title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=591
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814
link: https://peerj.com/articles/14593
last-modified: 2023-01-03
description: Two new species of temporary ectoparasitic isopods, Rocinela excavatasp. nov. and Gnathia obtusispinasp. nov., are reported from the southern Islands of the Korean Peninsula. Rocinela excavatasp. nov. is distinguishable from its related species by the following characteristics: (1) laterally stepped rostrum; (2) separated eyes; (3) propodal blade having eight robust setae; and (4) merus having four or five blunt robust setae in pereopods 1–3. Gnathia obtusispinasp. nov. differs from its congeners by the combination of the following characteristics: (1) body covered with numerous tubercles and setae, (2) cephalon having tooth-like paraocular ornamentations; and (3) frontal border having two inferior frontolateral processes. These two new species are the 13thRocinela species and 19thGnathia species in the temperate Northern Pacific region, respectively. Discovery of these new species represents high species diversity of the genera Rocinela Leach, 1818 and Gnathia Leach, 1814 worldwide as well as in the Northern Pacific region. In addition, faunal diversity analysis on the members of both genera revealed that Rocinela species show high-latitude diversity whereas Gnathia species have low-latitude diversity.
creator: Sung Hoon Kim
creator: Jong Guk Kim
creator: Seong Myeong Yoon
uri: https://doi.org/10.7717/peerj.14593
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Kim et al.

title: Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines
link: https://peerj.com/articles/14617
last-modified: 2023-01-03
description: BackgroundBud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear.MethodsWhole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation.ResultsIn two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine.ConclusionOur results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
creator: Jianquan Huang
creator: Guan Zhang
creator: Yanhao Li
creator: Mingjie Lyu
creator: He Zhang
creator: Na Zhang
creator: Rui Chen
uri: https://doi.org/10.7717/peerj.14617
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Huang et al.

title: Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes
link: https://peerj.com/articles/14431
last-modified: 2022-12-22
description: BackgroundEndogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation.ResultsIn this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily.ConclusionsWith the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
creator: Melissa Calero-Layana
creator: Carmen López-Cruz
creator: Agustín Ocaña
creator: Eduardo Tejera
creator: Vinicio Armijos-Jaramillo
uri: https://doi.org/10.7717/peerj.14431
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Calero-Layana et al.

title: Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study
link: https://peerj.com/articles/14056
last-modified: 2022-12-21
description: BackgroundThe aim of this study is to identify echocardiographic predictors of transient left ventricle dysfunction after pulmonary valve balloon dilatation (PVBD), in neonates with pulmonary valve stenosis (PVS) and atresia with intact septum (PAIVS) at birth.MethodsThe study includes patients admitted at the Bambino Gesù Children Hospital from January 2012 to January 2017. Clinical, echocardiographic and cardiac catheterization data before and after PVBD were retrospectively analyzed.ResultsTwenty-nine infants were included in the study (21 male and eight female). The median age was 5.8 ± 7.1 days. Eight patients developed transient LV dysfunction (three PAIVS and five PVS) and comparing data before and after the procedure, there was no difference in right ventricle geometrical and functional parameters except for evidence of at least moderate pulmonary valve regurgitation after PVBD.ConclusionModerate to severe degree pulmonary valve regurgitation was significant associated to LV dysfunction (p < 0.05) in PVS and PAIVS patients.
creator: Carolina D’Anna
creator: Alessio Franceschini
creator: Micol Rebonato
creator: Paolo Ciliberti
creator: Claudia Esposito
creator: Roberto Formigari
creator: Maria Giulia Gagliardi
creator: Paolo Guccione
creator: Gianfranco Butera
creator: Lorenzo Galletti
creator: Marcello Chinali
uri: https://doi.org/10.7717/peerj.14056
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 D’Anna et al.

title: Modeling the response of Japanese quail to arginine intake
link: https://peerj.com/articles/14337
last-modified: 2022-12-21
description: BackgroundUnderstanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails.MethodsThe experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient.ResultsThe arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for the daily production of 11 g of egg and 180 g of BW was determined to be 304 mg/bird. The current study provides procedures that researchers can easily adopt.
creator: Manoela Sousa
creator: Michele Lima
creator: Rita Brito Vieira
creator: Jaqueline Pavanini
creator: Nelson José Peruzzi
creator: Erikson Raimundo
creator: Daniel Santos
creator: Edney Silva
uri: https://doi.org/10.7717/peerj.14337
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Sousa et al.

title: A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace
link: https://peerj.com/articles/14418
last-modified: 2022-12-21
description: Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel’s cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel’s cartilage to the order Ctenacanthiformes with reservations.
creator: Merle Greif
creator: Humberto G. Ferrón
creator: Christian Klug
uri: https://doi.org/10.7717/peerj.14418
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Greif et al.

