title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=914 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: DXA reference values of the humanoid sheep model in preclinical studies link: https://peerj.com/articles/11183 last-modified: 2021-04-30 description: BackgroundMerino land sheep are a popular pre-clinical large animal model in research on systemic skeletal diseases such as osteoporosis. Interpretation of studies is difficult because many reference parameters are missing or not established. This study aims to determine the reference parameters of the skeletal system (peak bone mass = PBM, T-Score). A defined standard allows an easier comparison of the study data of the animal model with human studies (T-Score).Materials and methodsA total of 116 Dual Energy X-ray Absorptiometry DXA measurements were performed on 74 untreated sheep. The average age of the animals was 57 months. The BMD, BMC, and fat content of the sheep were determined by the relevant human region of interest (ROI). From this, the PBM and from this the T-score for each of the animals were calculated.ResultsUsing 682 DXA measurements BMD and BMC were determined to provide an indication to PBM. For BMD a significant correlation to the age of the animals was observed (p = 0.043). A significant correlation was also seen for BMC (B) (p ≤ 0.001). In the age-dependent analysis, a widespread of values above the linear regression line was measured for both BMD and BMC between the 50th and 90th months of life. From an age of about 90 months, a wider spread of values below the linear regression line was found, although the average values continued to rise.DiscussionThe evaluation of the 116 DXA measurements allowed the determination of the PBM for merino land sheep. With the help of the PBM, a T-score was calculated for each animal. The statistical analysis shows significant differences in BMD values between the different animal groups in each of the four ROIs investigated. Individual control or sham groups per study are therefore not sufficient. To improve comparability, an independent reference group should be established.ConclusionAn independent reference group for PBM and a T-score was established from four to six-year-old animals. The bone density increases with the age of the animals. Around the fourth year of life, a first peak could be observed. Also, after the seventh year of life, a further peak with the beginning plateau phase was observed. When compiling a group of animals for an osteoporosis model, animals from the age of seven years should, therefore, be used. creator: Christoph Biehl creator: Jakob Schmitt creator: Sabine Stoetzel creator: Deeksha Malhan creator: Fathi Hassan creator: Gero Knapp creator: Christian Heiss creator: Thaqif El Khassawna uri: https://doi.org/10.7717/peerj.11183 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Biehl et al. title: Response of net primary productivity to grassland phenological changes in Xinjiang, China link: https://peerj.com/articles/10650 last-modified: 2021-04-30 description: Determining the relationship between net primary productivity (NPP) and grassland phenology is important for an in-depth understanding of the impact of climate change on ecosystems. In this study, the NPP of grassland in Xinjiang, China, was simulated using the Carnegie-Ames-Stanford approach (CASA) model with Moderate Resolution Imaging Spectroradiometer (MODIS) grassland phenological (MCD12Q2) data to study trends in phenological metrics, grassland NPP, and the relations between these factors from 2001–2014. The results revealed advancement of the start of the growing season (SOS) for grassland in most regions (55.2%) in Xinjiang. The percentage of grassland area in which the end of the growing season (EOS) was delayed (50.9%) was generally the same as that in which the EOS was advanced (49.1%). The percentage of grassland area with an increase in the length of the growing season (LOS) for the grassland area (54.6%) was greater than that with a decrease in the LOS (45.4%). The percentage of grassland area with an increase in NPP (61.6%) was greater than that with a decrease in NPP (38.4%). Warmer regions featured an earlier SOS and a later EOS and thus a longer LOS. Regions with higher precipitation exhibited a later SOS and an earlier EOS and thus a shorter LOS. In most regions, the SOS was earlier, and spring NPP was higher. A linear statistical analysis showed that at various humidity (K) levels, grassland NPP in all regions initially increased but then decreased with increasing LOS. At higher levels of K, when NPP gradually increased, the LOS gradually decreased. creator: Renping Zhang creator: Jing Guo creator: Gang Yin uri: https://doi.org/10.7717/peerj.10650 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines link: https://peerj.com/articles/11275 last-modified: 2021-04-30 description: Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition. creator: Sophie Cowman creator: Barry Pizer creator: Violaine Sée uri: https://doi.org/10.7717/peerj.11275 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cowman et al. title: A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria link: https://peerj.com/articles/11282 last-modified: 2021-04-30 description: Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels. creator: Mengna Li creator: Hao Chen creator: Minxiao Wang creator: Zhaoshan Zhong creator: Hao Wang creator: Li Zhou creator: Huan Zhang creator: Chaolun Li uri: https://doi.org/10.7717/peerj.11282 