title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=409 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Loss of Farnesoid X receptor (FXR) accelerates dysregulated glucose and renal injury in db/db mice link: https://peerj.com/articles/16155 last-modified: 2023-09-29 description: BackgroundEnd-stage renal disease is primarily caused by diabetic kidney disease (DKD). The Farnesoid X receptor (FXR), a member of the nuclear receptor superfamily, has anti-inflammatory, lipid-lowering and hypoglycemic properties. It also inhibits renal fibrosis. Although its physiological role is not fully understood, it also plays a role in the control of diabetic nephropathy (DN).MethodsIn the present study, we examined male FXR & leptin receptor double knockout mice, in which weight, blood glucose, body fat, and other indicators were monitored. After 6 months of rearing, blood and urine samples were collected and biochemical parameters were measured. Fibrosis was assessed by Masson’s stain, while the assessment of the resuscitation case’s condition was performed using succinate dehydrogenase (SDHA) stain immunohistochemistry, which measures aerobic respiration. Expression of molecules such as connective tissue growth factor (CTGF), SMAD family members 3 (Smad3) and 7 (Smad7), and small heterodimer partner were detected by RT-PCR and Western blotting as part of the application.ResultsFXR knockout decreased body weight and body fat in db/db mice, but increased blood glucose, urine output, and renal fibrosis. Primary mesangial cells (P-MCs) from FXR+/ + mice stimulated with transforming growth factor β1 (TGFβ1) showed significantly higher levels of related fibrosis factors, TGFβ1 and Smad3 mRNA and protein, and significantly reduced levels of Smad7. These effects were reversed by the action of FXR agonist chenodeoxycholic acid (CDCA). P-MCs from FXR−/ − mice stimulated with TGFβ1 resulted in an increase in the expression and protein levels of collagen I and TGFβ1, and the addition of CDCA had no significant effect on TGFβ1 stimulation. However, compared with FXR+/ +db/db mice, the rate of oxygen consumption, the rate of carbon dioxide production, and the rate of energy conversion were increased in FXR−/ −db/db mice, whereas the SDHA succinate dehydrogenase, a marker enzyme for aerobic respiration, was significantly decreased.ConclusionsThese results provide evidence that FXR plays a critical role in the regulation of mesangial cells in DN. The likely mechanism is that aberrant FXR expression activates TGFβ1, which induces extracellular matrix accumulation through the classical Smad signaling pathway, leading to mitochondrial dysfunction. creator: Yuxiang Qiu creator: Ningsu Kang creator: Xi Wang creator: Yao Yao creator: Jun Cui creator: Xiaoyan Zhang creator: Lu Zheng uri: https://doi.org/10.7717/peerj.16155 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Qiu et al. title: Six-minute rowing test: a practical tool for training prescription, from ventilatory thresholds and power outputs, in amateur male rowers link: https://peerj.com/articles/16160 last-modified: 2023-09-29 description: BackgroundThe 6-minute rowing ergometer test (6-minRT) is valid and reliable for establishing maximal aerobic power (MAP) in amateur male rowers. However, ventilatory thresholds (VTs) have not yet been established with their mechanical correspondence in this test.ObjectiveThe primary objective was to determine the VTs in the 6-minRT achieved by amateur male rowers, while the secondary objective was to determine the correspondence between ventilatory, mechanical, and heart rate (HR) outcomes of the 6-minRT.MethodsSixteen amateur male rowers were part of the study. All participants were instructed to perform an incremental test (IT) and a 6-minRT. Determination of the ventilatory parameters for the first ventilatory threshold (VT1), the second ventilatory threshold (VT2), and 6minRTVO2max were performed by correlating the outcomes of VT1, VT2, and VO2max obtained in the IT, with the outcomes of 6-minRT. For these purposes, Pearson’s test was used, with the following criteria: trivial, <0.1; small, 0.1–0.3; moderate, 0.3–0.5; high, 0.5–0.7; very high, 0.7–0.9; or practically