title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=634 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Studying kinematic linkage of finger joints: estimation of kinematics of distal interphalangeal joints during manipulation link: https://peerj.com/articles/14051 last-modified: 2022-10-04 description: The recording of hand kinematics during product manipulation is challenging, and certain degrees of freedom such as distal interphalangeal (DIP) joints are difficult to record owing to limitations of the motion capture systems used. DIP joint kinematics could be estimated by taking advantage of its kinematic linkage with proximal interphalangeal (PIP) and metacarpophalangeal joints. This work analyses this linkage both in free motion conditions and during the performance of 26 activities of daily living. We have studied the appropriateness of different types of linear regressions (several combinations of independent variables and constant coefficients) and sets of data (free motion and manipulation data) to obtain equations to estimate DIP joints kinematics both in free motion and manipulation conditions. Errors that arise when estimating DIP joint angles assuming linear relationships using the equations obtained both from free motion data and from manipulation data are compared for each activity of daily living performed. Estimation using manipulation condition equations implies a lower mean absolute error per task (from 5.87° to 13.67°) than using the free motion ones (from 9° to 17.87°), but it fails to provide accurate estimations when passive extension of DIP joints occurs while PIP is flexed. This work provides evidence showing that estimating DIP joint angles is only recommended when studying free motion or grasps where both joints are highly flexed and when using linear relationships that consider only PIP joint angles. creator: Alba Roda-Sales creator: Joaquín L. Sancho-Bru creator: Margarita Vergara uri: https://doi.org/10.7717/peerj.14051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Roda-Sales et al. title: Theacrine alleviates sepsis-induced acute kidney injury by repressing the activation of NLRP3/Caspase-1 inflammasome link: https://peerj.com/articles/14109 last-modified: 2022-10-04 description: Acute kidney injury (AKI) is a frequent and serious complication of sepsis, which results in a rapid decline of kidney function. Currently, there are no curative therapies for AKI. Theacrine is a purine alkaloid and exerts significant role in regulating inflammation, oxidative stress, and mood elevation. The study aims to evaluate the biological role and potential mechanism of theacrine in septic AKI. The murine and cellular models of septic AKI were established in lipopolysaccharide (LPS)-treated C57BL/6 mice and HK-2 cells, respectively. The effect of theacrine on alleviating septic AKI was assessed after pretreatment with theacrine in vivo and in vitro. We found that theacrine treatment significantly alleviated LPS-induced kidney injury, as evidenced by decreased levels of kidney injury markers (blood urea nitrogen and creatinine), inflammatory factors (IL-1β and IL-18), and cell apoptosis in vivo and in vitro. Mechanistically, theacrine markedly repressed the activation of NOD-like receptor (NLR) pyrin domain-containing protein 3 (NLRP3)inflammasome. As expected, MCC950 (a specific inhibitor of NLRP3) treatment also decreased LPS-induced production of IL-18 and IL-1β and cell apoptosis in HK-2 cells. More important, Nigericin sodiumsalt (a NLRP3 agonist) damaged the effect of theacrine on repressing kidney injury markers (blood urea nitrogen and creatinine), pro-inflammatory cytokines (IL-18 and IL-1β), and cell apoptosis. Taken together, these results demonstrate that theacrine alleviates septic AKI, at least in part by repressing the activation of NLRP3 inflammasome. creator: Maoxian Yang creator: Peng Shen creator: Longsheng Xu creator: Min Kong creator: Congcong Yu creator: Yunchao Shi uri: https://doi.org/10.7717/peerj.14109 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Yang et al. title: Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance link: https://peerj.com/articles/14113 last-modified: 2022-10-04 description: The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization. creator: Alexey A. Kotov creator: Derek J. Taylor uri: https://doi.org/10.7717/peerj.14113 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kotov and Taylor title: Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages link: https://peerj.com/articles/14125 last-modified: 2022-10-04 description: BackgroundArmeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels.MethodsSeed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT).ResultsRapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding. creator: Yueliang Wu creator: Wenya Gao creator: Xinli Li creator: Shilin Sun creator: Jian Xu creator: Xiaoqiong Shi creator: Huiyan Guo uri: https://doi.org/10.7717/peerj.14125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wu et al. title: Specific lifestyle factors and in vitro fertilization outcomes in Romanian women: a pilot study link: https://peerj.com/articles/14189 last-modified: 2022-10-04 description: BackgroundInfertility is an important health concern worldwide. Although lifestyle habits and behaviors have been widely reported as predictors of IVF outcomes by previous studies, they have not been reported for Romanian women undergoing IVF. In this regard, our pilot study aimed to begin to address the data gap by assessing lifestyle predictors of in vitro fertilization (IVF) outcomes in Romanian women.Study designOur pilot study included 35 participants who completed a first IVF cycle at a single infertility center. We evaluated individual self-reported lifestyle habits and behaviors as predictors of IVF outcomes, and employed principal component analysis (PCA) to characterize multiple lifestyle habits and behaviors into personal care product (PCP) use, and healthy diet and physical activity patterns as predictors of IVF outcomes.ResultsOur PCA analysis showed that greater use of PCPs was associated with lower probabilities of pregnancy (RR: 0.92, 95% CI [0.87–0.98]) and live birth (RR: 0.94, 95% CI [0.88–1.01]) while, the healthy dietary habits and physical activity were associated with a higher likelihood of pregnancy, although without statistical significance (RR: 1.10, 95% CI [0.93–1.30]).ConclusionsIn this pilot study we identified associations between IVF outcomes among Romanian women and certain lifestyle habits and behaviors including stress, diet and physical activity, and certain PCP use. We also estimated the joint effects of multiple lifestyle factors using PCA and found that PCP use, healthy dietary habits