Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular clocks. In this study, we investigate the utility of nonreversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. [Bootstrap; nonreversible models; phylogenetic inference; root estimation.].

Co-occurrence of phthalic acid esters (PAEs) and cyclic volatile methylsiloxanes (cVMSs) in fine particulate matter (PM0.5 and PM0.1) collected from an industrial area in Vietnam.

Distribution patterns of 10 phthalic acid diesters (PAEs) and four cyclic volatile methylsiloxanes (cVMSs) were investigated in fine particulate matter (PM0.1 and PM0.5) collected from Bac Ninh, an industrial province in Vietnam during September-October in 2021. Total concentrations of PAEs found in PM0.1 and PM0.5 were in the ranges of 1.76-372 (median: 34.0 ng/m3) and 2.23-895 ng/m3 (median: 15.4 ng/m3), respectively. Among PAEs, di-n-butyl phthalate (DBP) was the most abundant compound found in PM0.1, whereas, di-2-(ethyl)hexyl phthalate (DEHP) was measured at the highest concentration in PM0.5. Total concentrations of cVMSs measured in PM0.1 and PM0.5 were in the ranges of method quantification limit (MQL)-203 (median: 2.10 ng/m3) and MQL-537 ng/m3 (median: 0.389 ng/m3), respectively. Among cVMSs, decamethylcyclopentasiloxane (D5) was found at the highest concentration in both PM0.1 and PM0.5 fractions of particulate matter. The concentration ratios between PAEs and cVMSs in PM0.1/PM0.5 were greater than 1 (except di-n-octyl phthalate: DnOP), suggesting that these chemicals tend to sorb to PM0.1 more preferentially than PM0.5. Among sampling locations, high concentrations of PAEs and cVMSs were found at traffic intersections (Que Vo district) and a craft village (Tu Son city). Relatively stronger correlations existed between cVMSs pairs in PM0.1 and PM0.5 (correlation coefficient: 0.73-1) than those of PAEs (-0.83-0.90). The human exposure doses to PAEs and cVMSs through inhalation of particulate matter were estimated based on the measured concentrations in PM0.1 and PM0.5 fractions. The estimated exposure doses of PAEs and cVMSs for infants (7.1 ng/kg-bw/d and 2.5 ng/kg-bw/d) were higher than those for adults (2.6 ng/kg-bw/d and 0.9 ng/kg-bw/d).

Arsenate removal by layered double hydroxides embedded into spherical polymer beads: Batch and column studies.

In this study, the performance of poly(layered double hydroxides) [poly(LDHs)] beads as an adsorbent for arsenate removal from aqueous solution was investigated. The poly(LDHs) beads were prepared by immobilizing LDHs into spherical alginate/polyvinyl alcohol (PVA)-glutaraldehyde beads (spherical polymer beads). Batch adsorption studies were conducted to assess the effect of contact time, solution pH, initial arsenate concentrations and co-existing anions on arsenate removal performance. The potential reuse of these poly(LDHs) beads was also investigated. Approximately 79.1 to 91.2% of arsenic was removed from an arsenate solution (50 mg As L(-1)) by poly(LDHs). The adsorption data were well described by the pseudo-second-order kinetics model and the Langmuir isotherm model, and the adsorption capacities of these poly(LDHs) beads at pH 8 were from 1.64 to 1.73 mg As g(-1), as calculated from the Langmuir adsorption isotherm. The adsorption ability of the poly(LDHs) beads decreased by approximately 5-6% after 5 adsorption-desorption cycles. Phosphates markedly decreased arsenate removal. The effect of co-existing anions on the adsorption capacity declined in the following order: HPO4 (2-) >> HCO3 (-) > SO4 (2-) > Cl(-). A fixed-bed column study was conducted with real-life arsenic-containing water. The breakthrough time was found to be from 7 to 10 h. Under optimized conditions, the poly(LDHs) removed more than 82% of total arsenic. The results obtained in this study will be useful for further extending the adsorbents to the field scale or for designing pilot plants in future studies. From the viewpoint of environmental friendliness, the poly(LDHs) beads are a potential cost-effective adsorbent for arsenate removal in water treatment.

Inhibitory nitric oxide production and cytotoxic activities of phenolic compounds from Gnetum montanum Markgr.

One new compound, styrene dimer-type listeanol-4-O-α-ʟ-rhamnopyranosyl-(1→4)-ß-ᴅ-glucopyranoside (1), and four known compounds namely listeanol (2), isorhapotigenin (3), genetifolin E (4), gnetifolin K (5) were isolated from the methanolic extract from the aerial part of the Gnetum montanum Markgr. in Viet Nam. Their chemical structures were determined by modern spectroscopic methods (NMR and HR-ESI-MS) and comparison with those of published data. These compounds were evaluated for their anti-inflammatory and cytotoxic activities. Among them, compound 3 exhibited the NO inhibitory production on the RAW264.7 cell line, and inhibited the HepG2 cell line with respective IC50 values of 79.88 ± 5.51 (µg/mL) (L-NMMA 7.90 ± 0.63 µg/mL), and 63.48 ± 3.63 (µg/mL) (Ellipticine 0.40 ± 0.01 µg/mL).

Stigmastane-type steroid saponins from the leaves of Vernonia amygdalina and their α-glucosidase and xanthine oxidase inhibitory activities.

Two new vernonioside K (1) and vernonioside L (2) and four known Δ7,9(11) stigmastane-type steroidal saponins-vernonioside B2 (3), vernoniacum B (4), vernonioside B1 (5), and vernoamyoside A (6)-were isolated from the leaves of Vernonia amygdalina. Their structures were determined by comprehensive spectroscopic analysis with one-dimensional nuclear magnetic resonance, two-dimensional nuclear magnetic resonance, and high-resolution mass spectrometry. All isolated compounds (1-6) were evaluated to determine their inhibitory effects on α-glucosidase and xanthine oxidase. Among them, two new compounds 1 and 2 showed significant inhibition of α-glucosidase with IC50 values of 78.56 ± 7.28 and 14.74 ± 1.57 (µM), respectively, comparable with acarbose as a positive control (127.53 ± 1.73 µM); none of these compounds inhibited xanthine oxidase activity. Compounds 1 and 2 are promising candidates for the development of antidiabetic agents from natural sources.

Isolation, structural elucidation and molecular docking studies against SARS-CoV-2 main protease of new stigmastane-type steroidal glucosides isolated from the whole plants of Vernonia gratiosa.

Phytochemical investigation of the whole plants of Vernonia gratiosa Hance. led in the isolation and identification of two new stigmastane-type steroidal glucosides (1-2), namely vernogratiosides A (1), and B (2). Their chemical structures were fully elucidated based on 1 D/2D NMR spectroscopic, HR-ESI-MS data analyses, and by producing derivatives by chemical reactions. The binding potential of the isolated compounds to replicase protein - main protease of SARS-CoV-2 were examined using the molecular docking simulations. Our results show that the isolated steroidal glucosides (1-2) bind to the substrate-binding site of SARS-CoV-2 main protease with binding affinities of -7.2 and -7.6 kcal/mol, respectively, as well as binding abilities equivalent to N3 inhibitor that has already been reported (-7.5 kcal/mol).