title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=193 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development link: https://peerj.com/articles/18578 last-modified: 2024-11-29 description: Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development. creator: Chao Mei creator: Yuwei Liu creator: Huiyang Song creator: Jinghao Li creator: Qianna Song creator: Yonghong Duan creator: Ruiyun Feng uri: https://doi.org/10.7717/peerj.18578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mei et al. title: Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure link: https://peerj.com/articles/18595 last-modified: 2024-11-29 description: BackgroundSodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed.ObjectiveEvaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients.MethodsWe conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value.ResultsAfter 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively.ConclusionThe optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients. creator: Tuong Le Trong Huynh creator: Phong Thanh Pham creator: Hien Dieu Tran creator: Nhan Dinh Tran creator: Duong Van Tran creator: Bao Lam Thai Tran creator: Khoa Dang Dang Tran creator: Toan Hoang Ngo creator: Son Kim Tran uri: https://doi.org/10.7717/peerj.18595 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Huynh et al. title: Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment link: https://peerj.com/articles/18603 last-modified: 2024-11-29 description: BackgroundExercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE.MethodsThirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%).ResultsThe net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05).ConclusionLow- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, a high-intensity load could increase the risk of inflammation. Therefore, low-intensity exercise may be more appropriate for an SBOE in HHE. creator: Yuhu Lv creator: Lin Cheng creator: Xiqian Zhang creator: Fenglin Peng creator: Yu Yuan creator: Xiquan Weng creator: Wen-Tao Lin uri: https://doi.org/10.7717/peerj.18603 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots link: https://peerj.com/articles/18624 last-modified: 2024-11-29 description: BackgroundEnhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments.MethodsTen maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods.Results and DiscussionAnalysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions. creator: Dedy Supriadi creator: Yusuf Mufti Bimantara creator: Yuniel Melvanolo Zendrato creator: Eko Widaryanto creator: Kuswanto Kuswanto creator: Budi Waluyo uri: https://doi.org/10.7717/peerj.18624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Supriadi et al. title: Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study link: https://peerj.com/articles/18631 last-modified: 2024-11-29 description: ObjectiveRheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, characterized by significant individual variations in treatment response. Predicting treatment response remains a formidable challenge. This study aims to identify predictors within the synovium associated with the response to JAK inhibitor therapy in RA patients, employing a retrospective approach.MethodsA retrospective analysis was conducted on 27 RA patients who underwent synovial biopsy and received JAK inhibitor therapy for at least three months at our center, from January to November 2023. These patients had comprehensive clinical records. Based on their response to JAK inhibitor therapy, as measured by the ACR20 criteria, they were categorized into non-responder and responder groups. We compared clinical data (including sex, age, disease duration), laboratory findings (RF, ACPA, ESR, CRP, etc.), DAS28-CRP scores, and synovial pathology features—such as synovial lining hyperplasia, neovascularization, stromal activation, inflammatory infiltration, and the expression of CD3, CD20, CD68, and CD138 markers in the synovium—between the two groups.ResultsThe rate of non-responder to JAKi was found to be 33.3% (nine cases out of a total of 27 patients). Non-responders, when compared to responders, exhibited longer disease duration, more pronounced synovial neovascularization alongside reduced infiltration of labeled CD20+ and CD138+ cells in the synovium. Multivariate regression analysis identified synovial neovascularization and disease duration as independent predictors of a poor response to JAK inhibitor treatment.ConclusionsThe presence of vascular phenotype with low inflammation within the synovium of RA patients is an indicator of poor response to JAK inhibitor therapy, highlighting its potential as a predictive marker for treatment outcomes. creator: Mengxia Liu creator: Pengcheng Liu creator: JianBin Li creator: Yiping Huang creator: Rui Wu uri: https://doi.org/10.7717/peerj.18631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma link: https://peerj.com/articles/18286 last-modified: 2024-11-28 description: BackgroundThe incidence of oropharyngeal squamous cell carcinoma (OPSCC) mediated by human papilloma virus (HPV) has been steadily increasing worldwide. The specific pathogenesis of HPV-mediated head and neck squamous cell carcinoma (HNSCC) usually induces carcinogenesis in the oropharynx and the roles of CK7, CK19 and p16 in the carcinogenesis mechanism of HPV-mediated OPSCC still remain uncertain.MethodsWe collected case data and paraffin samples of 69 cases of OPSCC and 40 cases of OSCC from July 2009 to December 2021. Immunohistochemistry was performed on serial paraffin sections from all cases to analyze the expression patterns of CK7, CK19, and p16. HPV-mediated (p16+) and non-HPV-mediated OPSCC were differentiated based on p16 expression. Three to six fields were selected from each case for observation of the expression intensity, localization, and interrelationship of the three proteins.ResultsIn both cancerous nests and pericancerous