title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=628 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Computational study of potential inhibitors for fat mass and obesity-associated protein from seaweed and plant compounds link: https://peerj.com/articles/14256 last-modified: 2022-10-21 description: BackgroundOver the past three decades, with substantial changes in lifestyle, the tendency to gain weight has increased, which is resulting in significant consequences affecting an individual’s well-being. The fat mass and obesity-associated (FTO) gene is involved in food intake and energy expenditure and plays a crucial role in regulating homeostasis and controlling energy expenditure by hindering signals that generate from the brain. Edible seaweeds have been shown to enhance satiety owing to their health benefits.MethodsExtensive screening of plant-derived anti-obesity compounds and seaweed compounds was conducted and validated for ADME properties and toxicity prediction. Further, the top ranked compounds were docked against the FTO protein to identify potential inhibitors and were subjected to molecular dynamic simulation studies to understand the binding stability of ligand protein complex. Finally, MM/PBSA studies were performed to calculate the binding free energy of the protein-ligand complexes.ResultsThrough the virtual screening of 1,210 compounds, 443 compounds showed good docking scores less than −7.00 kcal/mol. Drug likeness screenings of 443 compounds showed that only 369 compounds were in accordance with these properties. Further toxicity prediction resulted in 30 non-toxic compounds. Molecular docking studies revealed four top ranked marine compounds. Finally, RL074 (2-hydroxyluzofuranone B) and RL442 (10-acetoxyangasiol) from marine red alga Laurencia sp showed good stability from molecular dynamic simulation studies. MM/PBSA results revealed that BT012 (24ε-hydroperoxy-6β-hydroxy-24-ethylcholesta-4,-28(29)-dien-3-one), an oxygenated fucosterol from brown alga Turbinaria conoides, possessed higher binding energy. Hence, with all the data obtained it could be concluded that three seaweed compounds, BT012, RL074 and RL442, may act as a potential anti-obesity lead compound in targeting FTO. creator: Lavanya Prabhakar creator: Dicky John Davis G uri: https://doi.org/10.7717/peerj.14256 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Prabhakar and Davis G title: Tubular epithelial progenitors are excreted in urine during recovery from severe acute kidney injury and are able to expand and differentiate in vitro link: https://peerj.com/articles/14110 last-modified: 2022-10-20 description: BackgroundAcute kidney injury (AKI) is a serious condition associated with chronic kidney disease, dialysis requirement and a high risk of death. However, there are specialized repair mechanisms for the nephron, and migrated committed progenitor cells are the key players. Previous work has described a positive association between renal recovery and the excretion of tubular progenitor cells in the urine of kidney transplant recipients. The aim of this work was to describe such structures in non-transplanted AKI patients and to focus on their differentiation.MethodsMorning urine was obtained from four patients with AKI stage 3 and need for RRT on a consecutive basis. Urine sediment gene expression was performed to assess which part of the tubular or glomerular segment was affected by injury, along with measurement of neprilysin. Urine output and sediment morphology were monitored, viable hyperplastic tubular epithelial clusters were isolated and characterized by antibody or cultured in vitro. These cells were monitored by phase contrast microscopy, gene, and protein expression over 9 days by qPCR and confocal immunofluorescence. Furthermore, UMOD secretion into the supernatant was quantitatively measured.ResultsUrinary neprilysin decreased rapidly with increasing urinary volume in ischemic, toxic, nephritic, and infection-associated AKI, whereas the decrease in sCr required at least 2 weeks. While urine output increased, dead cells were present in the sediment along with debris followed by hyperplastic agglomerates. Monitoring of urine sediment for tubular cell-specific gene transcript levels NPHS2 (podocyte), AQP1 and AQP6 (proximal tubule), and SLC12A1 (distal tubule) by qPCR revealed different components depending on the cause of AKI. Confocal immunofluorescence staining confirmed the presence of intact nephron-specific epithelial cells, some of which appeared in clusters expressing AQP1 and PAX8 and were 53% positive for the stem cell marker PROM1. Isolated tubule epithelial progenitor cells were grown in vitro, expanded, and reached confluence within 5–7 days, while the expression of AQP1 and UMOD increased, whereas PROM1 and Ki67 decreased. This was accompanied by a change in cell morphology from a disproportionately high nuclear/cytoplasmic ratio at day 2–7 with mitotic figures. In contrast, an apoptotic morphology of approximately 30% was found at day 9 with the appearance of multinucleated cells that were associable with different regions of the nephron tubule by marker proteins. At the