title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1223 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Benchmarking protocols for the metagenomic analysis of stream biofilm viromes link: https://peerj.com/articles/8187 last-modified: 2019-12-20 description: Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms. creator: Meriem Bekliz creator: Jade Brandani creator: Massimo Bourquin creator: Tom J. Battin creator: Hannes Peter uri: https://doi.org/10.7717/peerj.8187 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bekliz et al. title: Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis link: https://peerj.com/articles/8201 last-modified: 2019-12-20 description: Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae. creator: Duncan Kiragu Gichuki creator: Lu Ma creator: Zhenfei Zhu creator: Chang Du creator: Qingyun Li creator: Guangwan Hu creator: Zhixiang Zhong creator: Honglin Li creator: Qingfeng Wang creator: Haiping Xin uri: https://doi.org/10.7717/peerj.8201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gichuki et al. title: Reduced GRAMD1C expression correlates to poor prognosis and immune infiltrates in kidney renal clear cell carcinoma link: https://peerj.com/articles/8205 last-modified: 2019-12-20 description: There has been an increase in the mortality rate and morbidity of kidney cancer (KC) with kidney renal clear cell carcinoma (KIRC) being the most common subtype of KC. GRAMD1C (GRAM Domain Containing 1C) has not been reported to relate to prognosis and immunotherapy in any cancers. Using bioinformatics methods, we judged the prognostic value of GRAMD1C expression in KIRC and investigated the underlying mechanisms of GRAMD1C affecting the overall survival of KIRC based on data downloaded from The Cancer Genome Atlas (TCGA). The outcome revealed that reduced GRAMD1C expression could be a promising predicting factor of poor prognosis in kidney renal clear cell carcinoma. Meanwhile, GRAMDIC expression was significantly correlated to several tumor-infiltrating immune cells (TIICs), particularly the regulatory T cells (Tregs). Furthermore, GRAMD1C was most significantly associated with the mTOR signaling pathway, RNA degradation, WNT signaling pathway, toll pathway and AKT pathway in KIRC. Thus, GRAMD1C has the potential to become a novel predictor to evaluate prognosis and immune infiltration for KIRC patients. creator: Haiyan Hao creator: Ziheng Wang creator: Shiqi Ren creator: Hanyu Shen creator: Hua Xian creator: Wenliang Ge creator: Wei Wang uri: https://doi.org/10.7717/peerj.8205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hao et al. title: Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’ link: https://peerj.com/articles/8210 last-modified: 2019-12-20 description: BackgroundSweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear.MethodsIn this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively.ResultsThe complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species. creator: Xueqing Zhao creator: Ming Yan creator: Yu Ding creator: Yan Huo creator: Zhaohe Yuan uri: https://doi.org/10.7717/peerj.8210 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Modelling the effect of curves on distance running performance link: https://peerj.com/articles/8222 last-modified: 2019-12-20 description: BackgroundAlthough straight ahead running appears to be faster, distance running races are predominately contested on tracks or roads that involve curves. How much faster could world records be run on straight courses?MethodsHere,we propose a model to explain the slower times observed for races involving curves compared to straight running. For a given running velocity, on a curve, the average axial leg force (${\overline{F}}_{a}$F¯a) of a runner is increased due to the need to exert centripetal force. The increased ${\overline{F}}_{a}$F¯a presumably requires a greater rate of metabolic energy expenditure than straight running at the same velocity. We assumed that distance runners maintain a constant metabolic rate and thus slow down on curves accordingly. We combined published equations to estimate the change in the rate of gross metabolic energy expenditure as a function of ${\overline{F}}_{a}$F¯a, where ${\overline{F}}_{a}$F¯a depends on curve radius and velocity, with an equation for the gross rate of oxygen uptake as a function of velocity. We compared performances between straight