Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study
Background Alzheimer’s disease (AD) is an age-related neurodegenerative disease caused by central nervous system disorders. Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Differences at the expression level of certain genes, resulting from either genetic variations or environmental interactions, might be one of the mechanisms underlying differential risks for developing AD. Peripheral blood genome transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tau for AD research. Methods This preliminary study explores molecular pathogenesis of LOAD-related inflammation through next generation sequencing, to assess RNA expression profiles in peripheral blood from five patients with LOAD and 10 healthy controls. Results The analysis of RNA expression profiles revealed 94 genes up-regulated and 147 down-regulated. Gene function analysis, including Gene Ontology (GO) and KOBAS-Kyoto Encyclopedia of DEGs and Genomes (KEGG) pathways indicated upregulation of interferon family (INF) signaling, while the down-regulated genes were mainly associated with the cell cycle process. KEGG metabolic pathways mapping showed gene expression alterations in the signaling pathways of JAK/STAT, chemokines, MAP kinases and Alzheimer disease. The results of this preliminary study provided not only a comprehensive picture of gene expression, but also the key processes associated with pathology for the regulation of neuroinflammation, to improve the current mechanisms to treat LOAD.
Cardona et al. (2021) Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PeerJ 9:e12016 https://doi.org/10.7717/peerj.12016
Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
Cryptosporidium spp. is a protozoan having the potential to cause zoonosis in humans and animals. Despite the zoonotic importance of this protozoan parasite, limited data are available about its prevalence in zoo felids in North-Eastern China. Hence, the current study was designed to determine the occurrence and molecular characterization of Cryptosporidium spp. from the fecal samples of captive zoo felids. Fecal samples (N = 244) were collected from different felids from five different zoos of North-Eastern China. 18S rRNA gene was amplified from the genomic DNA using species specific primers in nested polymerase chain reaction (nPCR) and Cryptosporidium parvum and Cryptosporidium spp. was found. The overall prevalence of Cryptosporidium was 9.43% (23/244). The 18S rRNA gene similarity analysis showed that 6 Cryptosporidium isolates were Cryptosporidium parvum and the remaining 17 Cryptosporidium isolates were resembling to a Cryptosporidium spp., which is similar to Cryptosporidium NEV10. Phylogenetic tree was constructed based on 18S rRNA of Cryptosporidium spp. The similarity of Cryptosporidium parvum was with its other isolates in China, India, Iran, Iraq, Turkey, Czech Republic, Spain and USA while Cryptosporidium NEV10 alike had a close relationship with Turkish isolates. In conclusion, Cryptosporidium was prevailing in feline animals of China zoo and zoo officials are directed to consider their control policy as it can be a cause of zoonosis.
Hussain et al. (2021) Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.. PeerJ 9:e11819 https://doi.org/10.7717/peerj.11819
Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
Liu et al. (2021) Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. PeerJ 9:e11842 https://doi.org/10.7717/peerj.11842
Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma
Background Lung cancer is a common malignant carcinoma of respiratory system with high morbidity and mortality. Kelch-like epichlorohydrin-related protein 1 (Keap1), a member of the BTB-Kelch protein family, has been reported as an important molecule in several cancers. However, its potential role in tumor is still controversial. Here we aim to clarify the effect of Keap1 on the biological characteristics and chemotherapy resistance in lung adenocarcinoma (LUAD). Methods Immunohistochemistry was conducted to compare Keap1 expression in lung adenocarcinoma tissues and matched non-cancerous tissues, and the correlation between Keap1 expression and clinicopathological features was analyzed. Subsequently, the stable A549 and H1299 cell lines with Keap1 knockdown or overexpression were constructed using lentivirus. The roles of Keap1 on the cell proliferation, migration, invasion and drug resistance were investigated by colony formation assay, cell proliferation assay, wound scratch test, transwell invasion assay and drug sensitivity assay, respectively. Results Keap1 was lowly expressed in tumor tissues compared to matched non-cancerous tissues, and its expression was correlated with TNM stage and lymph node metastasis. Early stage (I) tumors without lymph node metastasis had higher levels of Keap1 expression compared with late-stage tumors (II, III) with the presence of lymphatic metastasis. Colony formation assays showed that Keap1 knockdown promoted the proliferation of A549 and H1299 cells, and the cell growth curves further confirmed this feature. In contrast, wound scratch and transwell invasion experiments showed that Keap1 overexpression inhibited cell migration and invasive malignancy. The IC50 for cisplatin and paclitaxel were significantly increased by Keap1 knockdown in A549 and H1299 cell lines. Conclusion Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in LUAD. It may be a potential tumor marker to guide the staging and treatment of lung cancer.
