Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
Du et al. (2022) Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 10:e13689 https://doi.org/10.7717/peerj.13689
Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could be reflecting historical events.
Heredia-Pech et al. (2022) Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ 10:e13690 https://doi.org/10.7717/peerj.13690
Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
Yu et al. (2022) Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis). PeerJ 10:e13491 https://doi.org/10.7717/peerj.13491
Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
Berio et al. (2022) Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations. PeerJ 10:e13575 https://doi.org/10.7717/peerj.13575
Sea urchins: an update on their pharmacological properties
Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
Moreno-García et al. (2022) Sea urchins: an update on their pharmacological properties. PeerJ 10:e13606 https://doi.org/10.7717/peerj.13606
The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species
Background Ice-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce. Methods Samples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages. Results The disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
Kochman-Kędziora et al. (2022) The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species. PeerJ 10:e13624 https://doi.org/10.7717/peerj.13624
Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland
Excrement-shaped ferruginous masses have been recovered from the Miocene of Turów mine in south-western Poland. These siderite masses have been the subject of much controversy, having been interpreted either as being coprolites, cololithes or pseudofossils created by mechanical deformation of plastic sediment. Here we present the results of mineralogical, geochemical, petrographic and microtomographical analyses. Our data indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a fecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the presence of rare hair-like structures or coalified inclusions and (iii) the presence of rare fine striations on the surface. Importantly, comparative actualistic study of recent vertebrate feces shows overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas. Other potential producers (such as lizards and crocodiles) and even abiotic origins cannot be fully excluded but are less likely.
Brachaniec et al. (2022) Comparative actualistic study hints at origins of alleged Miocene coprolites of Poland. PeerJ 10:e13652 https://doi.org/10.7717/peerj.13652
Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation
Background Curcumin is an active compound derived from turmeric, Curcuma longa, and is known for its benefits to human health. The amoebicidal activity of curcumin against Acanthamoeba triangularis was recently discovered. However, a physiological change of intracellular pathways related to A. triangularis encystation mechanism, including autophagy in the surviving amoeba after curcumin treatment, has never been reported. This study aims to investigate the effect of curcumin on the survival of A. triangularis under nutrient starvation and nutrient-rich condition, as well as to evaluate the A. triangularis encystation and a physiological change of Acanthamoeba autophagy at the mRNA level. Methods In this study, A. triangularis amoebas were treated with a sublethal dose of curcumin under nutrient starvation and nutrient-rich condition and the surviving amoebas was investigated. Cysts formation and vacuolization were examined by microscopy and transcriptional expression of autophagy-related genes and other encystation-related genes were evaluated by real-time PCR. Results A. triangularis cysts were formed under nutrient starvation. However, in the presence of the autophagy inhibitor, 3-methyladenine (3-MA), the percentage of cysts was significantly reduced. Interestingly, in the presence of curcumin, most of the parasites remained in the trophozoite stage in both the starvation and nutrient-rich condition. In vacuolization analysis, the percentage of amoebas with enlarged vacuole was increased upon starvation. However, the percentage was significantly declined in the presence of curcumin and 3-MA. Molecular analysis of A. triangularis autophagy-related (ATG) genes showed that the mRNA expression of the ATG genes, ATG3, ATG8b, ATG12, ATG16, under the starvation with curcumin was at a basal level along the treatment. The results were similar to those of the curcumin-treated amoebas under a nutrient-rich condition, except AcATG16 which increased later. On the other hand, mRNA expression of encystation-related genes, cellulose synthase and serine proteinase, remained unchanged during the first 18 h, but significantly increased at 24 h post treatment. Conclusion Curcumin inhibits cyst formation in surviving trophozoites, which may result from its effect on mRNA expression of key Acanthamoeba ATG-related genes. However, further investigation into the mechanism of curcumin in A. triangularis trophozoites arrest and its association with autophagy or other encystation-related pathways is needed to support the future use of curcumin.
Boonhok et al. (2022) Curcumin effect on Acanthamoeba triangularis encystation under nutrient starvation. PeerJ 10:e13657 https://doi.org/10.7717/peerj.13657
Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.
Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, “MEblue” and “MEblack,” were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.
Yan et al. (2022) Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L.. PeerJ 10:e13659 https://doi.org/10.7717/peerj.13659
What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors
Artificial refuges provided by householders and/or conservation practitioners potentially represent one mechanism for mitigating declines in the availability of natural nest sites used for resting, breeding and hibernating in urban areas. The effectiveness of such refuges for different species is, however, not always known. In this study, we conducted a questionnaire survey of UK householders to identify factors associated with the use of ground-level nest boxes for West European hedgehogs (Erinaceus europaeus), a species of conservation concern. Overall, the percentage of boxes used at least once varied with season and type of use: summer day nesting (35.5–81.3%), breeding (7.2–28.2%), winter day nesting (20.1–66.5%) and hibernation (21.7–58.6%). The length of time the box had been deployed, the availability of artificial food and front garden to back garden access significantly increased the likelihood that a nest box had been used for all four nesting types, whereas other factors related to placement within the garden (e.g., in a sheltered location, on hardstanding such as paving, distance from the house) and resource provisioning (bedding) affected only some nesting behaviours. The factors most strongly associated with nest box use were the provisioning of food and bedding. These data suggest, therefore, that householders can adopt simple practices to increase the likelihood of their nest box being used. However, one significant limitation evident within these data is that, for welfare reasons, householders do not routinely monitor whether their box has been used. Consequently, future studies need to adopt strategies which enable householders to monitor their boxes continuously. Ultimately, such studies should compare the survival rates and reproductive success of hedgehogs within artificial refuges versus more natural nest sites, and whether these are affected by, for example, the impact of nest box design and placement on predation risk and internal microclimate.
Gazzard et al. (2022) What makes a house a home? Nest box use by West European hedgehogs (Erinaceus europaeus) is influenced by nest box placement, resource provisioning and site-based factors. PeerJ 10:e13662 https://doi.org/10.7717/peerj.13662