title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=293 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identifying the source rookery of green turtles (Chelonia mydas) found in feeding grounds around the Korean Peninsula link: https://peerj.com/articles/17560 last-modified: 2024-06-20 description: Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation. creator: Min-Woo Park creator: Il-Hun Kim creator: Jaejin Park creator: Changho Yi creator: Min-Seop Kim creator: In-Young Cho creator: Il-Kook Park creator: Hee-Jin Noh creator: Sang Hee Hong creator: Daesik Park uri: https://doi.org/10.7717/peerj.17560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al. title: VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19 link: https://peerj.com/articles/17504 last-modified: 2024-06-19 description: BackgroundThe development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low.MethodsHere, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE.ResultsA variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%.ConclusionsTherefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges. creator: Danusorn Lee creator: Unitsa Sangket uri: https://doi.org/10.7717/peerj.17504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lee and Sangket title: A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae) link: https://peerj.com/articles/17592 last-modified: 2024-06-19 description: The fossil record of true seals (Family Phocidae) is mostly made up of isolated bones, some of which are type specimens. Previous studies have sought to increase referral of non-overlapping and unrelated fossils to these taxa using the ‘Ecomorphotype Hypothesis’, which stipulates that certain differences in morphology between taxa represent adaptations to differing ecology. On this basis, bulk fossil material could be lumped to a specific ecomorphotype, and then referred to species in that ecomorphotype, even if they are different bones. This qualitative and subjective method has been used often to expand the taxonomy of fossil phocids, but has never been quantitatively tested. We test the proposed ecomorphotypes using morphometric analysis of fossil and extant northern true seal limb bones, specifically principal components analysis and discriminant function analysis. A large amount of morphological overlap between ecomorphotypes, and poor discrimination between them, suggests that the ‘Ecomorphotype Hypothesis’ is not a valid approach. Further, the analysis failed to assign fossils to ecomorphotypes designated in previous studies, with some fossils from the same taxa being designated as different ecomorphotypes. The failure of this approach suggests that all fossils referred using this method should be considered to have unknown taxonomic status. In light of this, and previous findings that phocid limb bones have limited utility as type specimens, we revise the status of named fossil phocid species. We conclude that the majority of named fossil phocid taxa should be considered nomina dubia. creator: James Patrick Rule creator: Gustavo Burin creator: Travis Park uri: https://doi.org/10.7717/peerj.17592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rule et al. title: The role of monocyte chemoattractant protein-1 (MCP-1) as an immunological marker for patients with leprosy: a systematic literature review link: https://peerj.com/articles/17400 last-modified: 2024-06-18 description: Leprosy, a significant global health concern affecting primarily the peripheral nerves and integumentary system, is influenced by the host immune system’s response, affecting its pathology, disease progression, and reaction occurrence. MCP-1, integral to leprosy’s immunological processes, holds promise as a diagnostic tool and predictor of reaction occurrence. This systematic review aimed to investigate MCP-1’s involvement in leprosy. Literature search, employing specified MeSH keywords, covered databases such as PubMed, Scopus, ScienceDirect, and Wiley Online Library until September 30th, 2023, yielding seventeen relevant studies. Assessing each study’s quality with the Newcastle-Ottawa Scale (NOS) and investigating bias using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), a narrative synthesis compiled findings. Seventeen distinct studies were included, each characterized by diverse designs, sample sizes, demographics, and outcome measures, highlighting MCP-1’s potential in diagnosing leprosy, differentiating it from control groups, and discerning leprosy types. Furthermore, MCP-1 shows promise in predicting leprosy reversal reactions. Although MCP-1 offers clinical benefits, including early diagnosis and type differentiation, further research with larger sample sizes and standardized methodologies is imperative to confirm its diagnostic utility fully. creator: Flora Ramona Sigit Prakoeswa creator: Ellen Josephine Handoko creator: Erika Diana Risanti creator: Nabila Haningtyas creator: Nasrurrofiq Risvana Bayu Pambudi creator: Muhana Fawwazy Ilyas uri: https://doi.org/10.7717/peerj.17400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Prakoeswa et al. title: Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer link: https://peerj.com/articles/17419 last-modified: 2024-06-18 description: BackgroundBreast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA.MethodsCuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the ‘limma’ package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines.ResultsThirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A.ConclusionTaken together, we constructed a signature for projecting the overall survival of BRCA patients and our findings authenticated the cuproptosis-relevant prognostic genes, which are expected to provide a basis for developing prognostic molecular biomarkers and an in-depth understanding of the relationship between cuproptosis and BRCA. creator: Xiang Chen creator: Hening Sun creator: Changcheng Yang creator: Wei Wang creator: Wenzhi Lyu creator: Kejian Zou creator: Fan Zhang creator: Zhijun Dai creator: Xionghui He creator: Huaying Dong uri: https://doi.org/10.7717/peerj.17419 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Chen et al. title: Serum proteomics study on cognitive impairment after cardiac valve replacement surgery: a prospective observational study link: https://peerj.com/articles/17536 last-modified: 2024-06-18 description: ObjectiveThe incidence of perioperative neurocognitive disorders (PND) is high, especially after cardiac surgeries, and the underlying mechanisms remain elusive. Here, we conducted a prospective observational study to observe serum proteomics differences in PND patients after cardiac valve replacement surgery.MethodsTwo hundred and twenty-six patients who