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Continuous bubble streams for controlling marine biofouling on static artificial structures link: https://peerj.com/articles/11323 last-modified: 2021-04-30 description: Biofouling accumulation is not proactively managed on most marine static artificial structures (SAS) due to the lack of effective options presently available. We describe a series of laboratory and field trials that examine the efficacy of continuous bubble streams in maintaining SAS free of macroscopic biofouling and demonstrate that this treatment approach is effective on surface types commonly used in the marine environment. At least two mechanisms were shown to be at play: the disruption of settlement created by the bubble stream, and the scouring of recently settled larvae through shear stress. Field trials conducted over a one-year period identified fouling on diffusers as a major issue to long-term treatment applications. Field measurements suggest that noise associated with surface mounted air blowers and sub-surface diffusers will be highly localised and of low environmental risk. Future studies should aim to develop and test systems at an operational scale. creator: Grant A. Hopkins creator: Fletcher Gilbertson creator: Oli Floerl creator: Paula Casanovas creator: Matt Pine creator: Patrick Cahill uri: https://doi.org/10.7717/peerj.11323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hopkins et al. title: Cinnamaldehyde inhibits the growth of Phytophthora capsici through disturbing metabolic homoeostasis link: https://peerj.com/articles/11339 last-modified: 2021-04-30 description: BackgroundPhytophthora capsici Leonian (P. capsici) can cause wilting and roots rotting on pepper and other cash crops. The new fungicide cinnamaldehyde (CA) has high activity against this pathogen. However, its potential mechanism is still unknown.MethodsIn order to gain insights into the mechanism, isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics was used to analyze P. capsici treated with CA. The iTRAQ results were evaluated by parallel reaction monitoring (PRM) analysis and quantitative real-time PCR (qRT-PCR) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to speculate the biochemical pathways that the agent may act on.ResultsThe results showed that 1502 differentially expressed proteins were identified, annotated and classified into 209 different terms (like metabolic process, cellular process, single-organism process) based on Gene Ontology (GO) functional enrichment analysis and nine different pathways (glyoxylate and dicarboxylate metabolism, fatty acid metabolism and so on) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. This study suggested that CA disordered fatty acid metabolism, polysaccharide metabolism and leucine metabolism. Based on PRM analysis, five proteins including CAMK/CAMK1 protein kinase, glucan 1,3-beta-glucosidase, 1,3-beta-glucanosyltransferase, methylcrotonoyl-CoA carboxylase subunit alpha and isovaleryl-CoA dehydrogenase were down-regulated in P. capsici treated with CA. Furthermore, the qRT-PCR analysis showed that the gene expression level of the interested proteins was consistent with the protein expression level, except for CAMK/CAMK1 protein kinase, acetyl-CoA carboxylase and fatty acid synthase subunit alpha.ConclusionsCA destroyed the metabolic homoeostasisof P. capsici, which led to cell death. This is the first proteomic analysis of P. capsici treated with CA, which may provide an important information for exploring the mechanism of the fungicide CA against P. capsici. creator: Yinan Wang creator: Mengke Wang creator: Min Li creator: Te Zhao creator: Lin Zhou uri: https://doi.org/10.7717/peerj.11339 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Low composite functional movement screen score associated with decline of gait stability in young adults link: https://peerj.com/articles/11356 last-modified: 2021-04-30 description: BackgroundThe functional movement screen (FMS)TM is a screening tool used to evaluate fundamental motor function. A score of 14 for the composite total FMS score (TFMS) is generally used as the cut-off point (≤14/21). In addition, gait analysis is used to evaluate fundamental motor function in humans. Thus, evaluating the fundamental motor function using the FMSTM test and gait analysis at various speeds can provide further understanding of any decline in gait stability. In this study, we aimed to investigate the association between gait ability and fundamental movement patterns in young adults according to the cut-off point.MethodsA total of 439 participants (male: 203, female: 236) successfully completed the FMS test and a 1 min treadmill test; the participants were classified into two groups: low TFMS (≤14) and high TFMS (>14).ResultsThe low TFMS group exhibited slower and shortened walking patterns and worsen gait variability than the high TFMS group. The coefficient of variance (CV) for the double support phase at a faster speed (male) and the stride length at a slower speed (female) were classifiers between the two groups. In addition, the low TFMS group demonstrated insufficient gait adaptation at the preferred and faster speeds based on the CV of the double support phase and gait asymmetry. Lower TFMS is associated with a decline in gait ability. Therefore, participants with a lower TFMS and poor gait ability may require intervention programs to prevent risk of future injury and to enhance motor function. creator: Myeounggon Lee creator: