title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=982 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral Pseudodiploria strigosa link: https://peerj.com/articles/10695 last-modified: 2021-02-02 description: Reef corals in the Mexican Reef System have been severely affected by the emergence of a white syndrome that resembles both White Plague II and SCTLD descriptions. Meandroid scleractinian coral species are among the most severely affected. To gain insight into this affliction we conducted a broad study in the brain coral Pseudodiploria strigosa at a rear reef site in the NE Mexican Caribbean. We describe macro and microscopical signals of the disease, characterize the outbreak dynamics, the tissue histopathology, explore immunological responses in the individuals, and compare microbial assemblages associated with the surface mucus layer of healthy and unhealthy colonies. At the study site, the white syndrome outbreak on P. strigosa showed a high incidence rate in summer-fall and a low one in winter, as well as low survival expectation of diseased colonies at the end of the study. After 306 days of observation, out of 96 tracked colonies, eight remained apparently healthy and seven were diseased. No effective resistance to colony disease progression was observed once white syndrome signs developed. Tissue loss rate during the study varied among colonies (mean = 10.8 cm2, s.d. = 7.8 cm2) suggesting a complex relation between causal agents and colony resistance. The deterioration of tissues was evidenced from the basal to the surface body wall of polyps (up to 66% hypertrophy and liquefactive necrosis in unhealthy colonies), implying that microscopic alterations begin before macroscopic signals develop, suggesting this may be a systemic disease. We measured high levels of phenoloxidase (two orders of magnitude higher PO activity than P. strigosa affected by BBD) and antibacterial activity without significant reduction in unhealthy samples from the mucus layer, indicative of an enhanced immunological response. Results showed that opportunistic bacteria dominated damaged colonies, where six genera of the Bacteroidia class were found with significant changes in unhealthy colonies after DeSeq2 analysis. Nevertheless, histological observations did not support infection of the tissues. The opportunistic overload seems to be contained within the mucus layer but may be associated with the mortality of tissues in a yet unclear way. Future research should focus on experimental infections, the tracking of natural infections, and the immunocompetence of corals in the face of environmental pressures due to local, regional, and global impacts. If environmental deterioration is the primary cause of the continuing emergence and re-emergence of lethal coral diseases, as has been proposed by many authors, the only true option to effectively help preserve the coral reef biodiversity and services, is to restore the environmental quality of reef waters at the local scale and reduce greenhouse gases at the global scale. creator: Patricia E. Thome creator: Jacqueline Rivera-Ortega creator: Jenny C. Rodríguez-Villalobos creator: Daniel Cerqueda-García creator: Edgar O. Guzmán-Urieta creator: José Q. García-Maldonado creator: Natalia Carabantes creator: Eric Jordán-Dahlgren uri: https://doi.org/10.7717/peerj.10695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Thome et al. title: Taxonomic, functional and expression analysis of viral communities associated with marine sponges link: https://peerj.com/articles/10715 last-modified: 2021-02-02 description: Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont. creator: Mary Nguyen creator: Bernd Wemheuer creator: Patrick W. Laffy creator: Nicole S. Webster creator: Torsten Thomas uri: https://doi.org/10.7717/peerj.10715 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Nguyen et al. title: Increased precipitation enhances soil respiration in a semi-arid grassland on the Loess Plateau, China link: https://peerj.com/articles/10729 last-modified: 2021-02-02 description: BackgroundPrecipitation influences the vulnerability of grassland ecosystems, especially upland grasslands, and soil respiration is critical for carbon cycling in arid grassland ecosystems which typically experience more droughty conditions.MethodsWe used three precipitation treatments to understand the effect of precipitation on soil respiration of a typical arid steppe in the Loess Plateau in north-western China. Precipitation was captured and relocated to simulate precipitation rates of 50%, 100%, and 150% of ambient precipitation.Results and DiscussionSoil moisture was influenced by all precipitation treatments. Shoot biomass was greater, though non-significantly, as precipitation increased. However, both increase and decrease of precipitation significantly reduced root biomass. There was a positive linear relationship between soil moisture and soil respiration