Gao et al. (2021) Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma. PeerJ 9:e11908 https://doi.org/10.7717/peerj.11908
The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust
Orchardgrass (Dactylis glomerata) is one of the top four perennial forages worldwide and, despite its large economic advantages, often threatened by various environmental stresses. WRKY transcription factors (TFs) can regulate a variety of plant processes, widely participate in plant responses to biotic and abiotic stresses, and are one of the largest gene families in plants. WRKYs can usually bind W-box elements specifically. In this study, we identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169 and 47 nucleotide-binding site-leucine-rich repeats (NBS-LRRs), leucine-rich repeats receptor-like protein kinases (LRR-RLKs), and leucine-rich repeats receptor-like proteins (LRR-RLPs), respectively. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stresses, it was found that many DgWRKY genes were differentially expressed under heat, drought, submergence, and rust stress. In particular, it was found that the greatest number of genes were differentially expressed under rust infection. Consistently, GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differentially expressed. Through cis-acting element prediction, 154 RGAs were found to contain W-box elements. Among them, DG6C02319.1 (a member of the LRR-RLK family) was identified as likely to interact with 14 DGWRKYs. Moreover, their expression levels in susceptible plants after rust inoculation were first up-regulated and then down-regulated, while those in the resistant plants were always up-regulated. In general, DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the response of orchardgrass to rust. This study provides meaningful insight into the molecular mechanisms of WRKY proteins in orchardgrass.
Ren et al. (2021) The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust. PeerJ 9:e11919 https://doi.org/10.7717/peerj.11919
Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones
Background Dupont’s Lark is an endangered bird, whose fragmented distribution in Europe is entirely restricted to Spain. This lark, suffering pronounced population decline and range contraction, inhabits steppes that have long been used for grazing sheep and are now threatened by rural abandonment and land use changes. Thus, for conservation of the lark, increasing knowledge about the connectivity of the Spanish metapopulation and identifying the most important connectivity nodes are crucial. Methods The study was carried out in Spain, using over 16,000 Dupont’s Lark georeferenced observations. We used distance buffers to define populations and subpopulations, based on the available scientific information. We identified potential stepping stones using a MaxEnt probability of presence model. Connectivity was assessed using Conefor software, using the centroid of each subpopulation and stepping stone as nodes. Each node was assigned a quantitative attribute based on total habitat area, within-node habitat quality and internal fragmentation. We evaluated different connectivity scenarios by potential movement thresholds (5–20–100 km) and presence or absence of stepping stones in the network. Results Dupont’s Lark Iberian metapopulation comprises 24 populations and 100 subpopulations, plus 294 potential stepping stones. Movement thresholds and stepping stones had a strong influence in the potential network connectivity. The most important nodes are located in the core of the metapopulation, which shows connectivity among subpopulations in the different indices and scenarios evaluated. Peripheral populations are more isolated and require stepping stones or medium (20 km) or long (100 km) potential movement thresholds to join the network. Discussion Metapopulation connectivity may be greater than expected, thanks to stepping stones and potential medium-distance movements. Connectivity is crucial for conservation and can be increased by preserving or improving adequate habitat in the most important nodes. Given the current species decline, steppe habitat should be urgently protected from land use changes and agriculture intensification, at least in the critical subpopulations and stepping stones. Long-term conservation of steppe lands and Dupont’s Lark in Spain requires the recovery of traditional grazing and more research on juvenile dispersion. Meanwhile, the conservation of potentially critical stepping stones should be incorporated to management plans.
