title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1017
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The use of artificial substrate units to improve inventories of cryptic crustacean species on Caribbean coral reefs
link: https://peerj.com/articles/10389
last-modified: 2020-11-23
description: Motile cryptofauna inhabiting coral reefs are complex assemblages that utilize the space available among dead coral stands and the surrounding coral rubble substrate. They comprise a group of organisms largely overlooked in biodiversity estimates because they are hard to collect and identify, and their collection causes disturbance that is unsustainable in light of widespread reef degradation. Artificial substrate units (ASUs) provide a better sampling alternative and have the potential to enhance biodiversity estimates. The present study examines the effectiveness of ASUs made with defaunated coral rubble to estimate the diversity of motile cryptic crustaceans in the back-reef zone of the Puerto Morelos Reef National Park, Mexico. Species richness, Simpson’s diversity index, Shannon–Wiener index and the composition of assemblages were compared between ASUs and samples from the surrounding coral rubble substrate. A combined total of 2,740 specimens of 178 different species, belonging to five orders of Crustacea (Amphipoda, Cumacea, Isopoda, Tanaidacea and Decapoda) were collected. Species richness was higher in the surrounding coral rubble and Shannon–Wiener and Simpson indexes were higher in ASUs. Species composition differed between methods, with only 71 species being shared among sampling methods. Decapoda was more speciose in ASUs and Peracarids in the surrounding coral rubble. Combining the use of ASUs with surrounding rubble provided a better inventory of motile cryptic crustacean biodiversity, as 65% of the species were represented by one or two specimens.
creator: Luz Verónica Monroy-Velázquez
creator: Rosa E. Rodríguez-Martínez
creator: Paul Blanchon
creator: Fernando Alvarez
uri: https://doi.org/10.7717/peerj.10389
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Monroy-Velázquez et al.

title: Sensation of the tiniest kind: the antennal sensilla of the smallest free-living insect Scydosella musawasensis (Coleoptera: Ptiliidae)
link: https://peerj.com/articles/10401
last-modified: 2020-11-23
description: Miniaturization is a major evolutionary trend prominent in insects, which has resulted in the existence of insects comparable in size to some unicellular protists. The adaptation of the complex antennal multisensory systems to extreme miniaturization is a fascinating problem, which remains almost unexplored. We studied the antennal sensilla of Scydosella musawasensisHall, 1999 (Coleoptera: Ptiliidae), the smallest free-living insect, using scanning electron microscopy. The antenna of S. musawasensis bears 131 sensilla; no intraspecific variation in the number or position of the sensilla has been revealed. Nine different morphological types of sensilla are described according to their external morphological features and distribution: four types of sensilla trichodea, one type of sensilla chaetica, two types of sensilla styloconica, and two types of sensilla basiconica. Morphometric analysis of the sensilla of S. musawasensis, based on measurements of the lengths and diameters of sensilla and their location and number, showed the absence of significant differences between females and males. Comparative allometric analysis of S. musawasensis and larger Coleoptera showed that the number of sensilla and the size of sensilla chaetica decrease with decreasing body size. However, the number of the types of sensilla and the length and diameter of the multiporous sensilla basiconica revealed no correlation with the body size. Comparison of the acquired data with the results of our earlier study of the antennal sensilla of some of the smallest parasitic wasps is used to put forward hypotheses on the common principles of miniaturization of the antennal sensory systems of insects.
creator: Anna V. Diakova
creator: Alexey A. Polilov
uri: https://doi.org/10.7717/peerj.10401
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Diakova and Polilov

title: Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis
link: https://peerj.com/articles/10419
last-modified: 2020-11-23
description: BackgroundPancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC.MethodsThe microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website.ResultsA total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype–Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracellular matrix, and calcium ion binding, respectively. The KEGG pathway analysis showed that the 20 hub genes were mainly enriched in ECM–receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and protein digestion and absorption. These findings indicated that FBN1 and COL8A1 appear to be involved in the progression of PDAC. Moreover, patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the expression levels of COL12A1 and MMP14 were correlated with a poor prognosis in PDAC patients (p < 0.05).ConclusionsThe results demonstrated that upregulation of MMP14 and COL12A1 is associated with poor overall survival, and these might be a combination of prognostic biomarkers in PDAC.
creator: Jingyi Ding
creator: Yanxi Liu
creator: Yu Lai
uri: https://doi.org/10.7717/peerj.10419
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Ding et al.