perfect, >0.9. The significance level was p < 0.05.ResultsThe IT analysis determined that VT1 and VT2 correspond to 55 and 80% of VO2max, respectively. A high correlation was observed between IT outcomes in VT1, VT2, and VO2max, with the outcomes of 6-minRT (r > 0.6).ConclusionBased on IT ventilatory parameters and concordance analysis, VT1 and VT2 of 6-minRT are determined at 55 and 80%, respectively, of both ventilatory parameters and their corresponding mechanical outcomes and HR. creator: Álvaro Huerta Ojeda creator: Miguel Riquelme Guerra uri: https://doi.org/10.7717/peerj.16160 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huerta Ojeda and Riquelme Guerra title: Genome-wide identification of DUF506 gene family in Oryzasativa and expression profiling under abiotic stresses link: https://peerj.com/articles/16168 last-modified: 2023-09-29 description: The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future. creator: Wei Dong creator: Jian Tu creator: Wei Deng creator: Jianhua Zhang creator: Yuran Xu creator: Anyu Gu creator: Hua An creator: Kui Fan creator: Rui Wang creator: Jianping Zhang creator: Limei Kui creator: Xiaolin Li uri: https://doi.org/10.7717/peerj.16168 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dong et al. title: Effects of the age of raised beds on the physicochemical characteristics of fruit orchard soil in the Vietnamese Mekong Delta link: https://peerj.com/articles/16178 last-modified: 2023-09-29 description: To grow fruit plants, farmers in the Vietnamese Mekong Delta (VMD) must use raised bed constructions to avoid waterlogging during the rainy season. This study aimed to evaluate the effects of the age of the raised beds on the soil physicochemical properties of longan orchards located in the VMD. Two raised bed systems were evaluated: a young bed constructed 10 years ago and an old bed constructed 42 years ago. Soil samples were collected from five different soil layers (0–20, 20–40, 40–60, 60–80, and 80–100 cm) with four replicates per layer. Soil samples were tested for pH, electrical conductivity (EC), available phosphorus (AP), total nitrogen (TN), soil organic matter (SOM), exchangeable cations (Ca2+, K+, Mg2+, and Na+), cation exchange capacity (CEC), bulk density (BD), soil porosity, available water-holding capacity (AWC), particle composition (sand, silt, and clay), and size. The soil pH was approximately 1.0 units lower in the old bed compared to the young bed at depths of 0–20 and 20–40 cm. The BD was higher in the old bed (0.15 g cm−3) than in the young bed at a soil depth of 0.4 m. SOM, AP, exchangeable cations (Ca2+, Na+, and Mg2+), AWC, and soil porosity were significantly lower in both the topsoil (0–20 cm) and subsoil (20–40 cm) layers in the old bed than in the young bed. In particular, the SOM, AP, AWC, and soil porosity contents in the old bed decreased by 18%, 20%, 15%, and 17%, respectively, compared with those in the young bed at soil depths of 0–40 cm. Therefore, cultivating raised bed soil for a longer period significantly reduced the soil exchangeable cations, porosity, and fertility of the surface and subsurface soils. Based on these results, farmers should use soil conservation practices, such as cover crops, rice straw mulching, and soil amendments in their orchards to mitigate topsoil degradation. creator: Le Van Dang creator: Ngo Ngoc Hung uri: https://doi.org/10.7717/peerj.16178 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dang and Hung title: Comparative Assessment of SSR and RAPD markers for genetic diversity in some Mango cultivars link: https://peerj.com/articles/15722 last-modified: 2023-09-28 description: Genetic improvement mainly depends on the level of genetic variability present in the population, and the degree of genetic diversity in a population largely determines the rate of genetic advancement. For analyzing genetic diversity and determining cultivar identities, a molecular marker is a useful tool. Using 30 SSR (simple sequence repeat) and 30 RAPD (randomly amplified polymorphic DNA) markers, this study evaluated the genetic divergence of 17 mango cultivars. The effectiveness of the two marker systems was evaluated using their genetic diversity