Resident microbes of lactation rooms and daycares
Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome.
Taft et al. (2019) Resident microbes of lactation rooms and daycares. PeerJ 7:e8168 https://doi.org/10.7717/peerj.8168
consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Extensive evaluation of RNA-seq methods have demonstrated that no single algorithm consistently outperforms all others. Removal of unwanted variation (RUV) has also been proposed as a method for stabilizing differential expression (DE) results. Despite this, it remains a challenge to run multiple RNA-seq algorithms to identify significant differences common to multiple algorithms, whilst also integrating and assessing the impact of RUV into all algorithms. consensusDE was developed to automate the process of identifying significant DE by combining the results from multiple algorithms with minimal user input and with the option to automatically integrate RUV. consensusDE only requires a table describing the sample groups, a directory containing BAM files or preprocessed count tables and an optional transcript database for annotation. It supports merging of technical replicates, paired analyses and outputs a compendium of plots to guide the user in subsequent analyses. Herein, we assess the ability of RUV to improve DE stability when combined with multiple algorithms and between algorithms, through application to real and simulated data. We find that, although RUV increased fold change stability between algorithms, it demonstrated improved FDR in a setting of low replication for the intersect, the effect was algorithm specific and diminished with increased replication, reinforcing increased replication for recovery of true DE genes. We finish by offering some rules and considerations for the application of RUV in a consensus-based setting. consensusDE is freely available, implemented in R and available as a Bioconductor package, under the GPL-3 license, along with a comprehensive vignette describing functionality: http://bioconductor.org/packages/consensusDE/.
Waardenberg et al. (2019) consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. PeerJ 7:e8206 https://doi.org/10.7717/peerj.8206
Vegetation dynamic analysis based on multisource remote sensing data in the east margin of the Qinghai-Tibet Plateau, China
This study focuses on the vegetation dynamic caused by global environmental change in the eastern margin of the Qinghai-Tibet Plateau (EMQTP). The Qinghai–Tibet Plateau (QTP) is one of the most sensitive areas responding to global environmental change, particularly global climate change, and has been recognized as a hotspot for coupled studies on changes in global terrestrial ecosystems and global climates. An important component of terrestrial ecosystems, vegetation dynamic has become a key issue in global environmental change, and numerous case studies have been conducted on vegetation dynamic trends using multi-source data and multi-scale methods across different study periods. The EMQTP is regarded as a transitional area located between the QTP and the Sichuan basin, and has special geographical and climatic conditions. Although this area is ecologically fragile and sensitive to climate change, few studies about vegetation dynamics have been carried out in this area. Thus, in this study, we used long-term series datasets of GIMMS 3g NDVI and VGT/PROBA-V NDVI to analyze the vegetation dynamics and phenological changes from 1982 to 2018. Validation was performed based on Landsat NDVI and Vegetation Index & Phenology (VIP) data. The results reveal that the year 1998 was a vital turning point in the start of growing season (SGS) in vegetation ecosystems. Before this turning point, the SGS had an average slope of 9.2 days/decade, and after, the average slope was 3.9 days/decade. The length of growing season (LGS) was slightly prolonged between 1982 to 2015. Additionally, the largest national alpine wetland grassland experienced significant vegetation degradation; in autumn, the degraded area accounted for 63.4%. Vegetation degradation had also appeared in the arid valleys of the Yalong River and the Jinsha River. Through validation analysis, we found that the main causes of vegetation degradation are the natural degradation of wetland grassland and human activities, specifically agricultural development and residential area expansion.
Spatial and Geographic Information Science
Wang et al. (2019) Vegetation dynamic analysis based on multisource remote sensing data in the east margin of the Qinghai-Tibet Plateau, China. PeerJ 7:e8223 https://doi.org/10.7717/peerj.8223
Development and characterization of a multiplex panel of microsatellite markers for the Reunion free-tailed bat Mormopterus francoismoutoui
The ecology and conservation status of many island-restricted bats remain largely unexplored. The free-tailed bat Mormopterus francoismoutoui is a small insectivorous tropical bat, endemic to Reunion Island (Indian Ocean). Despite being widely distributed on the island, the fine-scale genetic structure and evolutionary ecology of M. francoismoutoui remain under-investigated, and therefore its ecology is poorly known. Here, we used Illumina paired-end sequencing to develop microsatellite markers for M. francoismoutoui, based on the genotyping of 31 individuals from distinct locations all over the island. We selected and described 12 polymorphic microsatellite loci with high levels of heterozygosity, which provide novel molecular markers for future genetic population-level studies of M. francoismoutoui.