title: A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems
link: https://peerj.com/articles/10428
last-modified: 2020-11-23
description: Restoration of agricultural drylands globally, here farmlands and grazing lands, is a priority for ecosystem function and biodiversity preservation. Natural areas in drylands are recognized as biodiversity hotspots and face continued human impacts. Global water shortages are driving increased agricultural land retirement providing the opportunity to reclaim some of these lands for natural habitat. We used meta-analysis to contrast different classes of dryland restoration practices. All interventions were categorized as active and passive for the analyses of efficacy in dryland agricultural ecosystems. We evaluated the impact of 19 specific restoration practices from 42 studies on soil, plant, animal, and general habitat targets across 16 countries, for a total of 1,427 independent observations. Passive vegetation restoration and grazing exclusion led to net positive restoration outcomes. Passive restoration practices were more variable and less effective than active restoration practices. Furthermore, passive soil restoration led to net negative restoration outcomes. Active restoration practices consistently led to positive outcomes for soil, plant, and habitat targets. Water supplementation was the most effective restoration practice. These findings suggest that active interventions are necessary and critical in most instances for dryland agricultural ecosystems likely because of severe anthropogenic pressures and concurrent environmental stressors—both past and present.
creator: M. Florencia Miguel
creator: H. Scott Butterfield
creator: Christopher J. Lortie
uri: https://doi.org/10.7717/peerj.10428
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Miguel et al.

title: Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana
link: https://peerj.com/articles/10256
last-modified: 2020-11-20
description: Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.
creator: Lauren K. Hudson
creator: Lisha Constantine-Renna
creator: Linda Thomas
creator: Christina Moore
creator: Xiaorong Qian
creator: Katie Garman
creator: John R. Dunn
creator: Thomas G. Denes
uri: https://doi.org/10.7717/peerj.10256
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Hudson et al.

title: Morph-specific seasonal variation of aggressive behaviour in a polymorphic lizard species
link: https://peerj.com/articles/10268
last-modified: 2020-11-20
description: The persistence of colour polymorphism (CP) within a given population is generally associated with the coexistence of alternative reproductive strategies, each one involving specific trade-offs among behavioural, morphological, physiological, and other life histories. Common wall lizard (Podarcis muralis), is a medium-sized diurnal lizard, showing CP in three main colours (yellow, white, and red) on throat and belly, and a morph-specific pattern for both immunocompetence and seasonal variation of T levels. Yellow males show low stamina with high plasma T levels at the beginning of the season, while white males show high stamina with a higher plasma T levels at the end of the season. We hypothesised the presence of two strategies: a risky one, characterised by high aggressiveness played by yellow-morph, and a conservative one by white morph with low aggressiveness. Thus, we tested the aggressive response to conspecifics of yellow and white morphs using a mirror inserted into their cage, mimicking an intrusion of a stranger in their territories, throughout the breeding season (from April to July, 117 trials). We considered three types of aggressive response, with different levels of aggressiveness: (i) bite against the image reflected in the mirror, (ii) seconds spent by the individuals into the half mirrored cage, and (iii) number of times the lizard entered the half mirrored cage. We also considered the number of tongue flicking as explorative behaviour variable. All lizards were tested after a period of acclimatisation to the captivity conditions. Results demonstrate that yellow males showed a higher aggressive response in the early season and a decrease aggressive response towards the end, whereas white males showed an opposite pattern.
creator: Alan Jioele Coladonato
creator: Marco Mangiacotti
creator: Stefano Scali
creator: Marco A. L. Zuffi
creator: Carlotta Pasquariello
creator: Cristian Matellini
creator: Simone Buratti
creator: Mara Battaiola
creator: Roberto Sacchi
uri: https://doi.org/10.7717/peerj.10268
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Coladonato et al.

title: Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses
link: https://peerj.com/articles/10269
last-modified: 2020-11-20
description: BackgroundHost response diffuse large B-cell lymphoma (HR DLBCL) shares features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities, frequent splenic and bone marrow involvement, and younger age at presentation. HR DLBCL is inherently less responsive to the standard treatment for DLBCL. Moreover, the mechanism of infiltration of HR DLBCL with preexisting abundant T-cells and dendritic cells is unknown, and their associated underlying immune responses incompletely defined. Here, hub genes and pathogenesis associated with HR DLBCL were explored to reveal molecular mechanisms and treatment targets.MethodsDifferentially expressed genes were identified in three datasets (GSE25638, GSE44337, GSE56315). The expression profile of the genes in the GSE53786 dataset was used to constructed a co-expression network. Protein-protein interactions analysis in the modules of interest identified candidate hub genes. Then screening of real hub genes was carried out by survival analysis within the GSE53786 and GSE10846 datasets. Expression of hub genes was validated in the Gene expression profiling interactive analysis, Oncomine databases and human tissue specimens. Functional enrichment analysis and Gene set enrichment analysis were utilized to investigate the potential mechanisms. Tumor Immune Estimation Resource and The Cancer Genome Atlas were used to mine the association of the hub gene with tumor immunity, potential upstream regulators were predicted using bioinformatics tools.ResultsA total of 274 common differentially expressed genes were identified. Within the key module, we identified CXCL10 as a real hub gene. The validation of upregulated expression level of CXCL10 was consistent with our study. CXCL10 might have a regulatory effect on tumor immunity. The predicted miRNA (hsa-mir-6849-3p) and transcription factor (IRF9) might regulate gene expression in the hub module.
creator: Lingna Zhou
creator: Liya Ding
creator: Yuqi Gong
creator: Jing Zhao
creator: Gong Xin
creator: Ren Zhou
creator: Wei Zhang
uri: https://doi.org/10.7717/peerj.10269
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Zhou et al.

