title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=635 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Habitat selection of black grouse in an isolated population in northern Germany—the importance of mixing dry and wet habitats link: https://peerj.com/articles/14161 last-modified: 2022-10-17 description: Wildlife habitats in general must provide foraging, hiding and resting places as well as sites for reproduction. Little is known about habitat selection of black grouse in the lowlands of Central Europe. We investigated habitat selection of seven radio tagged birds in an open heath and grassland area surrounded by dense pine forests in the northern German Lüneburg Heath Nature Reserve. This site carries one of the last remaining populations in the Central European lowlands. Using resource selection functions based on presence/background data, we estimated the probability of black grouse occurrence by availability of, or distance to habitat types as well as vegetation diversity indices. Black grouse preferred undisturbed and heterogeneous habitats far from dense forests with wide sand heaths, natural grasslands and intermixed bogs, diverse vegetation and food sources, low density of (loose) shrub formations and solitary trees. Wetlands were extremely important in a landscape that is dominated by dry heaths and grasslands. About 4% (9 km2) of the nature reserve was a suitable habitat for black grouse, mostly due to lack of open areas due to the amount of dense forest, and because smaller, open heaths are only partly suitable. We suggest that to improve habitat quality and quantity for the grouse, habitat patch size and connectivity must be increased, along with a mosaic of heterogeneous landscape structures in these habitat islands. Our results may be used to inform and improve black grouse habitat management in the region and elsewhere. creator: Daniel Tost creator: Tobias Ludwig creator: Egbert Strauss creator: Klaus Jung creator: Ursula Siebert uri: https://doi.org/10.7717/peerj.14161 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tost et al. title: Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review link: https://peerj.com/articles/14174 last-modified: 2022-10-17 description: BackgroundThere have been promising results published regarding the potential of stem cells in regenerative medicine. However, the vast variety of choices of techniques and the lack of a standard approach to analyse human osteoblast and osteoclast differentiation may reduce the utility of stem cells as a tool in medical applications. Therefore, this review aims to systematically evaluate the findings based on stem cell differentiation to define a standard gene expression profile approach.MethodsThis review was performed following the PRISMA guidelines. A systematic search of the study was conducted by retrieving articles from the electronic databases PubMed and Web of Science to identify articles focussed on gene expression and approaches for osteoblast and osteoclast differentiation.ResultsSix articles were included in this review; there were original articles of in vitro human stem cell differentiation into osteoblasts and osteoclasts that involved gene expression profiling. Quantitative polymerase chain reaction (qPCR) was the most used technique for gene expression to detect differentiated human osteoblasts and osteoclasts. A total of 16 genes were found to be related to differentiating osteoblast and osteoclast differentiation.ConclusionQualitative information of gene expression provided by qPCR could become a standard technique to analyse the differentiation of human stem cells into osteoblasts and osteoclasts rather than evaluating relative gene expression. RUNX2 and CTSK could be applied to detect osteoblasts and osteoclasts, respectively, while RANKL could be applied to detect both osteoblasts and osteoclasts. This review provides future researchers with a central source of relevant information on the vast variety of gene expression approaches in analysing the differentiation of human osteoblast and osteoclast cells. In addition, these findings should enable researchers to conduct accurately and efficiently studies involving isolated human stem cell differentiation into osteoblasts and osteoclasts. creator: Shahrul Hisham Zainal Ariffin creator: Ker Wei Lim creator: Rohaya Megat Abdul Wahab creator: Zaidah Zainal Ariffin creator: Rus Dina Rus Din creator: Muhammad Ashraf Shahidan creator: Anis Nabilah Johari creator: Intan Zarina Zainol Abidin uri: https://doi.org/10.7717/peerj.14174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zainal Ariffin et al. title: isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting link: https://peerj.com/articles/14205 last-modified: 2022-10-17 description: Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5′-end variations (5′-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)—a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5′-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5′-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5′-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5′-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5′-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p—+1, hsa-miR-192-5p—+1 