in the study area during the summer (July and August), when most precipitation fell. Soil moisture, soil root biomass, pH, and fungal diversity were predictors of soil respiration based on partial least squares regression, and soil moisture was the best of these.ConclusionOur study highlights the importance of increased precipitation on soil respiration in drylands. Precipitation changes can cause significant alterations in soil properties, microbial fungi, and root biomass, and any surplus or transpired moisture is fed back into the climate, thereby affecting the rate of soil respiration in the future. creator: Yutao Wang creator: Yingzhong Xie creator: Gillian Rapson creator: Hongbin Ma creator: Le Jing creator: Yi Zhang creator: Juan Zhang creator: Jianping Li uri: https://doi.org/10.7717/peerj.10729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis link: https://peerj.com/articles/10739 last-modified: 2021-02-02 description: Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘Benihoppe’, ‘Xiaobai’, and ‘Snow White’, and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in ‘Benihoppe’ and ‘Xiaobai’ than in ‘Snow White’, consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation. creator: Fengli Zhao creator: Pan Song creator: Xiangfen Zhang creator: Gang Li creator: Panpan Hu creator: Ali Aslam creator: Xia Zhao creator: Houcheng Zhou uri: https://doi.org/10.7717/peerj.10739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: Intestinal fatty acid-binding protein, a biomarker of intestinal barrier dysfunction, increases with the progression of type 2 diabetes link: https://peerj.com/articles/10800 last-modified: 2021-02-02 description: ObjectiveTo investigate serum intestinal fatty acid-binding protein (I-FABP) in two groups of patients with different duration of hyperglycemia in a cross-sectional study.Materials and MethodsIn the present study, a total of 280 individuals (158 outpatients and 122 inpatients) suffering from hyperglycemia were recruited between May and September 2019. The clinical information of all participants was collected from the hospital information system, including the duration of hyperglycemia, age, gender, hemoglobin A1c (HbA1c), 75-g oral glucose tolerance test including fasting plasma glucose (FPG), 2-hour plasma glucose (2hPG), fasting C-peptide (FC-pep), 2-hour C-peptide (2hC-pep), fasting insulin (FIns), and 2-hour insulin (2hIns). In addition, the morbidity of diabetic complications (retinopathy, neuropathy, and nephropathy) in the inpatient group was determined. Furthermore, the difference between 2hPG and FPG (ΔPG), the difference between 2hC-pep and FC-pep (ΔC-pep), and the difference between 2hIns and FIns (ΔIns) were calculated. The level of serum I-FABP, a biomarker of intestinal barrier (IB) dysfunction, was estimated by an enzyme-linked immunosorbent assay.ResultsFor the outpatient group, the median duration of hyperglycemia was less than a year; the serum I-FABP level was positively correlated with age (R = 0.299, P < 0.001). For the inpatient group, the median duration of hyperglycemia was ten years; correlation analysis showed that the serum I-FABP level was positively associated with age and ΔPG (R = 0.286, P = 0.001; R = 0.250, P = 0.006, respectively) while negatively associated with FC-pep and 2hC-pep (R =  − 0.304, P = 0.001; R =  − 0.241, P = 0.008, respectively); multiple linear regression analysis showed that the serum I-FABP level was positively associated with the duration of hyperglycemia (β = 0.362, P < 0.001); moreover, patients with retinopathy had a significantly higher I-FABP level than those without retinopathy (P = 0.001).ConclusionsIn the outpatients whose duration of hyperglycemia was less than a year, the serum I-FABP level was positively associated with age. In the inpatients with different courses of diabetes, the serum I-FABP level was positively associated with the duration of hyperglycemia and glycemic variability but negatively associated with islet beta-cell function; moreover, the serum I-FABP level was higher in patients with retinopathy than in those without retinopathy, suggesting that the IB dysfunction got worse with the progression of diabetes. creator: Yifeng Wang creator: Licheng Ding creator: Jiayue Yang creator: Lijun Liu creator: Liang Dong uri: https://doi.org/10.7717/peerj.10800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Epigenetic identification of mitogen-activated protein kinase 10 as a functional tumor suppressor and clinical significance for hepatocellular carcinoma link: https://peerj.com/articles/10810 last-modified: 2021-02-02 description: BackgroundMitogen-activated protein kinase 10 (Mapk10) is a member of the c-jun N-terminal kinases (jnk) subgroup in the MAPK superfamily, and was proposed as a tumor suppressor inactivated epigenetically. Its role in hepatocellular carcinoma (HCC) has not yet been illustrated. We aimed to investigate the expression and