title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=739 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Novel decorating behaviour of silk retreats in a challenging habitat link: https://peerj.com/articles/12839 last-modified: 2022-03-22 description: Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat. creator: Alfonso Aceves-Aparicio creator: Donald James McLean creator: Zoe Wild creator: Jutta M. Schneider creator: Marie E. Herberstein uri: https://doi.org/10.7717/peerj.12839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aceves-Aparicio et al. title: Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds link: https://peerj.com/articles/13051 last-modified: 2022-03-22 description: Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian–early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural model is comparable to modern tree ferns or cycads and adapted to have grown in light-deficient lower-storey (sub-) tropical forests, usually not exceeding 15 m in height. Apical meristematic growth dominated, whereas only minor secondary growth occurred during ontogenesis. The densely attached frond bases followed a 3/8 phyllotaxis and were most likely abscised shortly after becoming photosynthetically inactive. A high water-conducting potential is assumed due to the tree’s cauline, petiolar and leaf vascular anatomies. Concerning the extensive leaf surface of the densely foliated fronds, considerable transpiration is hypothesised. Alethopteris schneideri foliage is stratigraphically significant for lower Permian (Asselian–Sakmarian) continental strata of central Europe, preferring habitats of wet clastic soils in sub-humid, seasonal palaeoclimate. The new insights provide a substantial step towards the first whole-plant concept of intramontane medullosaleans. creator: Ludwig Luthardt creator: Mathias Merbitz creator: Evgeny Fridland creator: Ronny Rößler uri: https://doi.org/10.7717/peerj.13051 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Luthardt et al. title: Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability link: https://peerj.com/articles/13076 last-modified: 2022-03-22 description: BackgroundPhosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils.MethodsIn this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities.ResultsCompared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90–32, xj120–12, xj120–31, and xj180–22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120–12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains.ConclusionsThe results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains. creator: Qiuju Peng creator: Yang Xiao creator: Su Zhang creator: Changwei Zhou creator: Ailin Xie creator: Zhu Li creator: Aijuan Tan creator: Lihong Zhou creator: Yudan Xie creator: Jinyi Zhao creator: Chenglin Wu creator: Lei Luo creator: Jie Huang creator: Tengxia He creator: Ran Sun uri: https://doi.org/10.7717/peerj.13076 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Peng et al. title: E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces link: https://peerj.com/articles/13099 last-modified: 2022-03-22 description: BackgroundThe SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein.MethodsHence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions.ResultsThe results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds.DiscussionMolecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve. creator: Vitor Pimentel Dos Santos creator: André Rodrigues creator: Gabriel Dutra creator: Luana Bastos creator: Diego Mariano creator: José Gutembergue Mendonça creator: Yan Jerônimo Gomes Lobo creator: Eduardo Mendes creator: Giovana Maia creator: Karina dos Santos Machado creator: Adriano Velasque Werhli creator: Gerd Rocha creator: Leonardo Henrique França de Lima creator: Raquel de Melo-Minardi uri: https://doi.org/10.7717/peerj.13099 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Dos Santos et al. title: The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia link: https://peerj.com/articles/13132 last-modified: 2022-03-22 description: BackgroundIndonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics.ObjectivesWe aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia.MethodsNasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT).ResultsWe successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general.ConclusionsWe demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response. creator: Anggia Prasetyoputri creator: Anik B. Dharmayanthi creator: Syam B. Iryanto creator: Ade Andriani creator: Isa Nuryana creator: Andri Wardiana creator: Asep M. Ridwanuloh creator: Sri Swasthikawati creator: Hariyatun Hariyatun creator: Herjuno A. Nugroho creator: Idris Idris creator: Indriawati Indriawati creator: Zahra Noviana creator: Listiana Oktavia creator: Yuliawati Yuliawati creator: Masrukhin Masrukhin creator: Erwin F. Hasrianda creator: Linda Sukmarini creator: Fahrurrozi Fahrurrozi creator: Nova Dilla Yanthi creator: Alfi T. Fathurahman creator: Ari S. Wulandari creator: Ruby Setiawan creator: Syaiful Rizal creator: Ahmad Fathoni creator: Wien Kusharyoto creator: Puspita Lisdiyanti creator: Ratih A. Ningrum creator: Sugiyono Saputra uri: https://doi.org/10.7717/peerj.13132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Prasetyoputri et al. title: The prognostic and clinicopathological significance of desmoglein 2 in human cancers: a systematic review and meta-analysis link: https://peerj.com/articles/13141 last-modified: 2022-03-22 description: ObjectiveThe survival and clinicopathological significance of desmoglein 2 (DSG2) in various cancers is controversial. Thus, we performed this systematic review and meta-analysis to explore the preliminary prognostic value of DSG2.MethodsEligible studies were identified from databases including PubMed, the Cochrane Library, Embase, Web of Science and Scopus. Hand searches were also conducted in relevant bibliographies. We then extracted and pooled hazard ratio (HR) of overall survival (OS) and odds ratio (OR) of clinicopathological features.ResultsA total of 11 eligible studies containing 1,488 patients were included. Our results demonstrated that in non-small cell lung cancer (NSCLC), high DSG2 expression is associated with poor OS. However, in digestive system cancer and female reproductive system cancer, there were no statistically significant associations between OS and DSG2.ConclusionsBased