and hsa-miR-148a-3p—0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer. creator: Stepan Nersisyan creator: Aleksandra Gorbonos creator: Alexey Makhonin creator: Anton Zhiyanov creator: Maxim Shkurnikov creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.14205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nersisyan et al. title: Signal peptidase 21 suppresses cell proliferation, migration, and invasion via the PTEN-PI3K/Akt signaling pathway in lung adenocarcinoma link: https://peerj.com/articles/14206 last-modified: 2022-10-17 description: BackgroundIn a previous study, a total of 568 differentially expressed proteins including the signal peptidase SPC21 were identified from lung adenocarcinoma (LUAD) and paired normal lung tissues. In this study, the role of SPC21 in LUAD progression was investigated.MethodsThe relationships and protein-protein interaction network of proteins differentially expressed between paired LUAD samples and adjacent normal tissues samples were identified via the String and Pajek software, respectively. The expression levels of the hub protein SPC21 were analyzed in 84 LUAD-normal paired tissues via immunohistochemistry. The prognostic value of SPC21 mRNA was investigated in 478 LUAD patients from TCGA and GTEx datasets. siRNAs were used in A549 and NCI-H1299 cells to knockdown SPC21. The SPC21 biological function was evaluated using the CCK-8, EdU, plate colony formation, transwell, wound healing, and adhesion assays.ResultsPatients with lower SPC21 mRNA levels tended to have worse prognosis (overall survival) than those with higher mRNA levels. SPC21 expression was significantly downregulated in LUAD tumor tissues compared with that in paired normal tissues (P < 0.001). Functionally, SPC21 knockdown promoted cell growth, migration, and invasion. Further analyses showed that SPC21 inactivated Akt signaling, and the Akt inhibitor MK-2206 blocked the tumor-promoting effects of SPC21 knockdown.ConclusionsSPC21 plays a tumor suppressor role in LUAD cells by targeting the PTEN-PI3K/Akt axis and might be used as a prognostic indicator and therapeutic target in LUAD patients. creator: Na Zhang creator: Shiguang Cao creator: Ruiying Sun creator: Yibei Wang creator: Luna Liu creator: Wei Wang creator: Xia Meng uri: https://doi.org/10.7717/peerj.14206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Hand port-site infection after hand-assisted laparoscopic donor nephrectomy for living-donor kidney transplantation: a retrospective cohort study link: https://peerj.com/articles/14215 last-modified: 2022-10-17 description: BackgroundHand-assisted laparoscopic donor nephrectomy (HALDN) is widely performed to minimize burden on living kidney donors. However, hand port-site infections after HALDN may occur. This study aimed to assess the impact of donor characteristics including preoperative comorbidities and operative factors on hand port-site infection after HALDN.MethodsIn this single-center, retrospective cohort study, 1,260 consecutive HALDNs for living-donor kidney transplantation performed between January 2008 and December 2021 were evaluated. All living donors met the living kidney donor guidelines in Japan. Hand port-site infections were identified in 88 HALDN cases (7.0%). To investigate risk factors for hand port-site infection, donor characteristics including preoperative comorbidities such as hypertension, glucose intolerance, dyslipidemia, obesity, and operative factors such as operative duration, blood loss, preoperative antibiotic prophylaxis, and prophylactic subcutaneous suction drain placement at the hand port-site were analyzed using logistic regression analysis.ResultsIn the multivariate analysis, significant differences were identified regarding sex (P = 0.021; odds ratio [OR], 1.971; 95% confidence interval [CI], 1.108–3.507), preoperative antibiotic prophylaxis (P < 0.001; OR, 0.037; 95% CI [0.011–0.127]), and prophylactic subcutaneous suction drain placement at the hand port-site (P = 0.041; OR, 2.005; 95% CI [1.029–3.907]). However, a significant difference was not identified regarding glucose intolerance (P = 0.572; OR, 1.148; 95% CI [0.711–1.856]). Preoperative comorbidities may not cause hand port-site infections within the donors who meet the living kidney donor guidelines. Preoperative antibiotic prophylaxis is crucial in preventing hand port-site infection, whereas prophylactic subcutaneous suction drain placement may increase the risk of hand port-site infection. creator: Takahisa Hiramitsu creator: Toshihide Tomosugi creator: Kenta Futamura creator: Manabu Okada creator: Norihiko Goto creator: Toshihiro Ichimori creator: Shunji Narumi creator: Kazuharu Uchida creator: Yoshihiko Watarai uri: https://doi.org/10.7717/peerj.14215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hiramitsu et al. title: Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms link: https://peerj.com/articles/14221 last-modified: 2022-10-17 description: Real-time quantitative PCR (RT-qPCR) is a widely applied technique for relative quantification of gene expression. In this context, the selection of a suitable reference gene (RG) is an essential step for obtaining reliable and biologically relevant RT-qPCR results. The present study aimed to determine the expression stability of commonly used RGs in mouse skeletal muscle tissue. The expression pattern of eight RGs (ACTB, GAPDH, HPRT, YWHAZ, B2M, PPIA, TUBA and 18S) were evaluated by RT-qPCR in different sample groups classified based on genetic background, muscle tissue type, and growth stage, as well as in a C2C12 myoblast cell line model. Five computational programs were included in the study (comparative ΔCq value, NormFinder, BestKeeper, geNorm, RefFinder) to evaluate the expression stability of RGs. Furthermore, the normalization effects of RGs in soleus (SOL) and gastrocnemius (GAS) muscle tissue were evaluated. Collectively, ACTB, HPRT and YWHAZ were shown to be the most stable RGs, while GADPH and 18S were the least stable. Therefore, the combined use of ACTB, HPRT and YWHAZ is recommended for the normalization of gene expression results in experiments with murine skeletal muscle. The results discussed herein provide a foundation for gene expression analysis by RT-qPCR in mammalian skeletal muscle. creator: Jianfeng Ma creator: Jingyun Chen creator: Mailin Gan creator: Lei Chen creator: Ye Zhao creator: Lili Niu creator: Yan Zhu creator: Shunhua Zhang creator: Xuewei Li creator: Zongyi Guo creator: Jinyong Wang creator: Li Zhu creator: Linyuan Shen uri: https://doi.org/10.7717/peerj.14221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ma et al. title: Effects of jasmonic acid in foliar spray and an humic acid amendment to saline soils on forage sorghum plants’ growth and antioxidant defense system link: https://peerj.com/articles/13793 last-modified: 2022-10-14 description: Salinity is one of the primary abiotic stresses that cause negative physiological and biochemical changes due to the oxidative stress caused by the generation of reactive oxygen species (ROS). The effect of jasmonic acid (JA) as foliar spray and humic acid (HA) as soil amendment on the growth and biochemical attributes of forage sorghum plants exposed to salinity stress was investigated. Soil treated with NaCl at levels of 0, 2, and 4 g NaCl kg−1 dry soil (designated as S0, S1, and S2) and soil amendment with humic acid at 0, 3, and 6 g HA kg−1 dry soil (designated as HA0, HA1, and HA2). The plants were sprayed with three JA levels, including 0, 5, and 10 mM JA. Salinity stress increased carotenoid and soluble protein content, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content. In contrast, salinity stress reduced plant height, leaf area, relative growth rate, proline content, and the activity of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). At the S2 salinity level, HA2 rate increased plant high by 9.7%, relative growth rate by 70.8% and CAT by 45.5, while HA1 increased leaf area by 12.5%, chlorophyll content by 22.3%, carotenoid content by 38.1%, SOD activity by 20.9%, MDA content by 18.0%, POD activity by 24.6% and APX value by 21.7%. At the S2 salinity level, the highest plant height, chlorophyll content, soluble protein content and APX value were recorded at 5 mM JA, while the highest leaf area, the content of carotenoid, proline, and MDA, and the activity of POD and CAT were achieved at 10 mM JA. Generally, 10 mM JA and 3 g HA kg−1 dry soil produced the best positive effects on forage sorghum plants physiological responses. Our study suggested that jasmonic acid and humic acid at appropriate rates can successfully mitigate the adverse effects of salinity stress on forage sorghum. creator: Adam Yousif Adam Ali creator: Guisheng Zhou creator: Aboagla Mohammed Elsiddig creator: Guanglong Zhu creator: Tianyao Meng creator: Xiurong Jiao creator: Irshad Ahmed creator: Ebtehal Gabralla Ibrahim Salih creator: Muhi Eldeen Hussien Ibrahim uri: https://doi.org/10.7717/peerj.13793 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ali et al. title: Virulence characteristics of Blumeria graminis f. sp. tritici and its genetic diversity by EST-SSR analyses link: https://peerj.com/articles/14118 last-modified: 2022-10-14 description: Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (an obligate biotrophic pathogen) is a worldwide threat to wheat production that occurs over a wide geographic area in China. For monitoring genetic variation and virulence structure of Blumeria graminis f. sp. tritici in Liaoning, Heilongjiang, and Sichuan in 2015, 31 wheat lines with known Powdery mildew resistance genes and 2 EST-SSR markers were used to characterize the virulence and genetic diversity. Results indicated that 90% of all isolates were virulent on Pm3c, Pm3e, Pm3f, Pm4a, Pm5, Pm6 (Timgalen), Pm7, Pm16, Pm19, and Pm1 + 2 + 9 and 62.6% to 89.9% of isolates were virulent on Pm3a, Pm3b, Pm3d, Pm4b, Pm6 (Coker747), Pm8, Pm17, Pm20, Pm23, Pm30, Pm4 + 8, Pm5 + 6, Pm4b + mli, Pm2 + mld, Pm4 + 2X, Pm2 + 6. The Pm13 and PmXBD genes were effective against most collected isolates from Liaoning and