same time, UMOD was detected in the culture supernatant.ConclusionDuring renal recovery, a high replicatory potential of tubular epithelial progenitor cells is found in urine. In vitro expansion and gene expression show differentiation into tubular cells with marker proteins specific for different nephron regions. creator: Daniela Gerges creator: Zsofia Hevesi creator: Sophie H. Schmidt creator: Sebastian Kapps creator: Sahra Pajenda creator: Barbara Geist creator: Alice Schmidt creator: Ludwig Wagner creator: Wolfgang Winnicki uri: https://doi.org/10.7717/peerj.14110 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gerges et al. title: A previously overlooked, highly diverse early Pleistocene elasmobranch assemblage from southern Taiwan link: https://peerj.com/articles/14190 last-modified: 2022-10-20 description: The Niubu fossil locality in Chiayi County, southern Taiwan is best known for its rich early Pleistocene marine fossils that provide insights into the poorly understood past diversity in the area. The elasmobranch teeth at this locality have been collected for decades by the locals, but have not been formally described and have received little attention. Here, we describe three museum collections of elasmobranch teeth (n = 697) from the Liuchungchi Formation (1.90–1.35 Ma) sampled at the Niubu locality, with an aim of constructing a more comprehensive view of the past fish fauna in the subtropical West Pacific. The assemblage is composed of 20 taxa belonging to nine families and is dominated by Carcharhinus and Carcharodon. The occurrence of †Hemipristis serra is of particular importance because it is the first Pleistocene record in the area. We highlight high numbers of large Carcharodon carcharias teeth in our sample correlating to body lengths exceeding 4 m, along with the diverse fossil elasmobranchs, suggesting that a once rich and thriving marine ecosystem in an inshore to offshore shallow-water environment during the early Pleistocene in Taiwan. creator: Chia-Yen Lin creator: Chien-Hsiang Lin creator: Kenshu Shimada uri: https://doi.org/10.7717/peerj.14190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: Effects of different fertilizers on nutrient quality and mineral elements in different economic forage groups in Qilian Mountain alpine meadows link: https://peerj.com/articles/14223 last-modified: 2022-10-20 description: The objective of this study was to examine the responses of nutrient quality and mineral elements of forages in different economic groups forages in the Qilian Mountains alpine meadows to different fertilization treatments. Eight fertilization treatments, potassium (K), nitrogen (N), zinc (Z), boric (B), copper (Cu), phosphorus (P), molybdenum (Mo), and selenium (Se), were sprayed onto forage roots, and no fertilizer was applied as a blank control (CK), with four replicates in each group. The forage trace element contents and nutritional quality of each economic group in to different treatments were determined in mid-August, and the trace element surplus and deficiency were analyzed. Compared with that in the control, the forage crude protein (CP) content in different economic groups under different fertilization treatments increased and fluctuated within the range of 7.7%–23.94%. The dry matter digestibility (DMD) ranged from 38.78% to 77.34% and showed no significant differences in DMD among treatments (P > 0.05). The DMD of legume forages was significantly higher than those of Gramineae grasses and sedges; there were no significant differences in forage acid detergent fiber (ADF) between any treatments and the control (P > 0.05), but ADF showed a decreasing trend in the treatments compared with that in the control. The P content increased by 81.81% in legumes (P < 0.05); however, it decreased by 38.46% and 61.29% in wilted grass and forbs (P < 0.05) and increased in Gramineae grasses and legumes under N treatment by 92.86% and 50% (P < 0.05), respectively. The Cu content under Cu, N, Zn, B and Se treatments increased significantly by 33.81%∼346.49% compared with that in the control. There were no significant differences in Zn content among the economic groups under different treatments (P > 0.05), but legumes showed better absorption of Zn. Consequently, the forages in this study were evaluated as having medium Cu (8.1–20 mg/kg), medium Se (0.11–1.0 mg/kg), and medium (30.1–60 mg/kg) to high (60.1–100 mg/kg) Zn contents. Comprehensive analysis showed that the application of different fertilizers could increase the CP and DMD of various forages, reduce ADF, and effectively improve the nutritional quality of pastures. The contents of N, Cu, Zn, and Se in forages increased under all treatments, and the contents of all forage elements were at appropriate levels. Applying K, N, P, Cu and Mo is beneficial to dominant species in Qilian Mountains alpine meadows. creator: Xin Chen creator: Ting Jiao creator: Zhongnan Nie creator: Degang Zhang creator: Juan Wang creator: Juan Qi uri: https://doi.org/10.7717/peerj.14223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: A novel risk factor of contrast associated acute kidney injury in patients after enhanced