title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=686 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Telomere-to-telomere genome assembly of Phaeodactylum tricornutum link: https://peerj.com/articles/13607 last-modified: 2022-07-05 description: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes. creator: Daniel J. Giguere creator: Alexander T. Bahcheli creator: Samuel S. Slattery creator: Rushali R. Patel creator: Tyler S. Browne creator: Martin Flatley creator: Bogumil J. Karas creator: David R. Edgell creator: Gregory B. Gloor uri: https://doi.org/10.7717/peerj.13607 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Giguere et al. title: Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity link: https://peerj.com/articles/13626 last-modified: 2022-07-05 description: BackgroundInterleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue.MethodsTo prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations.ResultsIL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future. creator: Jirakrit Saetang creator: Niran Roongsawang creator: Surasak Sangkhathat creator: Supayang Piyawan Voravuthikunchai creator: Natnaree Sangkaew creator: Napat Prompat creator: Teerapol Srichana creator: Varomyalin Tipmanee uri: https://doi.org/10.7717/peerj.13626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Saetang et al. title: Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2 link: https://peerj.com/articles/13680 last-modified: 2022-07-05 description: BackgroundThe COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions.MethodsTo gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant.ResultsThough mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface. creator: Priya Antony creator: Amie Jobe creator: Ranjit Vijayan uri: https://doi.org/10.7717/peerj.13680 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Antony et al. title: The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents link: https://peerj.com/articles/13687 last-modified: 2022-07-05 description: BackgroundExtensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents.MethodsThe data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms.ResultsThe obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience.DiscussionOur results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression. creator: Akihiro Masuyama creator: Takahiro Kubo creator: Hiroki Shinkawa creator: Daichi Sugawara uri: https://doi.org/10.7717/peerj.13687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Masuyama et al. title: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus link: https://peerj.com/articles/13689 last-modified: 2022-07-05 description: BackgroundCyclocarya 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.MethodsA 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.ResultsThe 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.ConclusionsLeaves 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). creator: Zhaokui Du creator: Weida Lin creator: Jinxing Zhu creator: Junmin Li uri: https://doi.org/10.7717/peerj.13689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Du et al. title: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area link: https://peerj.com/articles/13690 last-modified: 2022-07-05 description: 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. creator: Mauricio Heredia-Pech creator: Mariana Chávez-Pesqueira creator: Matilde M. Ortiz-García creator: Rubén Humberto Andueza-Noh creator: María Isabel Chacón-Sánchez creator: Jaime Martínez-Castillo uri: https://doi.org/10.7717/peerj.13690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Heredia-Pech et al. title: Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) link: https://peerj.com/articles/13491 last-modified: 2022-07-04 description: BackgroundWRKY (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.ResultsA 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.ConclusionsWe 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. creator: Zhenfan Yu creator: Dongdong Zhang creator: Bin Zeng creator: Xingyue Liu creator: Jiahui Yang creator: Wenwen Gao creator: Xintong Ma uri: https://doi.org/10.7717/peerj.13491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al. title: Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations link: https://peerj.com/articles/13575 last-modified: 2022-07-04 description: 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. creator: Fidji Berio creator: Yann Bayle creator: Daniel Baum creator: Nicolas Goudemand creator: Mélanie Debiais-Thibaud uri: https://doi.org/10.7717/peerj.13575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Berio et al. title: Sea urchins: an update on their pharmacological properties link: https://peerj.com/articles/13606 last-modified: 2022-07-04 description: 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. creator: Dulce María Moreno-García creator: Monica Salas-Rojas creator: Eduardo Fernández-Martínez creator: Ma del Rocío López-Cuellar creator: Carolina G. Sosa-Gutierrez creator: Armando Peláez-Acero creator: Nallely Rivero-Perez creator: Adrian Zaragoza-Bastida creator: Deyanira Ojeda-Ramírez uri: https://doi.org/10.7717/peerj.13606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Moreno-García et al. title: The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species link: https://peerj.com/articles/13624 last-modified: 2022-07-04 description: BackgroundIce-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.MethodsSamples 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.ResultsThe 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. creator: Natalia Kochman-Kędziora creator: Teresa Noga creator: Maria Olech creator: Bart Van de Vijver uri: https://doi.org/10.7717/peerj.13624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kochman-Kędziora et al.