on the findings of this study, high DSG2 expression is associated with worse prognosis in patients with NSCLC, and thus DSG2 expression could be a biomarker for prognosis in NSCLC. creator: Jiantao Wang creator: Siyuan Hao creator: Junjie Gu creator: Sean G. Rudd creator: Yan Wang uri: https://doi.org/10.7717/peerj.13141 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Bird protection treatments reduce bird-window collision risk at low-rise buildings within a Pacific coastal protected area link: https://peerj.com/articles/13142 last-modified: 2022-03-22 description: BackgroundIn North America, up to one billion birds are estimated to die annually due to collisions with glass. The transparent and reflective properties of glass present the illusion of a clear flight passage or continuous habitat. Approaches to reducing collision risk involve installing visual cues on glass that enable birds to perceive glass as a solid hazard at a sufficient distance to avoid it.MethodsWe monitored for bird-window collisions between 2013 and 2018 to measure response to bird protection window treatments at two low-rise buildings at the Alaksen National Wildlife Area in Delta, British Columbia, Canada. After 2 years of collision monitoring in an untreated state, we retrofitted one building with Feather Friendly® circular adhesive markers applied in a grid pattern across all windows, enabling a field-based assessment of the relative reduction in collisions in the 2 years of monitoring following treatment. An adjacent building that had been constructed with a bird protective UV-treated glass called ORNILUX® Mikado, was monitored throughout the two study periods. Carcass persistence trials were conducted to evaluate the likelihood that carcasses were missed due to carcass removal between scheduled searches.Results and ConclusionsAfter accounting for differences in area of glass between the two buildings, year, and observer effects, our best-fit model for explaining collision risk included the building’s treatment group, when compared to models that included building and season only. We found that the Feather Friendly® markers reduced collision risk at the retrofitted building by 95%. Collision incidence was also lower at the two monitored façades of the building with ORNILUX® glass compared to the building with untreated glass. Although more research is needed on the effectiveness of bird-protection products across a range of conditions, our results highlight the benefit of these products for reducing avian mortality due to collisions with glass. creator: Krista L. De Groot creator: Amy G. Wilson creator: René McKibbin creator: Sarah A. Hudson creator: Kimberly M. Dohms creator: Andrea R. Norris creator: Andrew C. Huang creator: Ivy B. J. Whitehorne creator: Kevin T. Fort creator: Christian Roy creator: Julie Bourque creator: Scott Wilson uri: https://doi.org/10.7717/peerj.13142 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 De Groot et al. title: Evaluation of change in trabecular bone structure surrounding dental implants by fractal dimension analysis and comparison with radiomorphometric indicators: a retrospective study link: https://peerj.com/articles/13145 last-modified: 2022-03-22 description: BackgroundThe trabecular bone surrounding dental implant show some structural changes during healing period. The purpose of this study is to observe the change in trabecular bone with fractal dimensional analysis from baseline to 3rd month of implant placement. It was also aimed to determine the correlation of fractal dimension (FD) change with morphometric indices, mandibular cortical index (MCI) and mandibular cortical width (MCW).MethodsDigital panoramic radiographs taken from 14 patients were evaluated in this study. A total of 30 implants which were placed on mandibular premolar or molar region were included. MCI and MCW assessments were made on baseline radiograph and FD were analyzed on baseline and 3rd month radiograph. FD change by time was recorded separately for every ROI. A paired sample t-test was used to evaluate the change between FD-baseline and FD-3rdmonth values. One-way ANOVA was used to determine the relationship between FD change and MCI. FD change and MCW measurements correlation was calculated by Pearson correlation analysisResultsFD value increased in 75 of 90 implant-adjacent regions evaluated in the 3rd month and it was observed that the FD values were statistically significantly increased in the mesial, distal and apical regions at the 3rd month measurements. There was no statistically significant relationship between mean FD change and MCI, and there was no correlation between mean FD change and MCW value.DiscussionThere are many studies evaluating the resorptive changes in bone. However, there are few studies investigating whether there is a correlation between pre- and post-operative trabecular pattern with MCI and MCW. The results of this study indicate that the implants have an improving effect on bone trabeculation in the region where they are placed. creator: Ilkim Karadag creator: Hasan Guney Yilmaz uri: https://doi.org/10.7717/peerj.13145 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Karadag and Yilmaz title: Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population link: https://peerj.com/articles/13149 last-modified: 2022-03-22 description: BackgroundDyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese.MethodsA total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method.ResultsWe found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese. creator: Prisca C. Limardi creator: Sukma Oktavianthi creator: Lidwina Priliani creator: Retno Lestari creator: Made Ratna Saraswati creator: Ketut Suastika creator: Safarina G. Malik uri: https://doi.org/10.7717/peerj.13149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Limardi et al. title: The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae) link: https://peerj.com/articles/13153 last-modified: 2022-03-22 description: The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges—followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene—the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus. creator: L. Lee Grismer creator: Nikolay A. Poyarkov creator: Evan S.H. Quah creator: Jesse L. Grismer creator: Perry L. Wood Jr uri: https://doi.org/10.7717/peerj.13153 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Grismer et al.