computed tomography: a retrospective study link: https://peerj.com/articles/14224 last-modified: 2022-10-20 description: BackgroundContrast associated acute kidney injury (CA-AKI) is a major cause of acute renal failure and the incidence of CA-AKI is still high in recent years. Risk stratification is traditionally based on glomerular filtration rate(GFR). Hence, the aim of this study was to explore the novel risk factors for CA-AKI after enhanced computed tomography (CT).MethodsA retrospective cohort study was conducted in 632 in-hospital patients undergoing enhanced CT. The patients were divided into CA-AKI and no-CA-AKI groups. For comparative analyses, we applied one-to-four cohorts of those two groups using propensity score-matching methods addressing the imbalances of age, gender, weight, and smoking. The baseline clinical and biochemical data were compared. Logistic regression analysis was employed to investigate the CA-AKI risk factors. The receiver operating characteristic (ROC) curve was adopted to test the value of RDW in predicting CA-AKI after enhanced CT.Results25 (3.96%) patients suffered from CA-AKI. Those subjects who developed CA-AKI had advanced age, severer renal functional injury, lower albumin, higher baseline RDW, neutrophil to lymphocyte ratio (NLR) and platelet to lymphocyte ratio (PLR) than those without CA-AKI. It also exhibited more severe anemia including decreased hemoglobin and red blood cell count (all p < 0.05). The baseline RDW, albumin and PLR between the two groups were statistically significant different after PSM. Binary logistic regression analysis showed that baseline RDW, albumin and eGFR were correlated with CA-AKI after contrast-enhanced CT examination. The RDW exhibited moderated discrimination ability for predicting CA-AKI beyond eGFR, with an AUC of 0.803 (95% CI [0.702–0.90]) vs 0.765 (95% CI [0.70–0.83]).ConclusionIncreased baseline RDW and decreased eGFR are risk factors for CA-AKI after enhanced CT. RDW exhibited good predictive value and can be used as an early warning marker for patients suffering from CA-AKI after enhanced CT. creator: You-Qi Li creator: Yongjun Shi creator: Wen-feng Deng creator: Shaobin Xiao creator: Wenwen Hu creator: Chengwen Huang creator: Xun Tang creator: Jun Zhang uri: https://doi.org/10.7717/peerj.14224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Integrated metabolomic and transcriptomic analysis of the anthocyanin and proanthocyanidin regulatory networks in red walnut natural hybrid progeny leaves link: https://peerj.com/articles/14262 last-modified: 2022-10-20 description: BackgroundWalnuts are among the most important dry fruit crops worldwide, typically exhibiting green leaves and yellow–brown or gray–yellow seed coats. A specific walnut accession with red leaves and seed coats, ‘RW-1’, was selected for study because of its high anthocyanin and proanthocyanidin (PA) contents. Anthocyanins and PAs are important secondary metabolites and play key roles in plant responses to biotic and abiotic stresses. However, few studies have focused on the molecular mechanism of anthocyanin biosynthesis in walnuts.MethodsIn this study, we determined the anthocyanin and PA components and their contents in different color leaves of ‘RW-1’ natural hybrid progenies at various developmental stages. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). We also performed conjoint analyses on DEGs and DAMs to ascertain the degree pathways, and explore the regulation of anthocyanin and PA biosynthesis.ResultsThe results of widely targeted metabolome profiling and anthocyanin detection revealed 395 substances, including four PAs and 26 anthocyanins, in red (SR) and green leaves (SG) of ‘RW-1’ natural hybrid progenies. From the research, the contents of all anthocyanin components in SR were higher than that in SG. Among them, the contents of delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-arabinoside and cyanidin 3-O-glucoside were significantly higher than others, and they were considered as the main types of anthocyanins. However, nine anthocyanins were detected only in SR. For PAs, the content of procyanidin C1 was higher in SR compared with SG, while procyanidin B1 and procyanidin B3 were higher in SR-1 and SR-3 but downregulated in SR-2 compared with the controls. Furthermore, transcriptome analysis revealed that the expressions of structural genes (C4H, F3H, F3′5′H, UFGT, LAR and ANR), three MYBs predicted as the activators of anthocyanin and PA biosynthesis, two MYBs predicted as the repressors of anthocyanin biosynthesis, and five WD40s in the anthocyanin and PA biosynthetic pathways were significantly higher in the SR walnuts. Gene-metabolite correlation analyses revealed a core set of 31 genes that were strongly correlated with four anthocyanins and one PA metabolites. The alteration of gene coding sequence altered the binding or regulation of regulatory factors to structural genes in different color leaves, resulting in the effective increase of anthocyanins and PAs accumulation in red walnut.ConclusionsThis study provides valuable information on anthocyanin and PA metabolites and candidate genes for anthocyanin and PA