Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis
Background Even if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia. Methods We recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS. Results The prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class. Conclusion CAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and schools. After controlling for clustering effects at the school and class levels, we found an association between CAS and increasing age, not always washing hands with soap after using latrine, walking barefoot, and T. trichiura infection. Using treated water for drinking was found to have a protective effect against CAS. Thus, educating children on personal hygiene and provision of safe drinking water could reduce the CAS burden in schoolchildren in rural areas of southern Ethiopia.
Amare et al. (2021) Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis. PeerJ 9:e11158 https://doi.org/10.7717/peerj.11158
First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics
Background The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. Methods Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. Results Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
Zheng et al. (2021) First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics. PeerJ 9:e11294 https://doi.org/10.7717/peerj.11294
Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama
Seagrass meadows are valued coastal habitats that provide ecological and economic benefits around the world. Despite their importance, many meadows are in decline, driven by a variety of anthropogenic impacts. While these declines have been well documented in some regions, other locations (particularly within the tropics) lack long-term monitoring programs needed to resolve seagrass trends over time. Effective and spatially-expansive monitoring within under-represented regions is critical to provide an accurate perspective on seagrass status and trends. We present a comprehensive dataset on seagrass coverage and composition across 24 sites in Bahía Almirante, a lagoon along the Caribbean coast of Panama. Using a single survey, we focus on capturing spatial variation in seagrass physical and elemental characteristics and provide data on key seagrass bio-indicators, such as leaf morphology (length and width), elemental content (% nitrogen and phosphorus) and stable isotopic signatures (δ13C and δ15N). We further explore relationships between these variables and water depth (proxy for light availability) and proximity to shore (proxy for terrestrial inputs). The seagrass assemblage was mostly monospecific (dominated by Thalassia testudinum) and restricted to shallow water (<3 m). Above-ground biomass varied widely, averaging 71.7 g dry mass m−2, yet ranging from 24.8 to 139.6 g dry mass m−2. Leaf nitrogen content averaged 2.2%, ranging from 1.76 to 2.57%, while phosphorus content averaged 0.19% and ranged from 0.15 to 0.23%. These values were high compared to other published reports for T. testudinum, indicating elevated nutrient availability within the lagoon. Seagrass stable isotopic characteristics varied slightly and were comparable with other published values. Leaf carbon signatures (δ13C) ranged from −11.74 to −6.70‰ and were positively correlated to shoreline proximity, suggesting a contribution of terrestrial carbon to seagrass biomass. Leaf nitrogen signatures (δ15N) ranged from −1.75 to 3.15‰ and showed no correlation with shoreline proximity, suggesting that N sources within the bay were not dominated by localized point-source discharge of treated sewage. Correlations between other seagrass bio-indicators and environmental metrics were mixed: seagrass cover declined with depth, while biomass was negatively correlated with N, indicating that light and nutrient availability may jointly regulate seagrass cover and biomass. Our work documents the response of seagrass in Bahía Almirante to light and nutrient availability and highlights the eutrophic status of this bay. Using the broad spatial coverage of our survey as a baseline, we suggest the future implementation of a continuous and spatially expansive seagrass monitoring program within this region to assess the health of these important systems subject to global and local stressors.
Gaubert-Boussarie et al. (2021) Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama. PeerJ 9:e11308 https://doi.org/10.7717/peerj.11308
Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
Karimi et al. (2021) Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 9:e11344 https://doi.org/10.7717/peerj.11344
Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum
Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum.
Zhou et al. (2021) Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum. PeerJ 9:e11345 https://doi.org/10.7717/peerj.11345
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing to interrogate and re-train the underlying classification model.
Hockenberry et al. (2021) BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. PeerJ 9:e11396 https://doi.org/10.7717/peerj.11396
Construction of an immune-related signature with prognostic value for colon cancer
Background Colon cancer is the third most common malignant tumor in the world. Although immunotherapy has been used in cancer treatment, there is still no first-line immunotherapy method for colon cancer. Therefore, it is essential to search for potential immunotherapy targets and molecular biomarkers for early diagnosis and prognosis. Methods In this study, we downloaded transcriptome data from The Cancer Genome Atlas (TCGA) and immune-related genes from the ImmPort database. Then we filtered genes with prognostic value and constructed an immune-related signature. Patients were classified into low- and high-risk groups, and we exerted a series of analysis between the signature and clinical phenotypes. Additionally, we used protein-protein interaction networks, gene set enrichment analysis (GSEA) and single-sample gene-set enrichment analysis (ssGSEA) to explore the underlying mechanism of this signature. Furthermore, the accuracy of this signature was verified, using two data sets from Gene Expression Omnibus (GEO). Results We selected 12 immune-related genes to construct the immune-related signature. Low-risk group had a higher level of immunity compared to high-risk group. The expression level of HLA genes and checkpoint-related genes were statistically different in low- and high-risk groups. This signature showed its prognostic value in TCGA cohort and 2 GEO data sets. The signature also had strong correlation with TNM classification, stage, survival state and lymphatic invasion. The mechanism of the signature may be related to several transcription factors and CD8+ T cell in the tumor microenvironment. Conclusion In conclusion, this immune-related signature is of great prognosis value for colon cancer and its biofunction might be correlated with HLA genes, checkpoint-related genes and high-infiltrating T cells in tumor tissues.
Lv et al. (2021) Construction of an immune-related signature with prognostic value for colon cancer. PeerJ 9:e10812 https://doi.org/10.7717/peerj.10812
Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types
Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
Langenfeld et al. (2021) Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types. PeerJ 9:e11111 https://doi.org/10.7717/peerj.11111
Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida
Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.
Jiang et al. (2021) Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida. PeerJ 9:e11212 https://doi.org/10.7717/peerj.11212
Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study
Background Lung adenocarcinoma (LUAD) is the leading histological subtype of non-small cell lung cancer (NSCLC). Methods In the present study, the gene matrixes of LUAD were downloaded from The Cancer Genome Atlas to infer immune and stromal scores with the ‘Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data’ (ESTIMATE) algorithm and identified immune-related differentially expressed genes (DEGs) between the high- and low-stromal/immune score groups. Next, all DEGs were subjected to univariate Cox regression and survival analyses to screen out prognostic biomarkers in the tumor microenvironment (TME), and were validated in the Gene Expression Omnibus database. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess the level of tumor-infiltrating immune cells (TIICs) and immune functions, and GSEA was used to identified pathways altered by prognostic biomarkers. Results Survival analysis showed that LUAD in the high-immune and stromal score group had a better clinical prognosis. A total of 303 immune-related DEGs were detected. Univariate Cox regression and survival analyses revealed that P2Y purinoceptor 13 (P2RY13) was a favorable factor for the prognosis of LUAD. ssGSEA and Spearman correlation analysis demonstrated that P2RY13 was highly correlated with various TIICs and immune functions. Several immune-associated pathways were enriched between the high- and low-expression P2RY13 groups. Conclusion P2RY13 may be a potential prognostic indicator and is highly associated with the TME in LUAD. However, further experimental studies are required to validate the present findings.
Lin et al. (2021) Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study. PeerJ 9:e11319 https://doi.org/10.7717/peerj.11319