characteristics. Additionally, the effects of SM (simple matching) and Dice similarity coefficients and their effects on mango clustering were evaluated. The findings showed that SSR markers generated 192 alleles, all of which were polymorphic (100%). With RAPD markers, 434 bands were obtained, 361 of which were polymorphic (83%). The average polymorphic information content (PIC) for RAPD and SSR was 0.378 and 0.735, respectively. Using SSR markers resulted in much higher values for other genetic diversity parameters compared to RAPD markers. Furthermore, grouping the genotypes according to the two similarity coefficients without detailed consideration of these coefficients could not influence the study results. The RAPD markers OPA_01, OPM_12 followed by OPO_12 and SSR markers MIAC_4, MIAC_5 followed by mMiCIR_21 were the most informative in terms of describing genetic variability among the cultivars under study; they can be used in further investigations such as genetic mapping or marker-assisted selection. Overall, ‘Zebda’ cultivar was the most diverse of the studied cultivars. creator: Mohammed A. A. Hussein creator: Manal Eid creator: Mehdi Rahimi creator: Faten Zubair Filimban creator: Diaa Abd El-Moneim uri: https://doi.org/10.7717/peerj.15722 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 A. A. Hussein et al. title: A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures link: https://peerj.com/articles/15758 last-modified: 2023-09-28 description: Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified—V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture. creator: Khor Waiho creator: Muhammad Syafiq Abd Razak creator: Mohd Zaidy Abdul Rahman creator: Zainah Zaid creator: Mhd Ikhwanuddin creator: Hanafiah Fazhan creator: Alexander Chong Shu-Chien creator: Nyok-Sean Lau creator: Ghazali Azmie creator: Ahmad Najmi Ishak creator: Mohammad Syahnon creator: Nor Azman Kasan uri: https://doi.org/10.7717/peerj.15758 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Waiho et al. title: Life on the edge—a changing genetic landscape within an iconic American pika metapopulation over the last half century link: https://peerj.com/articles/15962 last-modified: 2023-09-28 description: Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948–1949, 1988–1991, 2013–2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988–1991 and 2013–2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability. creator: Kelly B. Klingler creator: Lyle B. Nichols creator: Evon R. Hekkala creator: Joseph A. E. Stewart creator: Mary M. Peacock uri: https://doi.org/10.7717/peerj.15962 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Klingler et al. title: Basal sauropodomorph locomotion: ichnological lessons from the Late Triassic trackways of bipeds and quadrupeds (Elliot Formation, main Karoo Basin) link: https://peerj.com/articles/15970 last-modified: 2023-09-28 description: Using modern ichnological and stratigraphic tools, we reinvestigate two iconic sauropodomorph-attributed tetradactyl ichnogenera, Pseudotetrasauropus and Tetrasauropus, and their stratigraphic occurrences in the middle Upper Triassic of Lesotho. These tracks have been reaffirmed and are stratigraphically well-constrained to the lower Elliot Formation (Stormberg Group, Karoo Basin) with a maximum depositional age range of <219–209 Ma (Norian). This represents the earliest record of basal sauropodomorph trackways in Gondwana, if not globally. Track and trackway morphology, the sedimentary context of the tracks, and unique features (e.g., drag traces) have enabled us to discuss the likely limb postures and gaits of the trackmakers. Pseudotetrasauropus has bipedal (P. bipedoida) and quadrupedal (P. jaquesi) trackway states, with the oldest quadrupedal Pseudotetrasauropus track and trackway parameters suggestive of a columnar, graviportal limb posture in the trackmaker. Moreover, an irregularity in the intermanus distance and manus orientation and morphology, in combination with drag traces, is indicative of a non-uniform locomotory suite or facultative quadrupedality. Contrastingly, Tetrasauropus, the youngest trackway, has distinctive medially deflected, robust pedal and manual claw