title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=413
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genetic connectivity and population expansion inferred from multilocus analysis in Lutjanus alexandrei (Lutjanidae–Perciformes), an endemic snapper from Northeastern Brazilian coast
link: https://peerj.com/articles/15973
last-modified: 2023-09-26
description: Previous studies about the genetic diversity, connectivity and demographic history in Lutjanidae fishes have reported a common pattern of genetic homogeneity and expansion in populations from Western South Atlantic. In the present work, we inferred the population structure, the levels of genetic diversity and the demographic history of the Brazilian snapper Lutjanus alexandrei, a recently described and endemic species from Northeastern coast of Brazil. Five different fragments, including mitochondrial DNA (Control Region, Cyt b and ND4) and nuclear DNA (Myostatin and S7) regions were analyzed in 120 specimens of L. alexandrei from four localities in Northeastern Brazil, representing the first study of population genetics in this species. High levels of genetic diversity were observed following a panmictic pattern, probably related to the larval dispersal by the current tides along the Brazilian coast. In addition, both demographic history and neutrality tests indicated that L. alexandrei has undergone population expansion during Pleistocene. In this sense, the sea level variation from this period could have increased the available resources and suitable habitats for the Brazilian snapper.
creator: Ivana Veneza
creator: Raimundo da Silva
creator: Charles Ferreira
creator: Patrícia Mendonça
creator: Iracilda Sampaio
creator: Grazielle Evangelista-Gomes
uri: https://doi.org/10.7717/peerj.15973
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Veneza et al.

title: TLR7 promotes skin inflammation via activating NFκB-mTORC1 axis in rosacea
link: https://peerj.com/articles/15976
last-modified: 2023-09-26
description: Rosacea is a chronic inflammatory skin disease originated from damaged skin barrier and innate/adaptive immune dysregulation. Toll-like receptors (TLRs) sense injured skin and initiate downstream inflammatory and immune responses, whose role in rosacea is not fully understood. Here, via RNA-sequencing analysis, we found that the TLR signaling pathway is the top-ranked signaling pathway enriched in rosacea skin lesions, in which TLR7 is highlighted and positively correlated with the inflammation severity of disease. In LL37-induced rosacea-like mouse models, silencing TLR7 prevented the development of rosacea-like skin inflammation. Specifically, we demonstrated that overexpressing TLR7 in keratinocytes stimulates rapamycin-sensitive mTOR complex 1 (mTORC1) pathway via NFκB signaling. Ultimately, TLR7/NFκ B/mTORC1 axis promotes the production of cytokines and chemokines, leading to the migration of CD4+T cells, which are infiltrated in the lesional skin of rosacea. Our report reveals the crucial role of TLR7 in rosacea pathogenesis and indicatesa promising candidate for rosacea treatments.
creator: Yaqun Huang
creator: Da Liu
creator: Mengting Chen
creator: San Xu
creator: Qinqin Peng
creator: Yan Zhu
creator: Juan Long
creator: Tangxiele Liu
creator: Zhili Deng
creator: Hongfu Xie
creator: Ji Li
creator: Fangfen Liu
creator: Wenqin Xiao
uri: https://doi.org/10.7717/peerj.15976
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Huang et al.

title: Soil microbial and enzyme activities in different land use systems of the Northwestern Himalayas
link: https://peerj.com/articles/15993
last-modified: 2023-09-26
description: Soil microbial activity (SMA) is vital concerning carbon cycling, and its functioning is recognized as the primary factor in modifying soil carbon storage potential. The composition of the microbial community (MC) is significant in sustaining environmental services because the structure and activity of MC also influence nutrient turnover, distribution, and the breakdown rate of soil organic matter. SMA is an essential predictor of soil quality alterations, and microbiome responsiveness is imperative in addressing the escalating sustainability concerns in the Himalayan ecosystem. This study was conducted to evaluate the response of soil microbial and enzyme activities to land conversions in the Northwestern Himalayas (NWH), India. Soil samples were collected from five land use systems (LUSs), including forest, pasture, apple, saffron, and paddy-oilseed, up to a depth of 90 cm. The results revealed a significant difference (p < 0.05) in terms of dehydrogenase (9.97–11.83 TPF µg g−1 day−1), acid phosphatase (22.40–48.43 µg P-NP g−1 h−1), alkaline phosphatase (43.50–61.35 µg P-NP g−1 h−1), arylsulphatase (36.33–48.12 µg P-NP g−1 h−1), fluorescein diacetate hydrolase (12.18–21.59 µg g−1 h−1), bacterial count (67.67–123.33 CFU × 106 g−1), fungal count (19.33–67.00 CFU × 105 g−1), and actinomycetes count (12.00–42.33 CFU × 104 g−1), with the highest and lowest levels in forest soils and paddy-oilseed soils, respectively. Soil enzyme activities and microbial counts followed a pattern: forest > pasture > apple > saffron > paddy-oilseed at all three depths. Paddy-oilseed soils exhibited up to 35% lower enzyme activities than forest soils, implying that land conversion facilitates the depletion of microbiome diversity from surface soils. Additionally, reductions of 49.80% and 62.91% were observed in enzyme activity and microbial counts, respectively, with soil depth (from 0–30 to 60–90 cm). Moreover, the relationship analysis (principal component analysis and correlation) revealed a high and significant (p = 0.05) association between soil microbial and enzyme activities and physicochemical attributes. These results suggest that land conversions need to be restricted to prevent microbiome depletion, reduce the deterioration of natural resources, and ensure the sustainability of soil health.
creator: Yasir Hanif Mir
creator: Mumtaz Ahmad Ganie
creator: Tajamul Islam Shah
creator: Shabir Ahmed Bangroo
creator: Shakeel Ahmad Mir
creator: Aanisa Manzoor Shah
creator: Fehim Jeelani Wani
creator: Anzhen Qin
creator: Shafeeq Ur Rahman
uri: https://doi.org/10.7717/peerj.15993
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2023 Mir et al.

