A novel similarity score based on gene ranks to reveal genetic relationships among diseases
Knowledge of similarities among diseases can contribute to uncovering common genetic mechanisms. Based on ranked gene lists, a couple of similarity measures were proposed in the literature. Notice that they may suffer from the determination of cutoff or heavy computational load, we propose a novel similarity score SimSIP among diseases based on gene ranks. Simulation studies under various scenarios demonstrate that SimSIP has better performance than existing rank-based similarity measures. Application of SimSIP in gene expression data of 18 cancer types from The Cancer Genome Atlas shows that SimSIP is superior in clarifying the genetic relationships among diseases and demonstrates the tendency to cluster the histologically or anatomically related cancers together, which is analogous to the pan-cancer studies. Moreover, SimSIP with simpler form and faster computation is more robust for higher levels of noise than existing methods and provides a basis for future studies on genetic relationships among diseases. In addition, a measure MAG is developed to gauge the magnitude of association of anindividual gene with diseases. By using MAG the genes and biological processes significantly associated with colorectal cancer are detected.
Luo et al. (2021) A novel similarity score based on gene ranks to reveal genetic relationships among diseases. PeerJ 9:e10576 https://doi.org/10.7717/peerj.10576
Health status of Polychrus gutturosus based on physical examination, hematology and biochemistry parameters in Costa Rica
Studies evaluating the health status and characteristics of free-ranging wildlife populations are scarce or absent for most species. Saurian health assessments are usually performed in species that have conservation issues or that are kept in captivity. The Berthold’s bush anole (Polychrus guturossus) is one of eight species belonging to the genus Polychrus, the only representative of the family Polychrotidae. Only a handful of studies have been reported concerning these lizard’s morphological variation, ecology, and natural history, probably because P. gutturosus is a canopy dweller and it can be difficult to locate individuals. It is believed that deforestation and habitat modification could pose a threat for this species, although to date no health assessment has been done. The aim of this study was to generate health baseline data on P. gutturosus. Forty Berthold’s bush anoles (20 males and 20 females) were sampled at the Pacific versant in Costa Rica, where physical examination, skin and cloacal temperatures, and blood samples were obtained from individuals immediately after capture. Animals from the studied population were all healthy (body condition 2.5–3.0/5.0). No lesions or ectoparasites were detected, but hemoparasites were found in nine individuals. Hematological and biochemical values were obtained, and the morphology of leukocytes were found to be similar to other iguanians. A positive correlation was found between the tissue enzymes aspartate aminotransferase (AST) and creatinine kinase (CK) and a negative correlation was found between skin and cloacal temperatures and AST and CK. There were positive correlations between female weight and total protein, calcium, and the calcium and phosphorus ratio. No significant inter-sex differences were found in biochemical values, despite females being larger than males. This is the first health assessment performed on a free-ranging canopy dwelling lizard. These findings provide baseline data that may be useful for future monitoring if the species faces changes in health status due to anthropogenic causes or natural disturbances.
Arguedas et al. (2021) Health status of Polychrus gutturosus based on physical examination, hematology and biochemistry parameters in Costa Rica. PeerJ 9:e10649 https://doi.org/10.7717/peerj.10649
miR-875-5p exerts tumor-promoting function via down-regulation of CAPZA1 in esophageal squamous cell carcinoma
Esophageal squamous cell carcinoma (ESCC) is one of the leading causes of cancer deaths worldwide. Currently, efficient genetic markers for diagnosis and treatment of ESCC are lacking. MicroRNAs (miRNAs) are global genetic regulators that control cancer gene expression by binding to the 3′untranslated regions (3′UTRs) of targeting mRNAs. In addition, miRNAs function as oncogenes or tumor suppressors in the progression of tumors. In the current study, we found that hsa-miR-875-5p (miR-875-5p) exhibited amplification in ESCC according to the TCGA database. Then, xCELLigence Real-Time Cell Analyzer (RTCA)-MP system and colony formation assays were employed to detect cell proliferationand colony formationability. The results showed that miR-875-5p promoted the proliferation ESCC cells. Subsequently, transwell results indicated that miR-875-5p promoted the invasion and migration of ESCC cells. Furthermore, we showed that miR-875-5p was able to bind to CAPZA13’UTR, which contains the single nucleotide polymorphism (SNP), rs373245753, as reported in our previous study involving WGS and WES on ESCC. Subsequently, mRNA affinity pull-down assays verifiedthat the SNP disrupts miR-875-5p binding to CAPZA1. The current study is the first demonstration that miR-875-5p may function as an oncogene via down-regulation of CAPZA1 expression in ESCC.