García-Antón et al. (2021) Connectivity in Spanish metapopulation of Dupont’s lark may be maintained by dispersal over medium-distance range and stepping stones. PeerJ 9:e11925 https://doi.org/10.7717/peerj.11925
Nitrous oxide, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and straw in a semiarid environment
Background Soil application of biochar and straw alone or their combinations with nitrogen (N) fertilizer are becoming increasingly common, but little is known about their agronomic and environmental performance in semiarid environments. This study was conducted to investigate the effect(s) of these amendments on soil properties, nitrous oxide (N2O) and methane (CH4) emissions and grain and biomass yield of spring wheat (Triticum aestivum L.), and to produce background dataset that may be used to inform nutrient management guidelines for semiarid environments. Methods The experiment involved the application of biochar, straw or urea (46% nitrogen [N]) alone or their combinations. The treatments were: CN0–control (zero-amendment), CN50 –50 kg ha–1 N, CN100–100 kg ha–1 N, BN0 –15 t ha–1 biochar, BN50–15 t ha–1 biochar + 50 kg ha–1 N, BN100–15 t ha–1 biochar + 100 kg ha–1 N, SN0 –4.5 t ha–1 straw, SN50 –4.5 t ha–1 straw + 50 kg ha–1 N and SN100–4.5 t ha–1 straw + 100 kg ha–1 N. Fluxes of N2O, CH4 and grain yield were monitored over three consecutive cropping seasons between 2014 and 2016 using the static chamber-gas chromatography method. Results On average, BN100reported the highest grain yield (2054 kg ha–1), which was between 25.04% and 38.34% higher than all other treatments. In addition, biomass yield was much higher under biochar treated plots relative to the other treatments. These findings are supported by the increased in soil organic C by 17.14% and 21.65% in biochar amended soils (at 0–10 cm) compared to straw treated soils and soils without carbon respectively. The BN100treatment also improved bulk density and hydraulic properties (P < 0.05), which supported the above results. The greatest N2O emissions and CH4 sink were recorded under the highest rate of N fertilization (100 kg N ha–1). Cumulative N2O emissions were 39.02% and 48.23% lower in BN100 compared with CN0 and CN100, respectively. There was also a ≈ 37.53% reduction in CH4 uptake under BN100compared with CN0–control and CN50. The mean cumulative N2O emission from biochar treated soils had a significant decrease of 10.93% and 38.61% compared to straw treated soils and soils without carbon treatment, respectively. However, differences between mean cumulative N2O emission between straw treated soils and soils without carbon were not significant. These results indicate the dependency of crop yield, N2O and CH4 emissions on soil quality and imply that crop productivity could be increased without compromising on environmental quality when biochar is applied in combination with N-fertilizer. The practice of applying biochar with N fertilizer at 100 kg ha−1 N resulted in increases in crop productivity and reduced N2O and CH4soil emissions under dryland cropping systems.
Yeboah et al. (2021) Nitrous oxide, methane emissions and grain yield in rainfed wheat grown under nitrogen enriched biochar and straw in a semiarid environment. PeerJ 9:e11937 https://doi.org/10.7717/peerj.11937
A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus
We describe a new cryptic species of Phrynoglossus from Chattogram Division, Bangladesh based on an integrative taxonomic analysis based on morphology, phylogenetics, and bioacoustics which unambiguously support the placement of the species in the genus Phrynoglossus. We also present a compilation of published morphological characters for all twelve Phrynoglossus species and two species of Occidozyga as well as comments on taxonomy, morphology, and geographic distribution for the two genera. The new species is found to be most morphologically similar to P. martensii, however a provided set of character states visibly differentiates these two species. Finally, habitat for Phrynoglossus swanbornorum sp. nov. is highly fragmented and faces imminent threats from development and agriculture, and although it is confirmed to occur within government protected areas in the southeastern region of Bangladesh, few wildlife regulations are enforced within them. Thus, following IUCN criteria, we consider the new species as Endangered based on criteria B1ab(i,ii,iii,iv) + 2ab(i,ii,iii,iv).