biosynthesis, yielding new insights into anthocyanin and PA biosynthesis in walnuts. creator: Lei Wang creator: Lin Li creator: Wei Zhao creator: Lu Fan creator: Haijun Meng creator: Ganggang Zhang creator: Wenjiang Wu creator: Jiangli Shi creator: Guoliang Wu uri: https://doi.org/10.7717/peerj.14262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Anthropogenic influences on the distribution of a threatened apex-predator around sustainable-use reserves following hydropower dam installation link: https://peerj.com/articles/14287 last-modified: 2022-10-20 description: Although previous studies demonstrate declines in many large bodied species following hydropower dam installation, others suggest that some species, including the giant otter (Pteronura brasiliensis) may return to newly created reservoir habitats. Yet, there is a lack of evidence to support such theories. Here, we analyzed the effects of a hydropower dam on giant otters using a before-after control-impact study design in the eastern Brazilian Amazon. We collected data 3 years before (2011–2012 and 2015) and after (2017–2019) dam construction, totaling 6,459 km of surveys along rivers with 43 direct sightings of giant otters. Contrary to expectations, our results revealed that giant otters did not remain nor did they return to the dam reservoir. Beyond the zone directly impacted by the dam giant otter occurrence and relative abundance declined next to sustainable-use reserves where the river was more intensely used by people. Our study showed that in the absence of active management sustainable-use reserves and low human density were not sufficient to maintain this apex-predator. Our findings suggest a need to proactively create and maintain areas with low levels of anthropogenic disturbance to enable sustainable coexistence between energy demands and biodiversity across Amazonia. creator: Deborah C. Dávila Raffo creator: Darren Norris creator: Sandra Maria Hartz creator: Fernanda Michalski uri: https://doi.org/10.7717/peerj.14287 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Raffo et al. title: Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term black-legged tick studies link: https://peerj.com/articles/13916 last-modified: 2022-10-19 description: BackgroundUnderstanding how study design and monitoring strategies shape inference within, and synthesis across, studies is critical across biological disciplines. Many biological and field studies are short term and limited in scope. Monitoring studies are critical for informing public health about potential vectors of concern, such as Ixodes scapularis (black-legged ticks). Black-legged ticks are a taxon of ecological and human health concern due to their status as primary vectors of Borrelia burgdorferi, the bacteria that transmits Lyme disease. However, variation in black-legged tick monitoring, and gaps in data, are currently considered major barriers to understanding population trends and in turn, predicting Lyme disease risk. To understand how variable methodology in black-legged tick studies may influence which population patterns researchers find, we conducted a data synthesis experiment.Materials and MethodsWe searched for publicly available black-legged tick abundance dataset that had at least 9 years of data, using keywords about ticks in internet search engines, literature databases, data repositories and public health websites. Our analysis included 289 datasets from seven surveys from locations in the US, ranging in length from 9 to 24 years. We used a moving window analysis, a non-random resampling approach, to investigate the temporal stability of black-legged tick population trajectories across the US. We then used t-tests to assess differences in stability time across different study parameters.ResultsAll of our sampled datasets required 4 or more years to reach stability. We also found several study factors can have an impact on the likelihood of a study reaching stability and of data leading to misleading results if the study does not reach stability. Specifically, datasets collected via dragging reached stability significantly faster than data collected via opportunistic sampling. Datasets that sampled larva reached stability significantly later than those that sampled adults or nymphs. Additionally, datasets collected at the broadest spatial scale (county) reached stability fastest.ConclusionWe used 289 datasets from seven long term black-legged tick studies to conduct a non-random data resampling experiment, revealing that sampling design does shape inferences in black-legged tick population trajectories and how many years it takes to find stable patterns. Specifically, our results show the importance of study length, sampling technique, life stage, and geographic scope in understanding black-legged tick populations, in the absence of standardized surveillance methods. Current public health efforts based on existing black-legged tick datasets must take monitoring study parameters into account, to better understand if and how to use monitoring data to inform decisioning. We also advocate that potential future forecasting initiatives consider these parameters