title: Comparative sequence analysis elucidates the evolutionary patterns of Yersinia pestis in New Mexico over thirty-two years
link: https://peerj.com/articles/16007
last-modified: 2023-09-26
description: BackgroundYersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899.MethodsTo better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure.ResultsWe identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.
creator: Mary E. Warren
creator: Brett E. Pickett
creator: Byron J. Adams
creator: Crystal Villalva
creator: Alyssa Applegate
creator: Richard A. Robison
uri: https://doi.org/10.7717/peerj.16007
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Warren et al.

title: Association detection between multiple traits and rare variants based on family data via a nonparametric method
link: https://peerj.com/articles/16040
last-modified: 2023-09-26
description: BackgroundThe rapid development of next-generation sequencing technologies allow people to analyze human complex diseases at the molecular level. It has been shown that rare variants play important roles for human diseases besides common variants. Thus, effective statistical methods need to be proposed to test for the associations between traits (e.g., diseases) and rare variants. Currently, more and more rare genetic variants are being detected throughout the human genome, which demonstrates the possibility to study rare variants. Yet complex diseases are usually measured as a variety of forms, such as binary, ordinal, quantitative, or some mixture of them. Therefore, the genetic mapping problem can be attributable to the association detection between multiple traits and multiple loci, with sufficiently considering the correlated structure among multiple traits.MethodsIn this article, we construct a new non-parametric statistic by the generalized Kendall’s τ theory based on family data. The new test statistic has an asymptotic distribution, it can be used to study the associations between multiple traits and rare variants, which broadens the way to identify genetic factors of human complex diseases.ResultsWe apply our method (called Nonp-FAM) to analyze simulated data and GAW17 data, and conduct comprehensive comparison with some existing methods. Experimental results show that the proposed family-based method is powerful and robust for testing associations between multiple traits and rare variants, even if the data has some population stratification effect.
creator: Jinling Chi
creator: Meijuan Xu
creator: Xiaona Sheng
creator: Ying Zhou
uri: https://doi.org/10.7717/peerj.16040
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Chi et al.

title: Linking watershed nutrient loading to estuary water quality with generalized additive models
link: https://peerj.com/articles/16073
last-modified: 2023-09-26
description: Evaluating estuary water quality responses to reductions (or increases) in nutrient loading attributed to on the ground management actions can be challenging due to the strong influence of environmental drivers on nutrient loads and non-linear relationships. This study applied generalized additive models to calculate watershed nutrient loads and assess responses in estuary water quality to seasonally-adjusted freshwater inflow and flow-adjusted nutrient loads in Lavaca Bay, Texas. Lavaca Bay is a secondary embayment on the Texas coast displaying early potential for eutrophication and water quality degradation. Use of flow-adjusted nutrient loads allowed the study to evaluate the response in water quality to changes in nutrient loads driven by anthropogenic sources. Cross-validation indicated that, despite data constraints, semiparametric models performed well at nutrient load prediction. Based on these models, delivered annual nutrient loads varied substantially from year to year. In contrast, minimal changes in flow-normalized loads indicate that nutrient loadings were driven by natural variation in precipitation and runoff as opposed to changes in management of nonpoint sources. Models indicated no evidence of long-term changes in dissolved oxygen or chlorophyll-a within Lavaca Bay. However, site specific long-term increases in both organic and inorganic nitrogen are concerning for their potential to fuel eutrophication. Further analysis found freshwater inflow had strong influences on nutrient and chlorophyll-a concentrations but there was no evidence that changes in watershed nutrient loading explained additional variation in dissolved oxygen and limited evidence that watershed nutrient loadings explained chlorophyll-a concentrations. In addition to providing a baseline assessment of watershed nutrient loading and water quality responses in the Lavaca Bay watershed, this study provides methodological support for the use of semiparametric models in load regression models and estuary assessments.
creator: Michael P. Schramm
uri: https://doi.org/10.7717/peerj.16073
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Schramm