and physical activity were associated with IVF outcomes. creator: Iulia A. Neamtiu creator: Mihai Surcel creator: Thoin F. Begum creator: Eugen S. Gurzau creator: Ioana Berindan-Neagoe creator: Cornelia Braicu creator: Ioana Rotar creator: Daniel Muresan creator: Michael S. Bloom uri: https://doi.org/10.7717/peerj.14189 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Neamtiu et al. title: First eumonostiliferous nemertean from the Nishi-Shichito Ridge, Genrokunemertes obesa gen. et sp. nov. (Eumonostilifera, Nemertea) link: https://peerj.com/articles/13857 last-modified: 2022-10-03 description: Nemerteans are mostly marine, benthic invertebrates, inhabiting intertidal to hadal zones. Recently, they have been recognized from deep sea with environmental DNA (eDNA) metabarcoding of sediment samples whereas any records from the locations and/or the water depth have not been documented in nemertean taxonomic publications to date. It suggests that there are major gaps between deep-sea nemertean fauna observed with eDNA and taxonomic knowledge. During a research expedition in 2021, we obtained a single specimen of eumonostiliferous nemertean from the southern part of Genroku Seamount Chain, the Nishi-Shichito Ridge, where any nemertean species have never been reported. Subsequent morphological and molecular examination reveal that the species is placed in a new genus and herein described as Genrokunemertes obesa gen. et sp. nov. It resembles shallow-water-dwelling Kurilonemertes and Typhloerstedia, but differs from the former in lacking eyes and the latter in possessing well-developed cephalic glands and lacking accessory nerves of lateral nerve cords. In terms of genetic distances based on partial sequences of the cytochrome c oxidase subunit I gene, G. obesa gen. et sp. nov. is closest to Monostilifera sp. Owase collected from Japan, which is characterized by large four eyes; the COI distance is higher than commonly observed interspecific divergences in eumonostiliferans. creator: Natsumi Hookabe creator: Keita Koeda creator: Yoshihiro Fujiwara creator: Shinji Tsuchida creator: Rei Ueshima uri: https://doi.org/10.7717/peerj.13857 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hookabe et al. title: Does treating proximal cavities in primary molars non-restoratively affect intra-arch space and alignment of successor teeth negatively? A 4-year longitudinal study link: https://peerj.com/articles/14008 last-modified: 2022-10-03 description: BackgroundRemoving plaque with toothbrush and toothpaste from proximal cavities in primary molars without restoring them follows sound cariological principles. But does this treatment affect space for and alignment of their permanent successors negatively?HypothesisThere is no difference in impaction and displacement of the premolars, as well as in the D+E space in quadrants with three different statuses of the proximal surface of primary molars over a 4-year period.MethodsA total of 936 quadrants (466 maxillary and 470 mandibular quadrants) in 233 children were assessed. Treatment of cavities in the proximal surfaces of the primary molars consisted of amalgam and ART restorations using high-viscosity glass-ionomer cement, and cleaning of open large- and medium-sized cavities with toothbrush and toothpaste (UCT) under supervision for 220 days per year over 3 years. Dental casts were made at baseline, and after two, three, and 4 years. The D+E spaces were measured digitally. Status of the proximal surface of the primary molars was assessed by two calibrated examiners, and quadrants were grouped into normal anatomy, defective restoration, and proximal cavity. ANCOVA, ANOVA and LSD tests were applied.ResultsThere was a statistically significant difference between groups (p<= 0.001) and between evaluation times (p < 0.001), for the D+E space in both the maxilla and mandible. A sex difference related to the D+E space in the maxilla was found (p = 0.007). For boys, quadrants in the maxilla of the group ‘proximal cavity’ showed a significant shorter D+E space when compared to quadrants of the group ‘normal anatomy’ at the 3- and 4-year evaluation time. For girls the difference between the two groups was only present at the 3-year evaluation time. There was no significant difference between the D+E space in quadrants with defective restorations and those with normal anatomy in the mandible and in the maxilla. Displacement and impaction of the premolars showed no significant difference between groups.ConclusionPrimary molars with open proximal cavities that are cleaned with toothbrush and toothpaste do not result in displacement and impaction of the successor teeth, neither do primary molars with defective restorations in proximal tooth surfaces. creator: Rafael T. Gomide creator: Jo E. Frencken creator: Jorge Faber creator: Anne Marie Kuijpers-Jagtman uri: https://doi.org/10.7717/peerj.14008 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gomide et al. title: SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells link: https://peerj.com/articles/14084 last-modified: 2022-10-03 description: BackgroundRNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis.MethodsWe overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing.ResultsSERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis.ConclusionsWe for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression. creator: Junjie Zhou creator: Wenhao Chen creator: Qianwen He creator: Dong Chen creator: Chunguang Li creator: Congqing Jiang creator: Zhao Ding creator: Qun Qian uri: https://doi.org/10.7717/peerj.14084 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) link: https://peerj.com/articles/14087 last-modified: 2022-10-03 description: BackgroundDNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet.MethodsUsing the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns.ResultsFifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry. creator: Tianjie Li creator: Xiaoyu Wang creator: Dinakaran Elango creator: Weihua Zhang creator: Min Li creator: Fan Zhang creator: Qi Pan creator: Ying Wu uri: https://doi.org/10.7717/peerj.14087 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions link: https://peerj.com/articles/14088 last-modified: 2022-10-03 description: BackgroundNitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification.Materials and MethodsA simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively.Results and discussionsSoil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA.ConclusionsPNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions. creator: Xiaolan Zhang creator: Xuan Shan creator: Hongdan Fu creator: Zhouping Sun uri: https://doi.org/10.7717/peerj.14088 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al.