title: The cranial morphology of Tanystropheus hydroides (Tanystropheidae, Archosauromorpha) as revealed by synchrotron microtomography
link: https://peerj.com/articles/10299
last-modified: 2020-11-20
description: The postcranial morphology of the extremely long-necked Tanystropheus hydroides is well-known, but observations of skull morphology were previously limited due to compression of the known specimens. Here we provide a detailed description of the skull of PIMUZ T 2790, including a partial endocast and endosseous labyrinth, based on synchrotron microtomographic data, and compare its morphology to that of other early Archosauromorpha. In many features, such as the wide and flattened snout and the configuration of the temporal and palatal regions, Tanystropheus hydroides differs strongly from other early archosauromorphs. The braincase possesses a combination of derived archosaur traits, such as the presence of a laterosphenoid and the ossification of the lateral wall of the braincase, but also differs from archosauriforms in the morphology of the ventral ramus of the opisthotic, the horizontal orientation of the parabasisphenoid, and the absence of a clearly defined crista prootica. Tanystropheus hydroides was a ram-feeder that likely caught its prey through a laterally directed snapping bite. Although the cranial morphology of other archosauromorph lineages is relatively well-represented, the skulls of most tanystropheid taxa remain poorly understood due to compressed and often fragmentary specimens. The recent descriptions of the skulls of Macrocnemus bassanii and now Tanystropheus hydroides reveal a large cranial disparity in the clade, reflecting wide ecological diversity, and highlighting the importance of non-archosauriform Archosauromorpha to both terrestrial and aquatic ecosystems during the Triassic.
creator: Stephan N.F. Spiekman
creator: James M. Neenan
creator: Nicholas C. Fraser
creator: Vincent Fernandez
creator: Olivier Rieppel
creator: Stefania Nosotti
creator: Torsten M. Scheyer
uri: https://doi.org/10.7717/peerj.10299
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Spiekman et al.

title: Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions
link: https://peerj.com/articles/10357
last-modified: 2020-11-20
description: Ongoing anthropogenic climate change alters the local climatic conditions to which species may be adapted. Information on species’ climatic requirements and their intraspecific variation is necessary for predicting the effects of climate change on biodiversity. We used a climatic gradient to test whether populations of two allopatric varieties of an arctic seashore herb (Primula nutans ssp. finmarchica) show adaptation to their local climates and how a future warmer climate may affect them. Our experimental set-up combined a reciprocal translocation within the distribution range of the species with an experiment testing the performance of the sampled populations in warmer climatic conditions south of their range. We monitored survival, size, and flowering over four growing seasons as measures of performance and, thus, proxies of fitness. We found that both varieties performed better in experimental gardens towards the north. Interestingly, highest up in the north, the southern variety outperformed the northern one. Supported by weather data, this suggests that the climatic optima of both varieties have moved at least partly outside their current range. Further warming would make the current environments of both varieties even less suitable. We conclude that Primula nutans ssp. finmarchica is already suffering from adaptational lag due to climate change, and that further warming may increase this maladaptation, especially for the northern variety. The study also highlights that it is not sufficient to run only reciprocal translocation experiments. Climate change is already shifting the optimum conditions for many species and adaptation needs also to be tested outside the current range of the focal taxon in order to include both historic conditions and future conditions.
creator: Maria Hällfors
creator: Susanna Lehvävirta
creator: Tone Aandahl
creator: Iida-Maria Lehtimäki
creator: Lars Ola Nilsson
creator: Anna Ruotsalainen
creator: Leif E. Schulman
creator: Marko T. Hyvärinen
uri: https://doi.org/10.7717/peerj.10357
license: https://creativecommons.org/licenses/by-nc/4.0
rights: ©2020 Hällfors et al.

title: Genome-wide identification and analysis of the thiolase family in insects
link: https://peerj.com/articles/10393
last-modified: 2020-11-20
description: Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases.
creator: Shou-Min Fang
uri: https://doi.org/10.7717/peerj.10393
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Fang