title: Friend leukemia integration 1 overexpression decreases endometrial receptivity and induces embryo implantation failure by promoting PART1 transcription in the endometrial epithelial cells
link: https://peerj.com/articles/16105
last-modified: 2023-09-26
description: BackgroundIn vitro fertilization-embryo transfer (IVF-ET) is a crucial assisted reproductive technology for treating infertility. However, recurrent implantation failure (RIF), a significant challenge in IVF-ET success, remains unresolved. This study aimed to explore the role and mechanism of FLI1 in endometrial receptivity and RIF.MethodsDifferential endometrial cell proportions between patients with RIF and control subjects were assessed using single-cell RNA sequencing (scRNA-seq) analysis. The chromatin accessibility of FLI1 in the luteal endometrial tissue of patients with RIF and control subjects was examined using the single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq). FLI1 mRNA and protein levels were gauged by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Cell viability and migration were examined via cell counting kit (CCK)-8 and scratch healing assays. Epithelial-mesenchymal transition markers were analyzed using western blotting. Mechanisms underlying FLI1’s regulation of PART1 transcription and expression in endometrial epithelial cells were explored using chromatin immunoprecipitation and dual-luciferase reporter assays. Adeno-associated virus (AAV) carrying epithelial cell-specific FLI1/PART1 overexpression sequences was uterinely injected in mice to assess FLI1/PART1 effects.ResultsscRNA-seq revealed diminished endometrial epithelial cell proportions in RIF patients. Meanwhile, scATAC-seq indicated enhanced chromatin accessibility of FLI1 in these cells. FLI1 exhibited specific expression in RIF patients’ endometrial epithelial cells. Specific FLI1 overexpression inhibited embryo implantation, while knockdown enhanced it. Pregnant mice injected with AAV encoding FLI1 overexpression had significantly lower implantation than AAV-negative controls. FLI1 binding to PART1 promoter heightened PART1 transcription and expression in endometrial epithelial cells. Rescue experiments illustrated FLI1’s role in embryo implantation by boosting PART1 expression. PART1 was notably elevated in RIF patients’ luteal endometrial tissue and non-receptive endometrial epithelial cells (HEC-1-A). Specific PART1 overexpression dampened embryo implantation, whereas knockdown promoted it. Pregnant mice injected with AAV encoding PART1 had lower implantation than negative controls. PART1 knockdown mitigated FLI1’s inhibitory impact on HEC-1-A cell viability and migration.ConclusionsFLI1 overexpression in the endometrial epithelial cells of patients with RIF inhibited embryo implantation by binding to the PART1 promoter region to promote PART1 expression. These findings can aid in the development of novel therapeutic targets for RIF.
creator: Yile Zhang
creator: Beining Yin
creator: Sichen Li
creator: Yueyue Cui
creator: Jianrong Liu
uri: https://doi.org/10.7717/peerj.16105
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhang et al.

title: Numbers of fish species, higher taxa, and phylogenetic similarity decrease with latitude and depth, and deep-sea assemblages are unique
link: https://peerj.com/articles/16116
last-modified: 2023-09-26
description: Species richness has been found to increase from the poles to the tropics but with a small dip near the equator over all marine fishes. Phylogenetic diversity measures offer an alternative perspective on biodiversity linked to evolutionary history. If phylogenetic diversity is standardized for species richness, then it may indicate places with relatively high genetic diversity. Latitudes and depths with both high species and phylogenetic diversity would be a priority for conservation. We compared latitudinal and depth gradients of species richness, and three measures of phylogenetic diversity, namely average phylogenetic diversity (AvPD), the sum of the higher taxonomic levels (STL) and the sum of the higher taxonomic levels divided by the number of species (STL/spp) for modelled ranges of 5,619 marine fish species. We distinguished all, bony and cartilaginous fish groups and four depth zones namely: whole water column; 0 –200 m; 201–1,000 m; and 1,001–6,000 m; at 5°  latitudinal intervals from 75°S to 75°N, and at 100 m depth intervals from 0 m to 3,500 m. Species richness and higher taxonomic richness (STL) were higher in the tropics and subtropics with a small dip at the equator, and were significantly correlated among fish groups and depth zones. Species assemblages had closer phylogenetic relationships (lower AvPD and STL/spp) in warmer (low latitudes and shallow water) than colder environments (high latitudes and deep sea). This supports the hypothesis that warmer shallow latitudes and depths have had higher rates of evolution across a range of higher taxa. We also found distinct assemblages of species in different depth zones such that deeper sea species are not simply a subset of shallow assemblages. Thus, conservation needs to be representative of all latitudes and depth zones to encompass global biodiversity.
creator: Han-Yang Lin
creator: Shane Wright
creator: Mark John Costello
uri: https://doi.org/10.7717/peerj.16116
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Lin et al.

