Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and saponins all had bioactivity scores between −5.0 and 0.0 with respect to various receptor proteins and target enzymes. Solanidine, solasodine and solamargine had positive values of druglikeness which indicated that these compounds have the potential for development into future anticancer drugs. Toxicity potential evaluation revealed that glycoalkaloids and saponins had no toxicity, tumorigenicity or irritant effect(s). SAR analysis revealed that the number, type and location of sugar or the substitution of hydroxyl group on alkaloid backbone had an effect on the activity and that the presence of α-L-rhamnopyranose sugar at C-2 was critical for a compound to exhibit anticancer activity. Conclusion The present study revealed some cytoskeletal target(s) for S. nigrum phytoconstituents by docking analysis that have not been previously reported and thus warrant further investigations both in vitro and in vivo.
Ahmad (2019) Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis. PeerJ 7:e6012 https://doi.org/10.7717/peerj.6012
The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas
The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothesized island–mainland environmental differences (i.e., greater numbers of predators/competitors/environmental complexity on the mainland). Similarity between mainland and island anole radiations may indicate exceptional evolution in the anole clade overall or ordinary evolution in an extraordinarily studied clade.
Poe et al. (2019) The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas. PeerJ 6:e6040 https://doi.org/10.7717/peerj.6040
Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity
Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
Salas-Ovilla et al. (2019) Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity. PeerJ 7:e6102 https://doi.org/10.7717/peerj.6102
The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)
The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansion, likely related to sea-level and climatic oscillations during the Pleistocene, whereas the structure of the northern clade has probably been driven by dispersal through the Isthmus of Tehuantepec and isolation by the Motagua–Polochic–Jocotán fault system and the Mexican highlands.
Mendoza et al. (2019) The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae). PeerJ 7:e6115 https://doi.org/10.7717/peerj.6115
Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies
Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
Ondigo et al. (2019) Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies. PeerJ 7:e6120 https://doi.org/10.7717/peerj.6120
Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides
Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
Chen et al. (2019) Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 7:e6122 https://doi.org/10.7717/peerj.6122
Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.
The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
Rekulapally et al. (2019) Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.. PeerJ 6:e6138 https://doi.org/10.7717/peerj.6138
Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
Catanach et al. (2019) Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 7:e6142 https://doi.org/10.7717/peerj.6142
Otolith microchemistry and diadromy in Patagonian river fishes
Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
Alò et al. (2019) Otolith microchemistry and diadromy in Patagonian river fishes. PeerJ 7:e6149 https://doi.org/10.7717/peerj.6149
Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
Roncero-Ramos et al. (2019) Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 7:e6169 https://doi.org/10.7717/peerj.6169