epigenetic regulation of mapk10 as well as its clinical significance in HCC.ResultsMapk10 was expressed in almost all the normal tissues including liver, while we found that the protein expression of MAPK10 was significantly downregulated in clinical samples of HCC patients compared with these levels in adjacent normal tissues (29/46, P < 0.0001). Clinical significance of MAPK10 expression was then assessed in a cohort of 59 HCC cases, which indicated its negative expression was significantly correlated with advanced tumor stage (P = 0.001), more microsatellite nodules (P = 0.025), higher serum AFP (P = 0.001) and shorter overall survival time of HCC patients. Methylation was further detected in 58% of the HCC cell lines we tested and in 66% of primary HCC tissues by methylation-specific PCR (MSP), which was proved to be correlated with the silenced or downregulated expression of mapk10. To get the mechanisms more clear, the transcriptional silencing of mapk10 was reversed by pharmacological demethylation, and ectopic expression of mapk10 in silenced HCC cell lines significantly inhibited the colony formation ability, induced apoptosis, or enhanced the chemosensitivity of HCC cells to 5-fluorouracil.ConclusionMapk10 appears to be a functional tumor suppressor gene frequently methylated in HCC, which could be a valuable biomarker or a new diagnosis and therapy target in a clinical setting. creator: Liping Tang creator: Shasha Zhu creator: Weiyan Peng creator: Xuedong Yin creator: Cui Tan creator: Yaying Yang uri: https://doi.org/10.7717/peerj.10810 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tang et al. title: Comparison of physical fitness and mental health status among school-age children with different sport-specific training frequencies link: https://peerj.com/articles/10842 last-modified: 2021-02-02 description: This cross-sectional study compared the physical fitness and mental health status of 140 school-age children who participated in sport-specific training with 180 age-matched peers. All the participants were grouped by sport-specific training frequencies in extracurricular time into the following: (i) high sports training frequency group (HFG): training three to five times per week (n = 77, mean [SD] age: 9.60 [0.12] years); (ii) low sports training frequency group (LFG): training once per week (n = 63, mean [SD] age: 9.88 [0.14] years); and (iii) control group (CG): maintaining routine life (n = 180, mean (SD) age: 9.77(0.09) years). Physical fitness status, including body composition (body mass index), endurance (vital capacity; 50 × 8 round trip), speed and agility (50 m sprint), flexibility (sit-and-reach), coordination (1-min rope skipping), and core strength (1-min sit-ups) as well as mental health status was measured. Overall, the results showed that Grade 3 to 4 HFG students showed better total physical fitness scores than the LFG and CG students. Grade 2 and 5 participants in the three groups showed no significant difference in the total physical fitness score. Children in HFG performed better in several PF indicators (i.e., cardiopulmonary function, flexibility, core strength, and coordination) than those in LFG and CG, and children in LFG got a higher score than those in CG on a testing item of 1-min rope skipping. The mental health test results showed that HFG performed better than LFG and CG. The results indicated that participating in sport-specific training 3–5 times per week was beneficial for children’s physical and mental health. Additionally, there was a weak and negative correlation between physical fitness and mental health in LFG and CG, while no correlation was found between physical fitness and mental health in HFG. creator: Ruichen Jiang creator: Chun Xie creator: Jilong Shi creator: Xuechen Mao creator: Qin Huang creator: Fanying Meng creator: Zhiguang Ji creator: Anmin Li creator: Chunhua Zhang uri: https://doi.org/10.7717/peerj.10842 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: Undiagnosed cardiovascular risk factors in overweight and obese individuals: a low income country experience link: https://peerj.com/articles/10870 last-modified: 2021-02-02 description: BackgroundOverweight and obesity are associated with diabetes, hypertension and chronic kidney disease (CKD). However, there is scarce information from lower income countries about undiagnosed obesity-associated conditions. This information is necessary for healthcare planning and for assessment of Global Burden of Disease.MethodsWe assessed the prevalence of obesity-associated conditions in 656 overweight (n = 360) and obese (n = 296) adults from inner-city Portoviejo (Ecuador), in descriptive field research, based on an opportunistic and selective sampling strategy.ResultsOf 316 men and 340 women, 73% met criteria for prehypertension (27%) or hypertension (46%), 50% met criteria for prediabetes (30%) or diabetes (20%), 11% had an estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m2 