title: Optimization of oil industry wastewater treatment system and proposing empirical correlations for chemical oxygen demand removal using electrocoagulation and predicting the system’s performance by artificial neural network
link: https://peerj.com/articles/15852
last-modified: 2023-09-25
description: The alarming pace of environmental degradation necessitates the treatment of wastewater from the oil industry in order to ensure the long-term sustainability of human civilization. Electrocoagulation has emerged as a promising method for optimizing the removal of chemical oxygen demand (COD) from wastewater obtained from oil refineries. Therefore, in this study, electrocoagulation was experimentally investigated, and a single-factorial approach was employed to identify the optimal conditions, taking into account various parameters such as current density, pH, COD concentration, electrode surface area, and NaCl concentration. The experimental findings revealed that the most favorable conditions for COD removal were determined to be 24 mA/cm2 for current density, pH 8, a COD concentration of 500 mg/l, an electrode surface area of 25.26 cm2, and a NaCl concentration of 0.5 g/l. Correlation equations were proposed to describe the relationship between COD removal and the aforementioned parameters, and double-factorial models were examined to analyze the impact of COD removal over time. The most favorable outcomes were observed after a reaction time of 20 min. Furthermore, an artificial neural network model was developed based on the experimental data to predict COD removal from wastewater generated by the oil industry. The model exhibited a mean absolute error (MAE) of 1.12% and a coefficient of determination (R2) of 0.99, indicating its high accuracy. These findings suggest that machine learning-based models have the potential to effectively predict COD removal and may even serve as viable alternatives to traditional experimental and numerical techniques.
creator: Atef El Jery
creator: Hayder Mahmood Salman
creator: Nadhir Al-Ansari
creator: Saad Sh. Sammen
creator: Mohammed Abdul Jaleel Maktoof
creator: Hussein A. Z. AL-bonsrulah
uri: https://doi.org/10.7717/peerj.15852
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 El Jery et al.

title: Combined effects of temperature, photoperiod, and salinity on reproduction of the brine shrimp Artemia sinica (Crustacea: Anostraca)
link: https://peerj.com/articles/15945
last-modified: 2023-09-25
description: BackgroundArtemia sinica is a brine shrimp species distributed in hypersaline salt lakes in northern China and Siberia and a successful invasive species in some coastal salterns. Although it is a commercially harvested and cultured species, knowledge of its reproductive characteristics is limited, and existing studies are often contradictory. The combined effects of temperature, salinity, and photoperiod on reproduction characteristics are experimentally studied to better understand its reproductive features.MethodsThere were 36 combinations of three environmental factors (3 × 3 × 4), each with three or four levels, namely temperature (16, 25, 30 °C), photoperiod (6 L:18 D, 12 L:12D, 18 L:6D), and salinity (50, 100, 150, 200 PSU). In each treatment, 48 to 80 pairs of A. sinica from Yuncheng Salt Lake (Shanxi, China) were cultured. Females were observed daily for reproductive mode and the number of offspring produced.ResultsTemperature, photoperiod, salinity, and their interactions significantly affected the lifespan and reproduction of A. sinica. The reproductive period was the longest and accounted for the largest proportion of life span at moderate temperature (25 °C). Total offspring, offspring per brood, and offspring per day increased as salinity decreased, and the number of broods per female was highest at 25 °C. Temperature, photoperiod, and salinity significantly influenced reproductive modes, and interactions among these factors were identified. Artemia sinica primarily reproduces oviparously under low temperature and short daylight conditions, and ovoviviparously under high temperature and long daylight conditions, with the maximum oviparity ratio recorded in treatments of 16 °C, 6L:18D, and 50 or 100 PSU. The maximum ovoviviparity ratio was recorded under 30 °C, 12L:12D, and 100 PSU. Unlike that documented for other Artemia species or populations, the brood size of A. sinica kept increasing throughout the reproductive period. It did not decline even in the last two broods. For the same brood number, the sizes of oviparous and ovoviviparous broods were similar. The length of the oviparous interval was often greater than that of the ovoviviparous interval, suggesting that oviparous offspring might require additional energy and time to construct the multi-layered eggshell. Compared to other species and populations, the A. sinica from Yuncheng Salt Lake has a relatively shorter pre-reproductive development time, a preference for ovoviviparity, and relatively higher fecundity and population growth capacity, making it a suitable culture species for obtaining fresh biomass.
creator: Jing-Yu Yang
creator: Shi-Chun Sun
uri: https://doi.org/10.7717/peerj.15945
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Yang and Sun