Kang et al. (2021) miR-875-5p exerts tumor-promoting function via down-regulation of CAPZA1 in esophageal squamous cell carcinoma. PeerJ 9:e10020 https://doi.org/10.7717/peerj.10020
The reliability and validity of the weight-bearing lunge test in a Congenital Talipes Equinovarus population (CTEV)
Question What is the intra and inter-rater reliability and concurrent validity of the weight-bearing lunge test within a Congenital Talipes Equinovarus population? Design Test retest design for reliability and validity. The measure was taken, following preconditioning of the participants, using distance from wall, angle at distal posterior tibia using a digital inclinometer and the iPhone level function, twice by each rater. The raters included a clinician, clinician in training and a parent/carer. Outcome measures Weight bearing lunge test as a measure of ankle dorsiflexion. Results Twelve children aged 5–10 years were eligible to participate and consented, along with their parents. Intra-reliability of distance measures for all raters were good to excellent (ICC clinician 0.95, ICC training clinician 0.98 and ICC parent 0.89). Intra-rater reliability of the iPhone for all raters was good (ICCs > 0.751) and good to excellent for the inclinometer (ICC clinician 0.87, ICC training clinician 0.90). Concurrent validity between the clinician’s and parents distance measure was also high with ICC of 0.899. Inter-rater reliability was excellent for distance measure (ICC = 0.948), good for the inclinometer (ICC = 0.801) and moderate for the iPhone (ICC = 0.68). Standard error of measurement ranged from 0.70–2.05, whilst the minimal detectable change ranged from 1.90–5.70. Conclusion The use of the WBLT within this CTEV population has demonstrated good to excellent reliability and validity amongst clinicians, clinicians in training and parents/carers, supporting its use as an assessment measure of dorsiflexion range of motion. There is support for parents/carers to use the WBLT at home as a monitoring assessment measure which may assist with early detection of a relapse. Trial registration University of South Australia’s ethics committee (ID: 201397); Women’s and Children’s Hospital ethics committee (AU/1/4BD7310).
Gosse et al. (2021) The reliability and validity of the weight-bearing lunge test in a Congenital Talipes Equinovarus population (CTEV). PeerJ 9:e10253 https://doi.org/10.7717/peerj.10253
In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana
Background Genetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants. Methods The histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana. Results This study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers. This study shows the role of epigenetic marks in regulating gene expression and functional divergence after gene duplication in plants based on sequencing data.
Wang et al. (2021) In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana. PeerJ 9:e10426 https://doi.org/10.7717/peerj.10426
A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park
Munida diritas sp. nov. is described for the seamounts near Desventuradas Islands, in the intersection of the Salas & Gómez and Nazca Ridges, Chile. Specimens of the new species were collected in the summit (∼200 m depth) of one seamount and observed by ROV at two nearby ones. This species is characterized by the presence of distinct carinae on the thoracic sternites 6 and 7. Furthermore, it is not related with any species from the continental shelf nor the slope of America, while it is closely related to species of Munida from French Polynesia and the West-Pacific Ocean (i.e., M. ommata, M. psylla and M. rufiantennulata). In situ observations indicate that the species lives among the tentacles of ceriantarid anemones and preys on small crustaceans. The discovery of this new species adds to the knowledge of the highly endemic benthic fauna of seamounts of the newly created Nazca-Desventuradas Marine Park, emphasizing the relevance of this area for marine conservation.
Gallardo Salamanca et al. (2021) A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park. PeerJ 9:e10531 https://doi.org/10.7717/peerj.10531
Aerosol optical depth (AOD): spatial and temporal variations and association with meteorological covariates in Taklimakan desert, China
Aerosol optical depth (AOD) is a key parameter that reflects aerosol characteristics. However, research on the AOD of dust aerosols and various environmental variables is scarce. Therefore, we conducted in-depth studies on the distributions and variations of AOD in the Taklimakan Desert and its margins, China. We examined the correlation characteristics between AOD and meteorological factors combined with satellite remote sensing detection methods using MCD19A2-MODIS AOD products (from 2000, 2005, 2010, and 2015), MOD13Q1-MODIS normalized difference vegetation index products, and meteorological data. We analyzed the temporal and spatial distributions of AOD, periodic change trends, and important impacts of meteorological factors on AOD in the Taklimakan Desert and its margins. To explore the relationships between desert aerosols and meteorological factors, a random forest model was used along with environmental variables to predict AOD and rank factor contributions. Results indicated that the monthly average AOD exhibited a clear unimodal curve that reached its maximum in April. The AOD values followed the order spring (0.28) > summer (0.27) > autumn (0.18) > winter (0.17). This seasonality is clear and can be related to the frequent sandstorms occurring in spring and early summer. Interannual AOD showed a gradually increasing trend to 2010 then large changes to 2015. AOD tends to increase from south to north. Based on the general trend, the maximum value of AOD is more dispersed and its low-value area is always stable. The climatic index that has the most significant effect on AOD is relative humidity.