underwent cardiac valve surgery were included. They were categorized based on scoring into non-PND group (group non-P) and PND group (group P’). The risk factors associated with PND were analyzed. These patients were further divided into group C and group P by propensity score matching (PSM) to investigate the serum proteome related to the PND by serum proteomics.ResultsThe postoperative 6-week incidence of PND was 16.8%. Risk factors for PND include age, chronic illness, sufentanil dosage, and time of cardiopulmonary bypass (CPB). Proteomics identified 31 down-regulated proteins and six up-regulated proteins. Finally, GSTO1, IDH1, CAT, and PFN1 were found to be associated with PND.ConclusionThe occurrence of PND can impact some oxidative stress proteins. This study provided data for future studies about PND to general anaesthesia and surgeries. creator: Huanhuan Ma creator: Yiyong Wei creator: Wei Chen creator: Song Chen creator: Yan Wang creator: Song Cao creator: Haiying Wang uri: https://doi.org/10.7717/peerj.17536 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ma et al. title: Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato link: https://peerj.com/articles/17537 last-modified: 2024-06-18 description: The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants. creator: Hui Li creator: Tingrui Zou creator: Shuisen Chen creator: Ming Zhong uri: https://doi.org/10.7717/peerj.17537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis link: https://peerj.com/articles/17542 last-modified: 2024-06-18 description: BackgroundSepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis.MethodsGene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the “limma” R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes.ResultsBy WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e − 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Correlations between immune cells and these five key genes were assessed, revealing that plasma cells, macrophages M0, monocytes, T cells regulatory, eosinophils and NK cells resting were simultaneously and significantly associated with more than two key genes.ConclusionThis study suggests a critical role of LTF, LCN2, ELANE, MPO and CEACAM8 in sepsis and may provide potential diagnostic biomarkers and therapeutic targets for the treatment of sepsis. creator: Guoxin Lin creator: Nannan Li creator: Jishi Liu creator: Jian Sun creator: Hao Zhang creator: Ming Gui creator: Youjie Zeng creator: Juan Tang uri: https://doi.org/10.7717/peerj.17542 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Behavioral responses of a clonal fish to perceived predation risk link: https://peerj.com/articles/17547 last-modified: 2024-06-18 description: Predation threat is a major driver of behavior in many prey species. Animals can recognize their relative risk of predation based on cues in the environment, including visual and/or chemical cues released by a predator or from its prey. When threat of predation is high, prey often respond by altering their behavior to reduce their probability of detection and/or capture. Here, we test how a clonal fish, the Amazon molly (Poecilia formosa), behaviorally responds to predation cues. We measured aggressive and social behaviors both under ‘risk’, where chemical cues from predatory fish and injured conspecifics were present, and control contexts (no risk cues present). We predicted that mollies would exhibit reduced aggression towards a simulated intruder and increased sociability under risk contexts as aggression might increase their visibility to a predator and shoaling should decrease their chance of capture through the dilution effect. As predicted, we found that Amazon mollies spent more time with a conspecific when risk cues were present, however they did not reduce their aggression. This highlights the general result of the ‘safety in numbers’ behavioral response that many small shoaling species exhibit, including these clonal fish, which suggests that mollies may view this response as a more effective anti-predator response compared to limiting their detectability by reducing aggressive conspecific interactions. creator: Jonathan Aguiñaga creator: Sophia Jin creator: Ishita Pesati creator: Kate L. Laskowski uri: https://doi.org/10.7717/peerj.17547 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Aguiñaga et al. title: Knowledge, attitudes, and practices (KAPs) regarding tick-borne rickettsial disease among medical staff in endemic areas of China link: https://peerj.com/articles/17562 last-modified: 2024-06-18 description: Tick-borne rickettsial disease (TBRD) is a perilous acute infection that often eludes diagnosis in its early stages. The triad of knowledge, attitudes, and practices (KAPs) among medical professionals is key to reducing missed diagnosis rates. Therefore, a meticulous evaluation of KAPs is imperative. This study aimed to delve into the understanding of TBRD and explore the beliefs and practices related to personal prevention methods among individuals in Lu’an, a hotspot for TBRD. During the summer months of 2023, convenience sampling was employed by circulating a confidential questionnaire to 1,206 participants in the endemic regions of China. This questionnaire painted a comprehensive picture of the participants’ sociodemographic profiles and their KAPs levels vis-à-vis TBRD. The findings revealed that participants scored a mere 55.78% in knowledge, while their attitudes and practices garnered impressive scores of 90.09% and 90.83%, respectively. Upon further analysis using multiple linear regression, several intriguing patterns emerged. Male participants, employed in the Infectious Disease Department, held vice-senior or higher titles, or had prior medical training demonstrated superior knowledge scores. On the other hand, medical personnel who were younger than 30, possessed graduate degrees or higher qualifications, and had training excelled in attitudes and practices. Notably, when employing the Boston Consulting Group (BCG) matrix, a significant distribution of medical personnel was observed across the four quadrants. Specifically, 37.43%, 13.19%, 19.61%, and 29.77% fell into the first, second, third, and fourth quadrants. This survey underscores the commendable attitudes and practices of medical staff towards TBRD in endemic regions of China. However, their knowledge level remains wanting and demands urgent improvement. creator: Miaohui Shao creator: Peiyuan Hu creator: Pengpeng Xu creator: Jie Sun creator: Xiaqing Zhang creator: Dan Zhang creator: Yong Shen creator: Dawei Gao creator: Weigang Zhang creator: Wei Qin creator: Yong Lyu uri: https://doi.org/10.7717/peerj.17562 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shao et al.