title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=488 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants link: https://peerj.com/articles/15696 last-modified: 2023-07-11 description: Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants. creator: So Youn Won creator: Prabhakaran Soundararajan creator: Vadivelmurugan Irulappan creator: Jung Sun Kim uri: https://doi.org/10.7717/peerj.15696 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Won et al. title: Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China link: https://peerj.com/articles/15462 last-modified: 2023-07-10 description: The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases. creator: Yaru Zhao creator: Dulan Bao creator: Ying Sun creator: Yajie Meng creator: Ziteng Li creator: Rui Liu creator: Jiwei Lang creator: Li Liu creator: Li Gao uri: https://doi.org/10.7717/peerj.15462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Is retroflexion a stable cue for distributional learning for speech sounds across languages? Learning for some bilingual adults, but not generalisable to a wider population in a well powered pre-registered study link: https://peerj.com/articles/15467 last-modified: 2023-07-10 description: Bilinguals are widely reported to have certain kinds of cognitive advantages, including language learning advantages. One possible pathway is a language-specific transfer effect, whereby sensitivity to structural regularities in known languages can be brought to to-be-acquired languages that share particular features. Here we tested for transfer of a specific linguistic property, sensitivity to retroflexion as contrastive phonemic feature. We designed a task for bilinguals with homogeneous language exposure (i.e., bilingual in the same languages) and heterogeneous feature representation (i.e., differing levels of proficiency). Hindi and Mandarin Chinese both have retroflexion in phoneme contrasts (Hindi: stop consonants, Mandarin: sibilants). In a preregistered study, we conducted a statistical learning task for the Hindi dental-retroflex stop contrast with a group of early parallel English-Mandarin bilinguals, who varied in their Mandarin understanding levels. We based the target sample size on power analysis of a pilot study with a Bayesian stop-rule after minimum threshold. Contrary to the pilot study (N = 15), the main study (N = 50) did not find evidence for a learning effect, nor language-experience variance within the group. This finding suggests that statistical effects for the feature in question may be more fragile than commonly assumed, and may be evident in only a small subsample of the general population (as in our pilot). These stimuli have previously shown learning effects in children, so an additional possibility is that neural commitment to adults’ languages prevents learning of the fine-grained stimulus contrast in question for this adult population. creator: Hannah L. Goh creator: Luca Onnis creator: Suzy J. Styles uri: https://doi.org/10.7717/peerj.15467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Goh et al. title: Perceptions of the impact of COVID-19 in Tennessee, USA: a retrospective study link: https://peerj.com/articles/15473 last-modified: 2023-07-10 description: BackgroundDespite high incidence and mortality risks associated with COVID-19 during the pandemic, stay-at-home orders and vaccination recommendations were met with varying levels of acceptance in Tennessee. Understanding perceptions of individuals regarding the health and economic impacts of COVID-19 is necessary to address public concerns while ensuring appropriate public health response. Therefore, the objectives of this study were to (a) investigate differences in opinions among residents of Tennessee regarding the impacts of COVID-19; and (b) identify socioeconomic and demographic predictors/determinants of these opinions.MethodsThis retrospective cross-sectional study was conducted using survey data collected in nine waves during 2020. Distributions of survey-weighted sociodemographic characteristics and respondent perceptions of the impact of COVID-19 were computed. Weighted logistic models were used to investigate predictors of a number of perceptions: whether the health or economic impact was greater, concern for respondent’s health, concern for family’s health, and willingness to accept COVID-19 vaccine.ResultsThe study included a total of 9,754 survey respondents. Approximately equal percentages considered COVID-19 to have a greater economic (48.4%) versus health impact (51.6%). Just 40.1% of the respondents reported that they would definitely accept a COVID-19 vaccine. Age group, race, educational attainment, and