Spatial and Geographic Information Science
Li et al. (2021) Aerosol optical depth (AOD): spatial and temporal variations and association with meteorological covariates in Taklimakan desert, China. PeerJ 9:e10542 https://doi.org/10.7717/peerj.10542
Determining the influencing factors of preferential flow in ground fissures for coal mine dump eco-engineering
Ground fissures (GF), appearing in front of dumps, are one of the most obvious and harmful geological hazards in coal mining areas. Studying preferential flow and its influencing factors in the ground fissures of dumps may provide basic scientific support for understanding the rapid movement of water and vegetation restoration and reconstruction in mining areas. Based on field surveys of ground fissures, three typical ground fissures were selected in the studied dump. The morphological characteristics of preferential flow for ground fissures were determined through field dye tracing, laboratory experiments, and image processing technology. The results indicated that the lengths of the three ground fissures ranged from 104.84 cm to 120.83 cm, and the widths ranged from 2.86 cm to 9.85 cm. All of the ground fissure area densities were less than 10%, and the proportion of ground fissure surface area was small in the dump. The maximum fissure depth was 47 cm, and the minimum was 16 cm. The ground fissure widths ranged from 0 cm to 14.98 cm, and the fissure width and fissure width-to-depth ratios decreased with increasing soil depth. The stained area was greater than 90% in the 0–5 cm soil layers of the three fissures, and water movement was dominated by matrix flow. The stained width decreased from 90 cm to 20 cm with increasing soil depth. The preferential flow was mainly concentrated on both sides of the fissure, which was distributed as a “T” shape. The preferential flow stained area ratios were 27.23%, 31.97%, and 30.73%, respectively, and these values decreased with increasing soil depth. The maximum stained depths of the preferential flow among the three fissures were different, and the maximum stained depth of GF II was significantly larger than that of GF I and GF III (P < 0.05). The stained path numbers of the three fissures ranged from 0 to 49. With increasing soil depth, the stained path number first increased and then decreased. The stained path widths of the three fissures ranged from 0 cm to 90 cm. With the increase in soil depth, the stained path width decreased. The stained area ratio was significantly positively correlated with ground fissure width, the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity, soil organic matter, and sand content and was significantly negatively correlated with soil water content and clay content. The stained path number was significantly positively correlated with ground fissure width, the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity and soil organic matter. The stained path width was significantly positively correlated with the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity, soil organic matter and sand content and was significantly negatively correlated with clay content. Plant roots could significantly increase the stained area ratio, stained path number, and width and promote the formation and development of preferential flow.
Li et al. (2021) Determining the influencing factors of preferential flow in ground fissures for coal mine dump eco-engineering. PeerJ 9:e10547 https://doi.org/10.7717/peerj.10547
Improving insect conservation across heterogeneous landscapes using species–habitat networks
Background One of the biggest challenges in conservation is to manage multiple habitats for the effective conservation of multiple species, especially when the focal species are mobile and use multiple resources across heterogeneous protected areas. The application of ecological network tools and the analysis of the resulting species–habitat networks can help to describe such complex spatial associations and improve the conservation of species at the landscape scale. Methods To exemplify the application of species–habitat networks, we present a case study on butterflies inhabiting multiple grassland types across a heterogeneous protected area in North-East Italy. We sampled adult butterflies in 44 sites, each belonging to one of the five major habitat types in the protected area, that is, disturbed grasslands, continuous grasslands, evolved grasslands, hay meadows and wet meadows. First, we applied traditional diversity analyses to explore butterfly species richness and evenness. Second, we built and analyzed both the unipartite network, linking habitat patches via shared species, and the bipartite network, linking species to individual habitat patches. Aims (i) To describe the emerging properties (connectance, modularity, nestedness, and robustness) of the species–habitat network at the scale of the whole protected area, and (ii) to identify the key habitats patches for butterfly conservation across the protected area, that is, those supporting the highest number of species and those with unique species assemblages (e.g., hosting specialist species). Results The species–habitat network appeared to have a weak modular structure, meaning that the main habitat types tended to host different species assemblages. However, the habitats also shared a large proportion of species that were able to visit multiple habitats and use resources across the whole study area. Even butterfly species typically considered as habitat specialists were actually observed across multiple habitat patches, suggesting that protecting them only within their focal habitat might be ineffective. Our species–habitat network approach helped identifying both central habitat patches that were able to support the highest number of species, and habitat patches that supported rare specialist species.
Cappellari et al. (2021) Improving insect conservation across heterogeneous landscapes using species–habitat networks. PeerJ 9:e10563 https://doi.org/10.7717/peerj.10563
Bacterial meta-analysis of chicken cecal microbiota
Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.
Chica Cardenas et al. (2021) Bacterial meta-analysis of chicken cecal microbiota. PeerJ 9:e10571 https://doi.org/10.7717/peerj.10571