title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=894 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly link: https://peerj.com/articles/11845 last-modified: 2021-07-27 description: DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets. creator: Maxime Borry creator: Alexander Hübner creator: Adam B. Rohrlach creator: Christina Warinner uri: https://doi.org/10.7717/peerj.11845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Borry et al. title: Distribution, source, water quality and health risk assessment of dissolved heavy metals in major rivers in Wuhan, China link: https://peerj.com/articles/11853 last-modified: 2021-07-27 description: Heavy metals are released into the water system through various natural processes and anthropogenic activities, thus indirectly or directly endangering human health. The distribution, source, water quality and health risk assessment of dissolved heavy metals (V, Mn, Fe, Co, Ni, Zn, As, Mo, Sb) in major rivers in Wuhan were analyzed by correlation analysis (CA), principal component analysis (PCA), heavy metal pollution index (HPI), hazard index (HI) and carcinogenic risk (CR). The results showed that the spatial variability of heavy metal contents was pronounced. PCA and CA results indicated that natural sources controlled Mn, Fe, Co, Ni and Mo, and industrial emissions were the dominant factor for V, Zn and Sb, while As was mainly from the mixed input of urban and agricultural activities. According to the heavy metal pollution index (HPI, ranging from 23.74 to 184.0) analysis, it should be noted that As and Sb contribute most of the HPI values. The health risk assessment using HI and CR showed that V and Sb might have a potential non-carcinogenic risk and As might have a potential carcinogenic risk to adults and children in the study area (CR value exceeded target risk 10−4). At the same time, it was worth noting that As might have a potential non-carcinogenic risk for children around QLR (HI value exceeded the threshold value 1). The secular variation of As and Sb should be monitor in high-risk areas. The results of this study can provide important data for improving water resources management efficiency and heavy metal pollution prevention in Wuhan. creator: Xingyong Zhang creator: Qixin Wu creator: Shilin Gao creator: Zhuhong Wang creator: Shouyang He uri: https://doi.org/10.7717/peerj.11853 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhang et al. title: Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan link: https://peerj.com/articles/11857 last-modified: 2021-07-27 description: BackgroundBread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach.MethodsA collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits.ResultsOut of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach. creator: Akerke Amalova creator: Saule Abugalieva creator: Adylkhan Babkenov creator: Sandukash Babkenova creator: Yerlan Turuspekov uri: https://doi.org/10.7717/peerj.11857 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amalova et al. title: Proteomic analysis reveals some common proteins in the kidney stone matrix link: https://peerj.com/articles/11872 last-modified: 2021-07-27 description: BackgroundProteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research.MethodsWe conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue.ResultsWe included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no significant difference between healthy controls and kidney stone patients.ConclusionProteomic analysis revealed some common inflammation-related proteins in the kidney stone matrix. The role of these proteins in stone formation should be explored for their potential use as diagnostic biomarkers and therapeutic targets for urolithiasis. creator: Yuanyuan Yang creator: Senyuan Hong creator: Cong Li creator: Jiaqiao Zhang creator: Henglong Hu creator: Xiaolong Chen creator: Kehua Jiang creator: Fa Sun creator: Qing Wang creator: Shaogang Wang uri: https://doi.org/10.7717/peerj.11872 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures link: https://peerj.com/articles/11883 last-modified: 2021-07-27 description: BackgroundIn risk assessment, genotoxicity is a key factor to determine the safety for the consumer. Most in vitro genotoxicity assays were developed for the assessment of pure substances. However, in recent years more attention has been given to complex mixtures, where usually low amounts of a substance are present. For high-throughput screening, a toxicologically sensitive assay should be used, covering a broad range of genotoxic substances and detecting them at low concentrations. HepG2 cells have been recommended as one of the prime candidates for genotoxicity testing, as they are p53 competent, less prone towards cytotoxic effects and tend to have some metabolic activity.MethodsA HepG2 liver cell line was characterized for its suitability for genotoxicity assessment. For this, a luciferase based reporter gene assay revolving around the p53 pathway was validated for the analysis of pure substances and of complex mixtures. Further, the cell’s capability to detect genotoxins correctly with and without an exogenous metabolizing system, namely rat liver S9, was assessed.ResultsThe assay proved to have a high toxicological sensitivity (87.5%) and specificity (94%). Further, the endogenous metabolizing system of the HepG2 cells was able to detect some genotoxins, which are known to depend on an enzymatic system. When complex mixtures were added this did not lead to any adverse effects concerning the assays performance and cytotoxicity was not an issue.DiscussionThe HepGentox proved to have a high toxicological sensitivity and specificity for the tested substances, with similar or even lower lowest effective concentration (LEC) values, compared to other regulatory mammalian assays. This combines some important aspects in one test system, while also being less time and material consuming and covering several genotoxicity endpoints. As the assay performs well with and without an exogenous metabolizing system, no animal liver fractions have to be used, which application is discussed controversially and is considered to be expensive and laborious in sample testing. Because of this, the HepGentox is suitable for a cost-efficient first screening approach to obtain important information with human cells for further approaches, with a relatively fast and easy method. Therefore, the HepGentox is a promising assay to detect genotoxic substances correctly in complex mixtures even at low concentrations, with the potential for a high throughput application. In a nutshell, as part of an in vitro bioassay test battery, this assay could provide valuable information for complex mixtures. creator: Elisabeth Pinter creator: Christina Friedl creator: Alexandra Irnesberger creator: Thomas Czerny creator: Tina Piwonka creator: Alfonso Peñarroya creator: Manfred Tacker creator: Elisabeth Riegel uri: https://doi.org/10.7717/peerj.11883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pinter et al. title: Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology link: https://peerj.com/articles/11711 last-modified: 2021-07-26 description: Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats. creator: Raoul Manenti creator: Beatrice Piazza uri: https://doi.org/10.7717/peerj.11711 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Manenti and Piazza title: Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping link: https://peerj.com/articles/11724 last-modified: 2021-07-26 description: Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications. creator: Zeeshan Ahmed creator: Eduard Gibert Renart creator: Saman Zeeshan uri: https://doi.org/10.7717/peerj.11724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ahmed et al. title: Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels link: https://peerj.com/articles/11785 last-modified: 2021-07-26 description: BackgroudThis study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger.MethodsWe recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups.ResultsAlthough the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM).ConclusionWe concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive to persistent pregnancies. The E2 level on the day of trigger can still be used to predict the incidence of early onset severe OHSS in the fresh SBT cycle. creator: Yingfen Ying creator: Xiaosheng Lu creator: Huina Zhang creator: Samuel Kofi Arhin creator: Xiaohong Hou creator: Zefan Wang creator: Han Wu creator: Jieqiang Lu creator: Yunbing Tang uri: https://doi.org/10.7717/peerj.11785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ying et al. title: Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage link: https://peerj.com/articles/11834 last-modified: 2021-07-26 description: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize. creator: Baizhao Ren creator: Juan Hu creator: Peng Liu creator: Bin Zhao creator: Jiwang Zhang uri: https://doi.org/10.7717/peerj.11834 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ren et al. title: A bright idea—metabarcoding arthropods from light fixtures link: https://peerj.com/articles/11841 last-modified: 2021-07-26 description: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity. creator: Vasco Elbrecht creator: Angie Lindner creator: Laura Manerus creator: Dirk Steinke uri: https://doi.org/10.7717/peerj.11841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Elbrecht et al.