courses and courses with different curve radii and geometries.ResultsThe differences between our model predictions and the actual indoor world records, are between 0.45% in 3,000 m and 1.78% in the 1,500 m for males, and 0.59% in the 5,000 m and 1.76% in the 3,000 m for females. We estimate that a 2:01:39 marathon on a 400 m track, corresponds to 2:01:32 on a straight path and to 2:02:00 on a 200 m track.ConclusionOur model predicts that compared to straight racecourses, the increased time due to curves, is notable for smaller curve radii and for faster velocities. But, for larger radii and slower speeds, the time increase is negligible and the general perception of the magnitude of the effects of curves on road racing performance is not supported by our calculations. creator: Paolo Taboga creator: Rodger Kram uri: https://doi.org/10.7717/peerj.8222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Taboga and Kram title: New titanosauriform (Dinosauria: Sauropoda) specimens from the Upper Cretaceous Daijiaping Formation of southern China link: https://peerj.com/articles/8237 last-modified: 2019-12-20 description: Titanosauriform sauropod dinosaurs were once considered rare in the Upper Cretaceous of Asia, but a number of titanosauriforms from this stratigraphic interval have been discovered in China in recent years. In fact, all adequately known Cretaceous Asian sauropods are titanosauriforms, but only a few have been well studied, lending significance to any new anatomical information that can be extracted from Asia’s Cretaceous sauropod record. Here we give a detailed description of some titanosauriform bones recovered recently from the Upper Cretaceous Daijiaping Formation of Tianyuan County, Zhuzhou City, Hunan Province, southern China. The occurrence of this material in Hunan increases the known geographic range of titanosauriforms in eastern Asia. Although all of the specimens discussed in this paper can be assigned to Titanosauriformes at least tentatively, some bones display a limited number of features that are more typical of basal sauropods and/or derived diplodocoids, suggesting complex patterns of character evolution within Neosauropoda. creator: Fenglu Han creator: Xing Xu creator: Corwin Sullivan creator: Leqing Huang creator: Yu Guo creator: Rui Wu uri: https://doi.org/10.7717/peerj.8237 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2019 Han et al. title: Toward insights on determining factors for high activity in antimicrobial peptides via machine learning link: https://peerj.com/articles/8265 last-modified: 2019-12-20 description: The continued and general rise of antibiotic resistance in pathogenic microbes is a well-recognized global threat. Host defense peptides (HDPs), a component of the innate immune system have demonstrated promising potential to become a next generation antibiotic effective against a plethora of pathogens. While the effectiveness of antimicrobial HDPs has been extensively demonstrated in experimental studies, theoretical insights on the mechanism by which these peptides function is comparably limited. In particular, experimental studies of AMP mechanisms are limited in the number of different peptides investigated and the type of peptide parameters considered. This study makes use of the random forest algorithm for classifying the antimicrobial activity as well for identifying molecular descriptors underpinning the antimicrobial activity of investigated peptides. Subsequent manual interpretation of the identified important descriptors revealed that polarity-solubility are necessary for the membrane lytic antimicrobial activity of HDPs. creator: Hao Li creator: Chanin Nantasenamat uri: https://doi.org/10.7717/peerj.8265 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li and Nantasenamat title: A new species of Atrimitra Dall, 1918 (Gastropoda: Mitridae) from seamounts of the recently created Nazca-Desventuradas Marine Park, Chile link: https://peerj.com/articles/8279 last-modified: 2019-12-20 description: We describe Atrimitra isolata sp. n. (Gastropoda: Mitridae), collected on the summit of seamounts (~200 m water depth) in the vicinity of Desventuradas Islands, Chile insular territory. Additionally, we provide some insight into the habitat of this new species based on underwater imagery taken with a remotely operated vehicle. A. isolata sp. n. is characterized by its small size (up to 26 mm), elongate-ovate shape, solid shell and smooth appearance. It has a base brown color, with some specimens being tan or yellow. It is morphologically related to counterparts from shallow depths on the west coast of North, Central and South America (i.e., Atrimitra idae, Atrimitra orientalis and Atrimitra semigranosa), but has no affinities with species of the family reported from around Easter Island, on the far western side of the Salas y Gómez ridge (e.g., Strigatella flavocingulata, Imbricariopsis punctata and Neocancilla takiisaoi), or with other Indo-Pacific species. The present contribution adds to the knowledge of the poorly studied fauna of the seamounts in the southern portion of the Nazca ridge and easternmost section of the Sala y Gómez ridge, an area characterized by the high degree of endemism of its benthic fauna, and now protected within the large and newly created Nazca-Desventuradas Marine Park. creator: Javier Sellanes creator: Richard A. Salisbury creator: Jan M. Tapia creator: Cynthia M. Asorey uri: https://doi.org/10.7717/peerj.8279 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Sellanes et al. title: Production and characteristics of fish protein hydrolysate from parrotfish (Chlorurus sordidus) head link: https://peerj.com/articles/8297 last-modified: 2019-12-20 description: BackgroundFish byproducts are commonly recognized as low-value resources. In order to increase the value, fish byproducts need to be converted into new products with high functionality such as fish protein hydrolysate (FPH). In this study, FPH manufactured from parrotfish (Chlorurus sordidus) heads using different pH, time and sample ratio was investigated.MethodsHydrolysis reactions were conducted under different pHs (5, 7, and 9) and over different durations (12 and 24 h). Control treatment (without pH adjustment (pH 6.4)) and 0 h hydrolsisis duration were applied. Hydrolysates were characterized with respect to proximate composition, amino acid profile, and molecular weight distribution. The antioxidant activity of the hydrolysate was also observed.ResultsThe pH and duration of hydrolysis significantly affected (p < 0.05) the characteristics of FPH. The highest yield of hydrolysate (49.04 ± 0.90%), with a degree of hydrolysis of 30.65 ± 1.82%, was obtained at pH 9 after 24 h incubation. In addition, the FPH had high antioxidant activity (58.20 ± 0.55%), with a high level of essential amino acids. Results suggested that FPH produced using endogenous enzymes represents a promising additive for food and industrial applications. creator: Asep A. Prihanto creator: Rahmi Nurdiani creator: Annas D. Bagus uri: https://doi.org/10.7717/peerj.8297 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Prihanto et al. title: Expression and prognostic analyses of ITGA11, ITGB4 and ITGB8 in human non-small cell lung cancer link: https://peerj.com/articles/8299 last-modified: 2019-12-20 description: BackgroundIntegrins play a crucial role in the regulation process of cell proliferation, migration, differentiation, tumor invasion and metastasis. ITGA11, ITGB4 and ITGB8 are three encoding genes of integrins family. Accumulative evidences have proved that abnormal expression of ITGA11, ITGB4 and ITGB8 are a common phenomenon in different malignances. However, their expression patterns and prognostic roles for patients with non-small cell lung cancer (NSCLC) have not been completely illustrated.MethodsWe investigated the expression patterns and prognostic values of ITGA11, ITGB4 and ITGB8 in patients with NSCLC through using a series of databases and various datasets, including ONCOMINE, GEPIA, HPA, TCGA and GEO datasets.ResultsWe found that the expression levels of ITGA11 and ITGB4 were significantly upregulated in both LUAD and LUSC, while ITGB8 was obviously upregulated in LUSC. Additionally, higher expression level of ITGB4 revealed a worse OS in LUAD.ConclusionOur findings suggested that ITGA11 and ITGB4 might have the potential ability to act as diagnostic biomarkers for both LUAD and LUSC, while ITGB8 might serve as diagnostic biomarker for LUSC. Furthermore, ITGB4 could serve as a potential prognostic biomarker for LUAD. creator: Pancheng Wu creator: Yanyu Wang creator: Yijun Wu creator: Ziqi Jia creator: Yang Song creator: Naixin Liang uri: https://doi.org/10.7717/peerj.8299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wu et al.