Trageser et al. (2021) A new species of Phrynoglossus Peters, 1867; Dicroglossidae) from southeastern Bangladesh, with comments on the genera Occidozyga and Phrynoglossus. PeerJ 9:e11998 https://doi.org/10.7717/peerj.11998
Prevalence of abnormal urinary cadmium and risk of albuminuria as a primary bioindicator for kidney problems among a healthy population
Background The prevalence of chronic kidney disease is increasing globally, ranking 27th as the cause of death in the 1990s, rising to 18th in 2010 and 10th in 2019. Non-communicable diseases such as diabetes and hypertension have been identified as the common contributing factors, while there is also evidence linking environmental pollutants, especially cadmium, to kidney disease. This study aimed at investigating the level of urinary cadmium and its relationship to albuminuria as an early indicator of kidney problems in the Kepong community. Methods Respondents were surveyed as part of several health-related programs organized by the Kepong District Health Office involving local communities in and around the district from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the presence and level of urinary cadmium. Results A total of 240 respondents were enrolled from April 2019 to December 2019. Urinalysis of two urine samples was carried out using a Mission reagent strip and an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) test to detect the level of urinary cadmium. The respondents’ average age was 41-year-old (±13.23). Among them, 49.6% were male, 85.0% Malay, 5.8% Chinese and 8.3% Indian. 55.0% had background of tertiary, 39.6% secondary and 5.4% primary level of education. 52.1% were categorized in B40, 34.6% in M40 and 13.3% in T20 based on monthly household income category. 26.7% were hypertensive, 6.7% diabetic, 4.2% had dyslipidemia, 51.7% had urinary cadmium above the alert level, and 27.1% had albuminuria. Discussion Risk factors for albuminuria that have been identified are age with adjusted odds ratio (AOR) 3.53 (1.41–8.83; p < 0.05), highest educational level with AOR 2.18 (1.14–4.17; p < 0.05), diabetes with AOR 3.36 (1.07–10.52; p < 0.05), and urinary cadmium with AOR 4.72 (2.33–9.59; p < 0.001), with future screening programs placing greater attention to those at risk and further research is required to determine the cause of exposure to cadmium.
Madrim et al. (2021) Prevalence of abnormal urinary cadmium and risk of albuminuria as a primary bioindicator for kidney problems among a healthy population. PeerJ 9:e12014 https://doi.org/10.7717/peerj.12014
The relationship between characteristics of root morphology and grain filling in wheat under drought stress
Drought is a common yield limiting factor in wheat production and has become a significant threat to global food security. Root system is the organ responsible for water uptake from soil and root growth is closely associated with yield and quality of wheat. However, the relationship between morphological and structural characteristics of root growth and caryopsis enrichment in wheat under drought stress is unclear. In this study, two wheat cultivars (YM13 and YN19) were treated with drought from flowering to caryopsis maturity stage. The changes in morphological structure of roots and characteristics of endosperm enrichment were investigated. Drought stress significantly reduced the root length, plant height, root dry weight and aboveground parts dry weight, whereas the root-shoot ratio of YM13 and YN19 increased by 17.65% and 8.33% under drought stress, respectively. The spike length, spike weight, grains number per spike and 1,000-grains weight of mature wheat also significantly declined under drought stress. Meanwhile, the cross section structure of roots was changed with the enlargement of vascular cylinder and dense distribution of xylem vessels under drought stress. Additionally, drought stress affected the substance enrichment in wheat caryopses, decreasing starch accumulation and increasing protein accumulation of endosperm. Correlation analysis suggested that the root length was closely correlated with the relative areas of amyloplast (0.51) and protein body (0.70), and drought stress increased the correlation coefficient (0.79 and 0.78, respectively). While the root dry weight had a significantly positive correlation with the plant height and aboveground parts dry weight. The results can provide theoretical basis for root architecture optimization, water-saving and high-yield cultivation and quality improvement in wheat.
Chen et al. (2021) The relationship between characteristics of root morphology and grain filling in wheat under drought stress. PeerJ 9:e12015 https://doi.org/10.7717/peerj.12015