traces and a wide and uniform intermanus distance relative to the interpedal. These traits suggest a quadrupedal trackmaker with clawed and fleshy feet and forelimbs held in a wide, flexed posture. Altogether, these trackways pinpoint the start of the southern African ichnological record of basal sauropodomorphs with bipedal and quadrupedal locomotory habits to, at least, c. 215 Ma in the middle Late Triassic. creator: Lara Sciscio creator: Emese M. Bordy creator: Martin G. Lockley creator: Miengah Abrahams uri: https://doi.org/10.7717/peerj.15970 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sciscio et al. title: Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA link: https://peerj.com/articles/16047 last-modified: 2023-09-28 description: BackgroundThe Galapagos sea lion, Zalophus wollebaeki, is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for Zalophus genus—the other two species employed Sanger sequencing—by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case.Materials and MethodsWe used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial Zalophus DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock.ResultsFrom the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of Z. wollebaeki in a clade with Z. californianus, and Z. japonicus, and sister to Z. californianus; as well as establishing the divergence time for Z. wollebaeki 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals. creator: Pacarina Asadobay creator: Diego O. Urquía creator: Sven Künzel creator: Sebastian A. Espinoza-Ulloa creator: Miguel Vences creator: Diego Páez-Rosas uri: https://doi.org/10.7717/peerj.16047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Asadobay et al. title: Fluorofenidone alleviates liver fibrosis by inhibiting hepatic stellate cell autophagy via the TGF-β1/Smad pathway: implications for liver cancer link: https://peerj.com/articles/16060 last-modified: 2023-09-28 description: ObjectivesLiver fibrosis is a key stage in the progression of various chronic liver diseases to cirrhosis and liver cancer, but at present, there is no effective treatment. This study investigated the therapeutic effect of the new antifibrotic drug fluorofenidone (AKF-PD) on liver fibrosis and its related mechanism, providing implications for liver cancer.Materials and MethodsThe effects of AKF-PD on hepatic stellate cell (HSC) autophagy and extracellular matrix (ECM) expression were assessed in a carbon tetrachloride (CCl4)-induced rat liver fibrosis model. In vitro, HSC-T6 cells were transfected with Smad2 and Smad3 overexpression plasmids and treated with AKF-PD. The viability and number of autophagosomes in HSC-T6 cells were examined. The protein expression levels of Beclin-1, LC3 and P62 were examined by Western blotting. The Cancer Genome Atlas (TCGA) database was used for comprehensively analyzing the prognostic values of SMAD2 and SMAD3 in liver cancer. The correlation between SMAD2, SMAD3, and autophagy-related scores in liver cancer was explored. The drug prediction of autophagy-related scores in liver cancer was explored.ResultsAKF-PD attenuated liver injury and ECM deposition in the CCl4-induced liver fibrosis model. In vitro, the viability and number of autophagosomes in HSCs were reduced significantly by AKF-PD treatment. Meanwhile, the protein expression of FN, α-SMA, collagen III, Beclin-1 and LC3 was increased, and P62 was reduced by the overexpression of Smad2 and Smad3; however, AKF-PD reversed these effects. SMAD2 and SMAD3 were hazardous factors in liver cancer. SMAD2 and SMAD3 correlated with autophagy-related scores in liver cancer. Autophagy-related scores could predict drug response in liver cancer.ConclusionsAKF-PD alleviates liver fibrosis by inhibiting HSC autophagy via the transforming growth factor (TGF)-β1/Smadpathway. Our study provided some implications about how liver fibrosis was connected with liver cancer by SMAD2/SMAD3 and autophagy. creator: Xiongqun Peng creator: Huixiang Yang creator: Lijian Tao creator: Jingni Xiao creator: Ya Zeng creator: Yueming Shen creator: Xueke Yu creator: Fei Zhu creator: Jiao Qin uri: https://doi.org/10.7717/peerj.16060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Peng et al.