when projecting future black-legged tick population trends. creator: Rowan Christie creator: Kaitlin Stack Whitney creator: Julia Perrone creator: Christie A. Bahlai uri: https://doi.org/10.7717/peerj.13916 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Christie et al. title: Description of the new species Sigambra nkossa (Annelida, Pilargidae), with an analysis of the distribution patterns of polychaetes associated with artificially hydrocarbon-enriched bottoms link: https://peerj.com/articles/13942 last-modified: 2022-10-19 description: The monitoring of the N’Kossa offshore oil and gas fields in the Republic of Congo allowed us to assess the ecological traits of two polychaete species belonging to Sigambra (Annelida, Pilargidae). Sigambra parva occur in very low densities in all bottoms, except the most impacted, where it is totally absent; it is an undescribed species that reached >4,000 ind/m2 in hydrocarbon-enriched sediments. Their distribution patterns are compared with those of other polychaetes, showing a range of affinities for hydrocarbon-enriched sediments in the N’Kossa region. Our results suggest that S. parva would be a representative of the original local fauna, while the species associated with artificial hydrocarbon-enriched sediments, including the other Sigambra, six more polychaetes and a bivalve, could be natively associated with natural hydrocarbon-enriched sediments, using the former as alternative habitats and as dispersal stepping stones. This ecological segregation, together with a careful morphological and morphometric analyses led us to describe the latter as a new species, namely Sigambra nkossa sp. nov. Moreover, morphometric analysis allowed us to discuss on the taxonomic robustness of the key morphological characters of S. nkossa sp. nov., as well as to emend the generic diagnosis of Sigambra to accommodate the new species. creator: Daniel Martin creator: João Gil creator: Claude-Henri Chaineau creator: Sébastien Thorin creator: Romain Le Gall creator: Eric Dutrieux uri: https://doi.org/10.7717/peerj.13942 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Martin et al. title: Physical and chemical properties of the soils in selected communal property associations of South Africa link: https://peerj.com/articles/13960 last-modified: 2022-10-19 description: Communal Property Associations (CPAs) rangeland users need more knowledge on the state of their respective grazing lands and also the interaction of soil properties with grazing management implemented. This study aimed to investigate the effect grazing has on the physical and chemical properties of four different soil types found in selected CPAs of the Bela-Bela municipality, they are as follows: Mawela (Hutton-clay loam: HCL), Bela-Bela (Hutton-clay: HC), Moretele (Hutton-loamy sand: HLS) and Ramorula (Ecca sand-clay loam: ESCL).The macro and micro minerals, pH, nitrate-nitrogen, ammonium-nitrogen, organic carbon, soil particle size distribution, acidity and resistance were all measured. All data were subjected to two-way factorial analysis of variance (SAS, 2010). The topsoil was sampled at a depth of 300 mm at an interval of 100 m (100 and 200 m) from the same transect used for woody species data collection resulting in a total of 18 samples per CPA. In each CPA, three camps were selected. In each camp, three transects 200 m apart at the length of 200 m were set. In each transect, soils were drawn at 0, 100 and 200 m making a total of nine soil samples per each camp. The highest (P < 0.05) pH (7.14) recorded on the sub-soil was in HLS. Nitrate nitrogen (2.4 mg/kg) concentration on the topsoil was high (P < 0.05) in HC soil type. Soil organic carbon for both topsoil (0.66%) and subsoil (0.41%) was significantly lower (P < 0.05) in HLS soil type and ESCL soil type respectively. Phosphorus concentration was significantly high (P < 0.05) in ESCL soil type for both topsoil (12.86 mg/kg) and sub-soil (1.59 mg/kg). Iron concentration was high in both topsoil (11.8 mg/kg) and sub-soil (7.3 mg/kg) in ESCL soil type. Sub-soil manganese concentration was found to be higher (P < 0.05) in ESCL soil type (7.58 mg/kg). Soil resistance (2880 Ω ) measured in topsoil was high (P < 0.05) in HCL soil type compared to other soil types. Moreover, for the sub-soil the highest (P < 0.05) resistance (least salts) (3640 Ω) was recorded in ESCL soil type. For most of the soil types, the mineral concentration was higher in topsoil than in sub-soil, this trend explains that the uptake of these minerals by plants took place due to the inconsistencies of grazing management employed in these selected CPA farms. It is of colossal significance to properly manage rangelands, to allow a fair-to-good herbaceous layer in the presence of minerals in the soils and farmer should prioritize having enclosures and keeping N-fixing tree species in the rangelands to achieve the above mentioned conditions. creator: Malizo Ntalo creator: Khuliso Emmanuel Ravhuhali creator: Bethwell Moyo creator: Ntuwiseni Emile Mmbi creator: Kwena Hilda Mokoboki uri: https://doi.org/10.7717/peerj.13960 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ntalo et al.