household composition were significant (p < 0.05) predictors of all investigated perceptions regarding COVID-19. Lack of prior infection was the strongest predictor of the perception of COVID-19 having a greater impact on health (OR = 2.40, p < 0.001), concern for respondent’s health (OR = 1.86, p = 0.002), and concern for family members’ health (OR = 1.90, p = 0.001). Compared to males, females had higher odds of identifying the health impact of COVID-19 as greater (OR = 1.09, p = 0.041) and reporting concern for family health (OR = 1.14, p = 0.003). However, they had lower odds (OR = 0.63, p < 0.001) of willingness to accept vaccine than males.ConclusionThese findings improve our understanding of the drivers of health behaviors, including vaccine hesitancy, and are useful for guiding public health outreach/education programs. creator: Tamara L. Chavez-Lindell creator: Katie A. Cahill creator: Kristina W. Kintziger creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.15473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chavez-Lindell et al. title: Psychological flexibility, cognitive emotion regulation and mental health outcomes among patients with asthma in Pakistan link: https://peerj.com/articles/15506 last-modified: 2023-07-10 description: Background/ObjectiveAdults with asthma who experience difficulties in emotion regulation are prone to developing psychopathological symptoms that may affect their self-management activities and symptom control. The current research investigated the role of psychological flexibility and cognitive emotion regulation strategies in relation to mental health outcomes (psychological distress and quality of life) among patients with asthma in Pakistan.MethodA sample of 200 adults, diagnosed with asthma (32% men, 68% women; Mage = 42.32, SDage = 16.99), completed the acceptance and action questionnaire (AAQ-II) cognitive emotion regulation questionnaire (CERQ), depression, anxiety, stress scale-21 (DASS-21), asthma-related quality of life questionnaire (AQLQ) and a self-structured demographic sheet.ResultsResults of Pearson product moment correlation showed that most of the adaptive cognitive emotion regulation strategies (positive refocusing, refocus on planning, and positive reappraisal) were positively correlated with psychological flexibility and quality of life, whereas negatively correlated with psychological distress. All the maladaptive strategies of cognitive emotion regulation had a significant inverse relationship with psychological flexibility and quality of life, while positively correlated with psychological distress. Results of serial mediation analysis through PROCESS MACRO showed that catastrophising and anxiety fully mediated the relationship between psychological flexibility and asthma-related quality of life.ConclusionEvidence-based interventions should focus on developing psychological flexibility and identifying maladaptive patterns of cognitive emotion regulation strategies for improved mental health and quality of life outcomes for adults with asthma. creator: Samavia Hussain creator: Rabia Khawar creator: Rizwana Amin creator: Asma Hamdani creator: Asma Majeed uri: https://doi.org/10.7717/peerj.15506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hussain et al. title: A comparison of survey method efficiencies for estimating densities of zebra mussels (Dreissena polymorpha) link: https://peerj.com/articles/15528 last-modified: 2023-07-10 description: Abundance surveys are commonly used to estimate plant or animal densities and frequently require estimating detection probabilities to account for imperfect detection. The estimation of detection probabilities requires additional measurements that take time, potentially reducing the efficiency of the survey when applied to high-density populations. We conducted quadrat, removal, and distance surveys of zebra mussels (Dreissena polymorpha) in three central Minnesota lakes and determined how much survey effort would be required to achieve a pre-specified level of precision for each abundance estimator, allowing us to directly compare survey design efficiencies across a range of conditions. We found that the required sampling effort needed to achieve our precision goal depended on both the survey design and population density. At low densities, survey designs that could cover large areas but with lower detection probabilities, such as distance surveys, were more efficient (i.e., required less sampling effort to achieve the same level of precision). However, at high densities, quadrat surveys, which tend to cover less area but with high detection rates, were more efficient. These results demonstrate that the