normal epithelium of OPSCC, various expression combinations of CK7, CK19 and p16 were observed, including CK7+CK19+p16+, CK7−CK19+p16+, and CK7+CK19+p16−, while no expression of CK7+CK19−p16+ was found. The expression of CK7 with CK19, CK7 with p16, and CK19 with p16 all showed consistency in OPSCC (P < 0.05) while only the expression of CK7 and CK19 demonstrated consistency in OSCC (P < 0.05). The positive rates and H-scores for CK7/CK19 in HPV-mediated (p16+) OPSCC were significantly higher than those in non-HPV-mediated OPSCC and OSCC (P < 0.05).ConclusionsThese results suggest that CK7, CK19 and p16 may relate to HPV-mediated OPSCC. The interaction of CK7, CK19 and p16 may affect the development of HPV-mediated OPSCC. creator: Qizhang Yan creator: Pengning Chen creator: Xinyu Chen creator: Guanxi Chen creator: Lin Luo creator: Ping Ruan creator: Dahai Yu creator: Xiaojuan Zeng creator: Mengyu Zhou uri: https://doi.org/10.7717/peerj.18286 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yan et al. title: Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus link: https://peerj.com/articles/18298 last-modified: 2024-11-28 description: BackgroundUnderstanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons.MethodsThirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene.ResultsWe found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals.DiscussionThis is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota. creator: Ruber Rodríguez-Barreras creator: Eduardo L. Tosado-Rodríguez creator: Anelisse Dominicci-Maura creator: Filipa Godoy-Vitorino uri: https://doi.org/10.7717/peerj.18298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rodríguez-Barreras et al. title: Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics link: https://peerj.com/articles/18312 last-modified: 2024-11-28 description: IntroductionSevere early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, nearly 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM) was designed in this study.MethodsEleven fresh S-ECC dental plaque samples were collected and cultivated in both NEMM and SHI medium (reference medium) for 0, 1, 3, 6, 9, 15, 21 and 28 days under aerobic and anaerobic conditions. Thereafter, the cultures were harvested, together with their corresponding clinical S-ECC dental plaque samples, for high through-put 16S rRNA sequencing and culturomics. The single colonies were cultured for further confirmation by sequencing the full length of the 16S rRNA gene after bacterial genomic DNA extraction and PCR amplification.ResultsEither NEMM or SHI medium showed a significant decrease in bacterial alpha diversity compared to clinical dental plaque samples by high throughput 16S rRNA sequencing analysis, indicating a larger room for the improvement of both media. NEMM displayed more living bacteria, abundant bacteria species, uncultured bacteria and capacities in carbohydrate transport and metabolism than SHI medium. The dynamic changes in bacterial community composition over time indicated that some bacteria tended to be enriched at specific time points. Culturomics and identification of bacterial species results were further confirmed by the high throughput 16S rRNA sequencing results.ConclusionWe developed a new medium NEMM that could support S-ECC microbiota growth with a higher yield of living bacteria, higher abundance and capacity, and be suitable for cultivating oral uncultured bacteria via culturomics technology. creator: Yixin Zhang creator: Yang Chen creator: Chang Diao creator: Haojie Lin creator: Jingqi Zhu creator: Ruiqing Sun creator: Meng Wang creator: Yuke Chen creator: Hanzhang Zhou creator: Zixi Dong creator: Bin Xia creator: Yixiang Wang uri: https://doi.org/10.7717/peerj.18312 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231) link: https://peerj.com/articles/18420 last-modified: 2024-11-28 description: BackgroundNatural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231).MethodsThe optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways.ResultsELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell activation, promoting the apoptosis of triple-negative human breast cancer cells (MDA-MB-231), suggesting the potential use of MEPB leaves as an anti-cancer immunostimulant. creator: Taif Kareem Khalaf creator: Norzila Ismail creator: Nor Amalia Nazri creator: Naveed Ahmed creator: Aidy Irman Yajid creator: Rohimah Mohamud creator: Ramlah Kadir uri: https://doi.org/10.7717/peerj.18420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khalaf et al. title: Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China link: https://peerj.com/articles/18480 last-modified: 2024-11-28 description: BackgroundAs one of the most essential vegetation types, grasslands play a vital role in the global carbon cycle. However, current researches on the spatial variation (SV) of soil respiration (Rs) in grasslands faces great uncertainties.MethodsThe SV of Rs was analysed by obtaining Rs during the early growing season of three types of grasslands (i.e., alpine meadow, desert steppe, and typical steppe) and related impact factors at 19 sites.ResultsThe results demonstrated that during the early growing season, the Rs of the alpine meadow was the highest, followed by the typical steppe and desert steppe. Moreover, soil temperature was the primary factor affecting the SV of Rs in desert steppe. In contrast, soil water content influenced the SV of Rs in typical steppe. This study increases our understanding of the SV of Rs during the early growing season of different grasslands. It provides an important reference for accurately estimating the SV of Rs in grasslands at various time scales. creator: Jie Liu creator: Ni Huang creator: Li Wang creator: Xiaoyu Lin creator: Luying Zhu creator: Zheng Niu creator: Yuelin Zhang creator: Wensheng Duan uri: https://doi.org/10.7717/peerj.18480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al.