title: Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis
link: https://peerj.com/articles/14513
last-modified: 2022-12-21
description: Background and AimsA microscopic image has been used in cell analysis for cell type identification and classification, cell counting and cell size measurement. Most previous research works are tedious, including detailed understanding and time-consuming. The scientists and researchers are seeking modern and automatic cell analysis approaches in line with the current in-demand technology.ObjectivesThis article provides a brief overview of a general cell and specific stem cell analysis approaches from the history of cell discovery up to the state-of-the-art approaches.MethodologyA content description of the literature study has been surveyed from specific manuscript databases using three review methods: manuscript identification, screening, and inclusion. This review methodology is based on Prism guidelines in searching for originality and novelty in studies concerning cell analysis.ResultsBy analysing generic cell and specific stem cell analysis approaches, current technology offers tremendous potential in assisting medical experts in performing cell analysis using a method that is less laborious, cost-effective, and reduces error rates.ConclusionThis review uncovers potential research gaps concerning generic cell and specific stem cell analysis. Thus, it could be a reference for developing automated cells analysis approaches using current technology such as artificial intelligence and deep learning.
creator: Nurul Syahira Mohamad Zamani
creator: Wan Mimi Diyana Wan Zaki
creator: Zariyantey Abd Hamid
creator: Aqilah Baseri Huddin
uri: https://doi.org/10.7717/peerj.14513
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Mohamad Zamani et al.

title: OPA1 supports mitochondrial dynamics and immune evasion to CD8+ T cell in lung adenocarcinoma
link: https://peerj.com/articles/14543
last-modified: 2022-12-21
description: BackgroundMitochondrial fusion and fission were identified to play key roles during multiple biology process. Thus, we aim to investigate the roles of OPA1 in mitochondria fusion and immune evasion of non-small cell lung cancer cells.MethodsThe transcriptional activation of genes related to mitochondrial dynamics was determined by using multi-omics data in lung adenocarcinoma (LUAD). We elucidated the molecular mechanism and roles of OPA1 promoting lung cancer through single-cell sequencing and molecular biological experiments.ResultsHere, we found that copy number amplification of OPA1 and MFN1 were co-occurring and synergistically activated in tumor epithelial cells in lung cancer tissues. Both of OPA1 and MFN1 were highly expressed in LUAD tumor tissues and OPA1 high expression was associated with poor prognosis. In terms of mechanism, the damaged mitochondria activated the apoptotic signaling pathways, inducing cell cycle arrest and cell apoptosis. More interestingly, OPA1 deficiency damaged mitochondrial dynamics and further blocked the respiratory function to increase the sensitivity of tumor epithelial to CD8+ T cells in non-small cell lung cancer.ConclusionsOur study demonstrated the high co-occurrence of copy number amplification and co-expression of OPA1 and MFN1 in LUAD tissue, and further revealed the contribution of OPA1 in maintaining the mitochondria respiratory function and the ability of immune evasion to CD8+ T cells of LUAD.
creator: Ying Wang
creator: Yadong Li
creator: Xuanwei Jiang
creator: Yayun Gu
creator: Hui Zheng
creator: Xiaoxuan Wang
creator: Haotian Zhang
creator: Jixiang Wu
creator: Yang Cheng
uri: https://doi.org/10.7717/peerj.14543
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: The diversity, evolution, and development of setal morphologies in bumble bees (Hymenoptera: Apidae: Bombus spp.)
link: https://peerj.com/articles/14555
last-modified: 2022-12-21
description: Bumble bees are characterized by their thick setal pile that imparts aposematic color patterns often used for species-level identification. Like all bees, the single-celled setae of bumble bees are branched, an innovation thought important for pollen collection. To date no studies have quantified the types of setal morphologies and their distribution on these bees, information that can facilitate understanding of their adaptive ecological function. This study defines several major setal morphotypes in the common eastern bumble bee Bombus impatiens Cresson, revealing these setal types differ by location across the body. The positions of these types of setae are similar across individuals, castes, and sexes within species. We analyzed the distribution of the two most common setal types (plumose and spinulate) across the body dorsum of half of the described bumble bee species. This revealed consistently high density of plumose (long-branched) setae across bumble bees on the head and mesosoma, but considerable variation in the amount of metasomal plumosity. Variation on the metasoma shows strong phylogenetic signal at subgeneric and smaller group levels, making it a useful trait for species delimitation research, and plumosity has increased from early Bombus ancestors. The distribution of these setal types suggests these setae may serve several functions, including pollen-collecting and thermoregulatory roles, and probable mechanosensory functions. This study further examines how and when setae of the pile develop, evidence for mechanosensory function, and the timing of pigmentation as a foundation for future genetic and developmental research in these bees.
creator: Heather M. Hines
creator: Shelby Kerrin Kilpatrick
creator: István Mikó
creator: Daniel Snellings
creator: Margarita M. López-Uribe
creator: Li Tian
uri: https://doi.org/10.7717/peerj.14555
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Hines et al.

title: Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing
link: https://peerj.com/articles/14567
last-modified: 2022-12-21
description: Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
creator: Julia Moll
creator: Björn Hoppe
uri: https://doi.org/10.7717/peerj.14567
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Moll and Hoppe