best survey design is likely to be context-specific, requiring some prior knowledge of the underlying population density and the cost/time needed to collect additional information for estimating detection probabilities. creator: Jake M. Ferguson creator: Laura Jiménez creator: Aislyn A. Keyes creator: Austen Hilding creator: Michael A. McCartney creator: Katherine St. Clair creator: Douglas H. Johnson creator: John R. Fieberg uri: https://doi.org/10.7717/peerj.15528 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ferguson et al. title: Comparative analysis of quantitative phosphoproteomics between two tilapias (Oreochromis niloticus and Oreochromis aureus) under low-temperature stress link: https://peerj.com/articles/15599 last-modified: 2023-07-10 description: As an important farmed fish, tilapia has poor tolerance to low-temperatures. At the same time, different tilapia strains have apparent differences in low-temperature tolerance. In this study, using the iTRAQ method, the phosphorylated proteomics of two tilapia strains (Oreochromis niloticus and Oreochromis aureus) with different tolerances to low-temperature stress were quantitatively and comparatively analyzed, to clarify the physiological mechanism of tilapia’s response to low-temperature stress. Through the GO and IPR analyses of differentially phosphorylated proteins, a number of similarities in physiological activities and regulatory effects were found between the two tilapias in response to low-temperature stress. Many differentially phosphorylated proteins are mainly involved in lipid metabolism, cell proliferation and apoptosis. However, the difference in endurance of low temperature of these two tilapias might be related to the differences in categories, expression and modification level of genetic products which were involved in the aforementioned physiological processes. And meanwhile, the enrichment results of KEGG showed the changes of multiple immune-related and growth-related phosphorylated proteins in the cytokine-cytokine receptor interaction pathway in O. aureus are more prominent. Furthermore, the significantly enriched pathway of carbohydrate digestion and absorption in O. niloticus may indicate that low-temperature stress exerts a more severe impact on energy metabolism. The relative results would help elucidating the molecular mechanism by which tilapia responds to low-temperature stress, and developing culture of tilapia species. creator: Changgeng Yang creator: Hua Fan creator: Liya Ge creator: Qian Ma creator: Ming Jiang creator: Hua Wen uri: https://doi.org/10.7717/peerj.15599 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Analysis of self-renewing and differentiation-related microRNAs and transcription factors in multilineage mouse hematopoietic stem/progenitor cells induced by 1,4-benzoquinone link: https://peerj.com/articles/15608 last-modified: 2023-07-10 description: BackgroundHSPCs are targets for benzene-induced hematotoxicity and leukemogenesis. However, benzene toxicity targeting microRNAs (miRNAs) and transcription factors (TF) that are involve in regulating self-renewing and differentiation of HSPCs comprising of different hematopoietic lineages remains poorly understood. In this study, the effect of a benzene metabolite, 1,4-benzoquinone (1,4-BQ) exposure, in HSPCs focusing on the self-renewing (miRNAs: miR-196b and miR-29a; TF: HoxB4, Bmi-1) and differentiation (miRNAs: miR-181a, TF: GATA3) pathways were investigated.MethodsFreshly isolated mouse BM cells were initially exposed to 1,4-BQ at 1.25 to 5 µM for 24 h, followed by miRNAs and TF studies in BM cells. Then, the miRNAs expression was further evaluated in HSPCs of different lineages comprised of myeloid, erythroid and pre-B lymphoid progenitors following 7–14 days of colony forming unit (CFU) assay.ResultsExposure to 1,4-BQ in BM cells significantly (p < 0.05) reduced the miR-196b (2.5 and 5 µM), miR-181a (1.25, 2.5 and 5 µM) and miR-29a (1.25 µM) along with upregulation of miR-29a at 2.5 µM. Meanwhile, 1,4-BQ exposure in HSPCs significantly increased the miR-196b expression level (p < 0.05) only in myeloid and pre-B lymphoid progenitors at 2.5 and 5 µM. Significant (p < 0.05) reduction in expression of miR-181a in myeloid (1.25 µM), erythroid (5 µM) progenitors along with miR-29a in myeloid (1.25 µM) and pre-B lymphoid (5 µM) progenitors were noted following exposure to 1,4-BQ. Meanwhile, increased expression of miR-181a was observed in pre-B lymphoid progenitor upon exposure to 1,4-BQ, but only at 5 µM. As for TF studies, expression of HoxB4 protein was significantly increased (p < 0.05) at all 1,4-BQ concentrations as compared to Bmi-1 and GATA3, which were