Dietrich et al. (2019) Development and characterization of a multiplex panel of microsatellite markers for the Reunion free-tailed bat Mormopterus francoismoutoui. PeerJ 7:e8036 https://doi.org/10.7717/peerj.8036
Body height and waist circumference of young Swiss men as assessed by 3D laser-based photonic scans and by manual anthropometric measurements
Overweight and obesity are considered among the major health concerns worldwide. The body mass index is a frequently used measure for overweight and obesity and is associated with common non-communicable diseases such as diabetes type II, cardiovascular diseases and certain cancers. However, the body mass index does not account for the distribution of body fat and relative fat to muscle mass. 3D laser-based photonic full body scans provide detailed information on various body circumferences, surfaces, and volumes as well as body height and weight (using an integrated scale). In the literature, body scans showed good feasibility, reliability, and validity, while also demonstrating a good correlation with health parameters linked to the metabolic syndrome. However, systematic differences between body scan derived measurements and manual measurements remain an issue. This study aimed to assess these systematic differences for body height, waist circumference, and body mass index using cross-sectional data from a homogenous sample of 52 young Swiss male volunteers. In addition to 3D laser-based photonic full body scans and correlative manual measurements, body fat distribution was assessed through bioelectrical impedance analysis. Overall, an excellent correlation was found between measurements of waist circumference and body mass index, and good correlation between body mass index and total fat mass, as well as between waist circumference and visceral fat mass as assessed by bioelectrical impedance analysis. Volunteers were shorter in height measured by body scan when compared to manual measurements. This systematic difference became smaller when volunteers stood in the scanner in a completely upright position with their feet together. Waist circumference was slightly smaller for manual measurements than for body scan derived values. This systematic difference was larger in overweight volunteers compared to leaner volunteers.
Beckmann et al. (2019) Body height and waist circumference of young Swiss men as assessed by 3D laser-based photonic scans and by manual anthropometric measurements. PeerJ 7:e8095 https://doi.org/10.7717/peerj.8095
Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences
Background Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information. Methods We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry. Results We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades. Conclusions Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.
Xuan et al. (2019) Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PeerJ 7:e8158 https://doi.org/10.7717/peerj.8158
MemCat: a new category-based image set quantified on memorability
Images differ in their memorability in consistent ways across observers. What makes an image memorable is not fully understood to date. Most of the current insight is in terms of high-level semantic aspects, related to the content. However, research still shows consistent differences within semantic categories, suggesting a role for factors at other levels of processing in the visual hierarchy. To aid investigations into this role as well as contributions to the understanding of image memorability more generally, we present MemCat. MemCat is a category-based image set, consisting of 10K images representing five broader, memorability-relevant categories (animal, food, landscape, sports, and vehicle) and further divided into subcategories (e.g., bear). They were sampled from existing source image sets that offer bounding box annotations or more detailed segmentation masks. We collected memorability scores for all 10 K images, each score based on the responses of on average 99 participants in a repeat-detection memory task. Replicating previous research, the collected memorability scores show high levels of consistency across observers. Currently, MemCat is the second largest memorability image set and the largest offering a category-based structure. MemCat can be used to study the factors underlying the variability in image memorability, including the variability within semantic categories. In addition, it offers a new benchmark dataset for the automatic prediction of memorability scores (e.g., with convolutional neural networks). Finally, MemCat allows the study of neural and behavioral correlates of memorability while controlling for semantic category.
