors and contemporary environmental variations across African river systems. This is suggestive of the influence of historical biogeographic factors and climatic conditions on population divergence of S. intermedius across African river systems. Given our discovery of previously underappreciated diversity within S. intermedius, we recommend that this species be considered for increased conservation and management.

Antioxidation and active constituents analysis of flower residue of Rosa damascena.

Objective: To make full usage of resource and turn waste into treasure, the chemical constituents and bioactivity were firstly investigated on Damask rose (Rosa damascena) flower residue (DRFR). Methods: DPPH and ABTS experiments were applied to assess the antioxidant activity of DRFR. Then, column chromatography was used to purify compounds from an antioxidation extract (DRFR-A), and the chemical structure was identified using NMR. The total phenolic acid content was measured by Folin-Ciocalteu colorimetric method, and the content of gallic acid of the indicator ingredient was detected by HPLC. Results: DRFR-A was found to show a high activity both on DPPH (IC50: 2.760 µg/mL) and ABTS (IC50: 2.258 µg/mL) compared to positive control VC. Ten compounds were isolated and identified as quercetin (1), kaempferol (2), gallic acid (3), protocatechuic acid (4), pyrogallic acid (5), 2-phenylethyl 3,4,5-trihydroxybenzoate (6), methyl gallate (7), p-hydroxybenzoic acid (8), p-hydroxyphenethyl alcohol (9) and astragalin (10) from DRFR-A. Among them, pyrogallic acid, 2-phenylethyl-3, 4, 5-trihydroxybenzoate, p-hydroxybenzoic acid and p-hydroxyphenethyl alcohol are obtained from the plant for the first time. The content of total phenolic acids and gallic acid, main ingredient in DRFR-A was determined as 63.73% and 24.67%, respectively. Conclusion: This study provides a reliable data and lays the foundation for the development and utilization of rose residue, and hence for the full utilization of rose resources.

DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity.

This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.

Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos.

Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.

High-precision deformation mapping in finFET transistors with two nanometre spatial resolution by precession electron diffraction.

Precession electron diffraction has been used to systematically measure the deformation in Si/SiGe blanket films and patterned finFET test structures grown on silicon-on-insulator type wafers. Deformation maps have been obtained with a spatial resolution of 2.0 nm and a precision of ±0.025%. The measured deformation by precession diffraction for the blanket films has been validated by comparison to energy dispersive x-ray spectrometry, X-Ray diffraction, and finite element simulations. We show that although the blanket films remain biaxially strained, the patterned fin structures are fully relaxed in the crystallographic planes that have been investigated. We demonstrate that precession diffraction is a viable deformation mapping technique that can be used to provide useful studies of state-of-the-art electronic devices.

Diversity and human perceptions of bees (Hymenoptera: Apoidea) in Southeast Asian megacities.

Urbanization requires the conversion of natural land cover to cover with human-constructed elements and is considered a major threat to biodiversity. Bee populations, globally, are under threat; however, the effect of rapid urban expansion in Southeast Asia on bee diversity has not been investigated. Given the pressing issues of bee conservation and urbanization in Southeast Asia, coupled with complex factors surrounding human-bee coexistence, we investigated bee diversity and human perceptions of bees in four megacities. We sampled bees and conducted questionnaires at three different site types in each megacity: a botanical garden, central business district, and peripheral suburban areas. Overall, the mean species richness and abundance of bees were significantly higher in peripheral suburban areas than central business districts; however, there were no significant differences in the mean species richness and abundance between botanical gardens and peripheral suburban areas or botanical gardens and central business districts. Urban residents were unlikely to have seen bees but agreed that bees have a right to exist in their natural environment. Residents who did notice and interact with bees, even though being stung, were more likely to have positive opinions towards the presence of bees in cities.

DNA barcodes and species distribution models evaluate threats of global climate changes to genetic diversity: a case study from Nanorana parkeri (Anura: Dicroglossidae).

Anthropogenic global climate changes are one of the greatest threats to biodiversity. Distribution modeling can predict the effects of climate changes and potentially their effects on genetic diversity. DNA barcoding quickly identifies patterns of genetic diversity. As a case study, we use DNA barcodes and distribution models to predict threats under climate changes in the frog Nanorana parkeri, which is endemic to the Qinghai-Tibetan Plateau. Barcoding identifies major lineages W and E. Lineage W has a single origin in a refugium and Lineage E derives from three refugia. All refugia locate in river valleys and each greatly contributes to the current level of intraspecific genetic diversity. Species distribution models suggest that global climate changes will greatly influence N. parkeri, especially in the level of genetic diversity, because two former refugia will fail to provide suitable habitat. Our pipeline provides a novel application of DNA barcoding and has important implications for the conservation of biodiversity in southern areas of the Qinghai-Tibetan Plateau.