significantly (p < 0.05) elevated starting at 2.5 µM of 1,4-BQ.Conclusion1,4-BQ induces aberration of miRNAs and transcription factors protein expression that are involved in regulating self-renewing and differentiation pathways of HSPCs. Moreover, epigenetic toxicity as evidenced from the miRNAs expression was found to be mediated by a lineage-driven mechanism. The role of cell lineage in governing the toxicity of 1,4-BQ in HSPCs lineages deserves further investigation. creator: Ramya Dewi creator: Nur Afizah Yusoff creator: Siti Razila Abdul Razak creator: Zariyantey Abd Hamid uri: https://doi.org/10.7717/peerj.15608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dewi et al. title: Network neighborhood operates as a drug repositioning method for cancer treatment link: https://peerj.com/articles/15624 last-modified: 2023-07-10 description: Computational drug repositioning approaches are important, as they cost less compared to the traditional drug development processes. This study proposes a novel network-based drug repositioning approach, which computes similarities between disease-causing genes and drug-affected genes in a network topology to suggest candidate drugs with highest similarity scores. This new method aims to identify better treatment options by integrating systems biology approaches. It uses a protein-protein interaction network that is the main topology to compute a similarity score between candidate drugs and disease-causing genes. The disease-causing genes were mapped on this network structure. Transcriptome profiles of drug candidates were taken from the LINCS project and mapped individually on the network structure. The similarity of these two networks was calculated by different network neighborhood metrics, including Adamic-Adar, PageRank and neighborhood scoring. The proposed approach identifies the best candidates by choosing the drugs with significant similarity scores. The method was experimented on melanoma, colorectal, and prostate cancers. Several candidate drugs were predicted by applying AUC values of 0.6 or higher. Some of the predictions were approved by clinical phase trials or other in-vivo studies found in literature. The proposed drug repositioning approach would suggest better treatment options with integration of functional information between genes and transcriptome level effects of drug perturbations and diseases. creator: Ali Cüvitoğlu creator: Zerrin Isik uri: https://doi.org/10.7717/peerj.15624 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cüvitoğlu and Isik title: Effect of prolactin on cytotoxicity and oxidative stress in ovine ovarian granulosa cells link: https://peerj.com/articles/15629 last-modified: 2023-07-10 description: BackgroundProlactin (PRL) has been reported to be associated with oxidative stress, which is an important contributor leading to cell apoptosis. However, little is known about the mechanisms underlying the effects of PRL on cytotoxicity and oxidative stress in ovine ovarian granulosa cells (GCs).MethodsOvine ovarian GCs were treated with 0, 4, 20, 100 and 500 ng/mL of PRL. Then, the cytotoxicity, cell viability, malondialdehyde (MDA), reactive oxygen species (ROS), superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) of GCs were detected. Additionally, 500 ng/mL PRL was chosen as the high PRL concentration (HPC) due to its high cytotoxicity and oxidative stress. Proteomic and metabonomic were performed to examine the overall difference in proteins and metabolic pathways between C (control: 0 ng/mL PRL) and P groups (500 ng/mL PRL).ResultsThe results indicated that GCs treated with 4 ng/mL PRL significantly decreased (P < 0.05) the cytotoxicity, ROS and MDA, increased (P < 0.05) the cell viability, SOD and T-AOC, and the GCs treated with 500 ng/mL PRL showed the opposite trend (P < 0.05). Supplementation with 500 ng/mL PRL significantly increased the proteins of MT-ND1, MAPK12, UBA52 and BCL2L1, which were enriched in ROS and mitophagy pathways. Pathway enrichment analysis showed that the pentose phosphate pathway was significantly enriched in the P group.ConclusionA low concentration of PRL inhibited cytotoxicity and oxidative stress. HPC induced oxidative stress in ovine ovarian GCs via the pentose phosphate pathway by modulating the associated proteins MT-ND1 in ROS pathway and UBA52, MAPK12 and BCL2L1 in mitophagy pathway, resulting in cytotoxicity. creator: Ruochen Yang creator: Shuo Zhang creator: Chunhui Duan creator: Yunxia Guo creator: Xinyu Shan creator: Xinyan Zhang creator: Sicong Yue creator: Yingjie Zhang creator: Yueqin Liu uri: https://doi.org/10.7717/peerj.15629 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al.