Goetschalckx et al. (2019) MemCat: a new category-based image set quantified on memorability. PeerJ 7:e8169 https://doi.org/10.7717/peerj.8169
The effect of voluntary head movements on postural kinetics in the standing cat
Background Although the postural instability accompanying bilateral vestibular loss in human and quadrupeds during lateral head movements are well-known, it is still unclear whether or not lateral head turns would indeed activate the postural control system to maintain balance. This study aimed to examine the kinetic parameters in freely standing intact cats during head movements in order to further answer the above question. Methods Six intact cats were trained to stand, unrestrained on a force plate and perform voluntary head movements to the left and right positions in response to visual cues. Each trial was divided into two phases, quiet standing with the cat’s head maintaining a straight forward and lateral head position after voluntary head movements. Kinetic parameters including peak pressure and contact area under each limb as well as center of pressure (COP) displacements of the whole body were measured. Results Compared to the neutral head position, peak pressure and contact area of the left head position were significantly smaller for the left forelimb while greatly larger for the right forelimb. An exact opposite case of peak pressure and contact area in the forelimbs was found between the right and neutral head positions. In addition, the COP displacements altered oppositely to the head movements, and presented a significantly right shift in the left position and a significantly left shift in the right position. Conclusion These results demonstrate that the lateral displacement of the head in standing intact cats does activate the postural adjustment to maintain balance, which is consistent with the concept that vestibular input can contribute to postural balance during voluntary head turns.
Song et al. (2019) The effect of voluntary head movements on postural kinetics in the standing cat. PeerJ 7:e8186 https://doi.org/10.7717/peerj.8186
Identification of key genes in non-small cell lung cancer by bioinformatics analysis
Background Non-small cell lung cancer (NSCLC) is one of the most common malignant tumors in the world, and it has become the leading cause of death of malignant tumors. However, its mechanisms are not fully clear. The aim of this study is to investigate the key genes and explore their potential mechanisms involving in NSCLC. Methods We downloaded gene expression profiles GSE33532, GSE30219 and GSE19804 from the Gene Expression Omnibus (GEO) database and analyzed them by using GEO2R. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. We constructed the protein-protein interaction (PPI) network by STRING and visualized it by Cytoscape. Further, we performed module analysis and centrality analysis to find the potential key genes. Finally, we carried on survival analysis of key genes by GEPIA. Results In total, we obtained 685 DEGs. Moreover, GO analysis showed that they were mainly enriched in cell adhesion, proteinaceous extracellular region, heparin binding. KEGG pathway analysis revealed that transcriptional misregulation in cancer, ECM-receptor interaction, cell cycle and p53 signaling pathway were involved in. Furthermore, PPI network was constructed including 249 nodes and 1,027 edges. Additionally, a significant module was found, which included eight candidate genes with high centrality features. Further, among the eight candidate genes, the survival of NSCLC patients with the seven high expression genes were significantly worse, including CDK1, CCNB1, CCNA2, BIRC5, CCNB2, KIAA0101 and MELK. In summary, these identified genes should play an important role in NSCLC, which can provide new insight for NSCLC research.
Zhang et al. (2019) Identification of key genes in non-small cell lung cancer by bioinformatics analysis. PeerJ 7:e8215 https://doi.org/10.7717/peerj.8215
Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia
Background In extant ecosystems, complex networks of ecological interactions between organisms can be readily studied. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in past terrestrial ecosystems we know comparatively little about plant biotic interactions besides saprotrophy, herbivory, mycorrhizal associations, and oviposition. Due to taphonomic biases, epiphyte communities are particularly rare in the plant-fossil record, despite their prominence in modern ecosystems. Accordingly, little is known about how terrestrial epiphyte communities have changed across geologic time. Here, we describe a tiny in situ fossil epiphyte community that sheds light on plant-animal and plant-plant interactions more than 50 million years ago. Methods A single silicified Todea (Osmundaceae) rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco (Patagonia, Argentina) was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms and mapping and quantifying their distribution. A 200 × 200 µm grid was superimposed onto the rhizome cross section, and the colonizers present at each node of the grid were tallied. Results Preserved in situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes outside of amber deposits; as well as several types of fungal hyphae and spores; microsclerotia with possible affinities in several ascomycete families; and evidence for oribatid mites. Discussion The community associated with the Patagonian rhizome enriches our understanding of terrestrial epiphyte communities in the distant past and adds to a growing body of literature on osmundaceous rhizomes as important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained virtually unchanged over time and space and are abundant in the fossil record, they provide a paleoecological model system that could be used to explore epiphyte community structure through time.
Bippus et al. (2019) Fossil fern rhizomes as a model system for exploring epiphyte community structure across geologic time: evidence from Patagonia. PeerJ 7:e8244 https://doi.org/10.7717/peerj.8244