Heilongjiang Provinces. Only Pm21 exhibited an immune infection response to all isolates. Furthermore, closely related isolates within each region were distinguished by cluster analyses using EST-SSR representing some gene exchanges and genetic relationships between the flora in Northeast China (Liaoning, Heilongjiang) and Sichuan. Only 45% of the isolates tested show a clear correlation between EST-SSR genetic polymorphisms and the frequency of virulence gene data. However, the EST-SSR polymorphism of isolated genes did not correspond to the virulence diversity of isolates in the single-gene lineage identification of hosts. creator: Yazhao Zhang creator: Xianxin Wu creator: Wanlin Wang creator: Yiwei Xu creator: Huiyan Sun creator: Yuanyin Cao creator: Tianya Li creator: Mansoor Karimi-Jashni uri: https://doi.org/10.7717/peerj.14118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: The correlation between illness perception, pain intensity and quality of life in elderly with low back pain in Denmark: a cross-sectional study link: https://peerj.com/articles/14129 last-modified: 2022-10-14 description: BackgroundIllness perception is related to management patterns and pain intensity, but among elderly with low back pain, this relation is unclear. The aims of this study were to analyse the associations between illness perception, pain intensity and health related quality of life in a group of elderly with low back pain and explore how different illness perception profiles would cluster and differ in terms of pain, quality of life and choice of management.MethodThis was a cross-sectional survey based on a cohort of originally 640 Danish children. Of the 311 respondents in 2019, 69% reported low back pain within last year and were included. Associations between illness perceptions (Brief illness perception questionnaire), health related quality of life (EuroQol-5 Domain-3L) and low back pain intensity were assessed, and participants were clustered based on their perceptions using hierarchical and K-means cluster analysis. Cluster differences in pain, quality of life and use of pharmacological and non-pharmacological treatments were explored.ResultsAmong the 213 individuals with low back pain, 33% reported severe or fluctuating pain intensity. Higher pain intensity was associated with perceiving low back pain as a greater threat. Participants reporting fluctuating pain perceived their low back pain almost as threatening as participants reporting severe pain. Two clusters were identified. Cluster 1 reported lower quality of life (difference in medians: −0.176 (95% CI [−0.233–−0.119 ])) and was more likely to report severe or fluctuating pain (37.7% vs. 4.5% [P < 0.0001]) and to use pharmacological treatments than Cluster 2 (37.7% vs. 14.9% [P < 0.001]). No association was found between clusters concerning use of non-pharmacological treatments (P = 0.134).ConclusionBased on illness perceptions, two clusters differing in pain intensity, quality of life and use of pharmacological treatments were identified. Targeting illness perceptions may be beneficial during rehabilitation or when guiding patients with low back pain in choice of management. creator: Elisabeth Ginnerup-Nielsen creator: Mette Harreby creator: Robin Christensen creator: Henning Bliddal creator: Marius Henriksen uri: https://doi.org/10.7717/peerj.14129 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ginnerup-Nielsen et al. title: Fermentation characteristics of bedded pack barn dairy cattle manure on methane yield, carbon, and nitrogen content in solid-state anaerobic digestion link: https://peerj.com/articles/14134 last-modified: 2022-10-14 description: This study aimed to estimate the fermentation characteristics of bedded pack barn dairy cattle manure (BDCM) in terms of methane yield, fibrous material, and nitrogen content in batch solid-state anaerobic digestion (SSAD). SSAD was performed in triplicate using a 1,400 ml polypropylene bottle at a constant temperature of 39 °C until less than 1% methane was produced. The cumulative methane content of BDCM was 142.5 N mL/g volatile solids (VSs). The methane content rapidly increased for 18 days, reaching 63.4 ± 4.6% until the end of the experiment. The ultimate biodegradability and total VS removal of BDCM were 23.1 and 19.0%, respectively. The slopes of the non-fibrous and hemicellulose carbon fractions, and acid detergent insoluble carbon by digestion time were −0.174 (p < 0.001), −0.141 (p = 0.003), and −0.051 (p < 0.001), respectively. The non-fibrous and hemicellulose nitrogen fraction contents quadratically decreased during SSAD (p = 0.001 and p = 0.008). No significant decrease was observed in the acid detergent insoluble nitrogen content (p = 0.840). The results of the present study provide basic data on the digestion characteristics of BDCM and could help determine fermentation conditions in the anaerobic digestion of BDCM. creator: Yongjun Choi creator: Sangrak Lee creator: Duck-Min Ha creator: Youngjun Na creator: Doo-Hwan Kim uri: https://doi.org/10.7717/peerj.14134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Choi et al.