Changhong Youm creator: Byungjoo Noh creator: Hwayoung Park uri: https://doi.org/10.7717/peerj.11356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lee et al. title: Mycophenolate suppresses inflammation by inhibiting prostaglandin synthases: a study of molecular and experimental drug repurposing link: https://peerj.com/articles/11360 last-modified: 2021-04-30 description: Mycophenolate mofetil is an established anti-proliferative and immune-suppressive agent that minimizes the proliferation of inflammatory cells by interfering with nucleic acid synthesis. Herein, we report our discovery of the prostaglandin inhibiting properties of MMF, which offers new applications for the drug in the treatment of inflammatory diseases. The estimated values of IC50MMFCOX-1, IC50MMFCOX-2, and IC50MMF5-LOX were 5.53, 0.19, and 4.47 µM, respectively. In contrast, mycophenolic acid (MPA) showed slightly stronger inhibition: IC50MPACOX-1, IC50MPACOX-2, and IC50MPA5-LOX were 4.62, 0.14, and 4.49 µM, respectively. These results indicate that MMF and MPA are, respectively, 28.6 and 33 times more selective for cyclooxygenase-2 than for cyclooxygenase-1, which implies that MMF would have less impact on the gastric mucosa than most nonselective, nonsteroidal anti-inflammatory drugs. Furthermore, MMF provided dose-dependent relief of acute inflammation in the carrageenan-induced rat paw edema test, with results comparable to those of celecoxib and indomethacin. Molecular dynamics simulations indicated that the MMF bond with COX-2 was stable, as evidenced by a low root-mean-square deviation of atomic positions, complementary per-residue root-mean-square fluctuation, and 0–4 hydrogen bonds during the 50-ns simulation time. Therefore, MMF provides immune-suppressing, cyclooxygenase-inhibiting, and inflammation-relieving properties. Our results indicate that MMF can be 1) repositioned for inflammation treatment without the need for further expensive clinical trials, 2) used for local acute inflammations, and 3) used as a sparing agent for other steroid and non-steroid anti-inflammatory medications, especially in topical applications. creator: Fahad Al-Hizab creator: Mahmoud Kandeel uri: https://doi.org/10.7717/peerj.11360 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Al-Hizab and Kandeel title: The hypoferremic response to acute inflammation is maintained in thalassemia mice even under parenteral iron loading link: https://peerj.com/articles/11367 last-modified: 2021-04-30 description: BackgroundHepcidin controls iron homeostasis by inducing the degradation of the iron efflux protein, ferroportin (FPN1), and subsequently reducing serum iron levels. Hepcidin expression is influenced by multiple factors, including iron stores, ineffective erythropoiesis, and inflammation. However, the interactions between these factors under thalassemic condition remain unclear. This study aimed to determine the hypoferremic and transcriptional responses of iron homeostasis to acute inflammatory induction by lipopolysaccharide (LPS) in thalassemic (Hbbth3/+) mice with/without parenteral iron loading with iron dextran.MethodsWild type and Hbbth3/+ mice were intramuscularly injected with 5 mg of iron dextran once daily for two consecutive days. After a 2-week equilibration, acute inflammation was induced by an intraperitoneal injection of a single dose of 1 µg/g body weight of LPS. Control groups for both iron loading and acute inflammation received equal volume(s) of saline solution. Blood and tissue samples were collected at 6 hours after LPS (or saline) injection. Iron parameters and mRNA expression of hepcidin as well as genes involved in iron transport and metabolism in wild type and Hbbth3/+ mice were analyzed and compared by Kruskal–Wallis test with pairwise Mann–Whitney U test.ResultsWe found the inductive effects of LPS on liver IL-6 mRNA expression to be more pronounced under parenteral iron loading. Upon LPS administration, splenic erythroferrone (ERFE) mRNA levels were reduced only in iron-treated mice, whereas, liver bone morphogenetic protein 6 (BMP6) mRNA levels were decreased under both control and parenteral iron loading conditions. Despite the altered expression of the aforementioned hepcidin regulators, the stimulatory effect of LPS on hepcidin mRNA expression was blunt in iron-treated Hbbth3/+ mice. Contrary to the blunted hepcidin response, LPS treatment suppressed FPN1 mRNA expression in the liver, spleen, and duodenum, as well as reduced serum iron levels of Hbbth3/+ mice with parenteral iron loading.ConclusionOur study suggests that a hypoferremic response to LPS-induced acute inflammation is maintained in thalassemic mice with parenteral iron loading in a hepcidin-independent manner. creator: Chanita Sanyear creator: Buraporn Chiawtada creator: Punnee Butthep creator: Saovaros Svasti creator: Suthat Fucharoen creator: Patarabutr Masaratana uri: https://doi.org/10.7717/peerj.11367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sanyear et al. title: Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.) link: https://peerj.com/articles/11398 last-modified: 2021-04-30 description: Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1–CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16–17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments. creator: Yuanyuan Dan creator: Yuan Niu creator: Chunlei Wang creator: Mei Yan creator: Weibiao Liao uri: https://doi.org/10.7717/peerj.11398 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Dan et al.