consistent with chronic kidney disease (CKD) and 5.5% had pathological albuminuria for a total CKD prevalence of 16%. Age-related prevalence data were generated. In all participants, serum total cholesterol and triglycerides were >200 and >150 mg/dl, respectively. Hyperuricemia and microhematuria (<2%) were uncommon. Women were more likely to have low eGFR (18 vs 5%, p 0.000). Diabetes and pathological albuminuria prevalence were higher in obese than in overweight participants (15 vs 12%, p 0.018; and 8 vs 4%, p 0.0199, respectively).DiscussionIn conclusion, undiagnosed hypertension, diabetes and CKD were more common than expected in overweight and obese persons from Ecuador. Detection rates exceeded official estimates of prevalene of these conditions. Screening the overweight/obese for these conditions, especially at the age ranges at higher risk, may be cost-effective to identify a high number of persons who may benefit from early inexpensive intervention. creator: Patricio Alfredo Vallejo-Valdivieso creator: Graciela Zambrano-Pincay creator: Alberto Ortiz uri: https://doi.org/10.7717/peerj.10870 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vallejo-Valdivieso et al. title: The long non-coding RNA GHSROS reprograms prostate cancer cell lines toward a more aggressive phenotype link: https://peerj.com/articles/10280 last-modified: 2021-02-01 description: It is now appreciated that long non-coding RNAs (lncRNAs) are important players in orchestrating cancer progression. In this study we characterized GHSROS, a human lncRNA gene on the opposite DNA strand (antisense) to the ghrelin receptor gene, in prostate cancer. The lncRNA was upregulated by prostate tumors from different clinical datasets. Transcriptome data revealed that GHSROS alters the expression of cancer-associated genes. Functional analyses in vitro showed that GHSROS mediates tumor growth, migration and survival, and resistance to the cytotoxic drug docetaxel. Increased cellular proliferation of GHSROS-overexpressing PC3, DU145, and LNCaP prostate cancer cell lines in vitro was recapitulated in a subcutaneous xenograft model. Conversely, in vitro antisense oligonucleotide inhibition of the lncRNA reciprocally regulated cell growth and migration, and gene expression. Notably, GHSROS modulates the expression of PPP2R2C, the loss of which may drive androgen receptor pathway-independent prostate tumor progression in a subset of prostate cancers. Collectively, our findings suggest that GHSROS can reprogram prostate cancer cells toward a more aggressive phenotype and that this lncRNA may represent a potential therapeutic target. creator: Patrick B. Thomas creator: Penny Jeffery creator: Manuel D. Gahete creator: Eliza Whiteside creator: Carina Walpole creator: Michelle Maugham creator: Lidija Jovanovic creator: Jennifer Gunter creator: Elizabeth Williams creator: Colleen Nelson creator: Adrian Herington creator: Raul M. Luque creator: Rakesh Veedu creator: Lisa K. Chopin creator: Inge Seim uri: https://doi.org/10.7717/peerj.10280 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Thomas et al. title: Seasonal patterns in nest survival of a subtropical wading bird, the Hawaiian Stilt (Himantopus mexicanus knudseni) link: https://peerj.com/articles/10399 last-modified: 2021-02-01 description: Nest survival is influenced by where and when birds decide to breed. For ground-nesting species, nest-site characteristics, such as vegetation height and proximity to water, may impact the likelihood of nest flooding or depredation. Further, habitat characteristics, and thus nest survival, may fluctuate across the breeding season. The Hawaiian Stilt (‘Ae‘o; Himantopus mexicanus knudseni) is an endangered Hawaiian waterbird that nests in wetlands across the Hawaiian Islands. In this study, we used observational surveys and nest cameras to examine the impact of nest-site characteristics and day of nesting season on nest survival of the Hawaiian Stilt. Early nests had a higher chance of survival than late nests. For most of the nesting season, taller vegetation was correlated with increased nest survival, while shorter vegetation was correlated with increased nest survival late in the nesting season. Seasonal patterns in nest survival may be due to changes in parental behavior or predator activity. Nest depredation was responsible for 55% of confirmed nest failures and introduced mammals were the primary nest predators. Our study is the first to examine seasonality in nest survival of Hawaiian Stilts and suggests that, despite longer nesting seasons and year-round occupation of wetlands, late nesters in subtropical regions may have lower nest survival than early nesters, similar to trends observed in temperate regions. creator: Kristen C. Harmon creator: Nathaniel H. Wehr creator: Melissa R. Price uri: https://doi.org/10.7717/peerj.10399 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Harmon et al.