Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders
Background Vaginal lubrication is a crucial physiological response that occurs at the beginning of sexual arousal. However, research on lubrication disorders (LD) is still in its infancy, and the role of long non-coding RNAs (lncRNAs) in LD remains unclear. This study aimed to explore the function of lncRNAs in the pathogenesis of vaginal LD. Methods The expression profiles of LD and normal control (NC) lncRNAs were examined using next-generation sequencing (NGS), and eight selected differentially expressed lncRNAs were verified by quantitative real-time PCR. We conducted GO annotation and KEGG pathway enrichment analyses to determine the principal functions of significantly deregulated genes. LncRNA-mRNA co-expression and protein-protein interaction (PPI) networks were constructed and the lncRNA transcription factors (TFs) were predicted. Results From the results, we identified 181,631 lncRNAs and 145,224 mRNAs in vaginal epithelial tissue. Subsequently, our preliminary judgment revealed a total of 499 up-regulated and 337 down-regulated lncRNAs in LD. The top three enriched GO items of the dysregulated lncRNAs included the following significant terms: “contractile fiber part,” “actin filament-based process,” and “contractile fiber”. The most enriched pathways were “cell-extracellular matrix interactions,” “muscle contraction,” “cell-cell communication,” and “cGMP-PKG signaling pathway”. Our results also showed that the lncRNA-mRNA co-expression network was a powerful platform for predicting lncRNA functions. We determined the three hub genes, ADCY5, CXCL12, and NMU, using PPI network construction and analysis. A total of 231 TFs were predicted with RHOXF1, SNAI2, ZNF354C and TBX15 were suspected to be involved in the mechanism of LD. Conclusion In this study, we constructed the lncRNA-mRNA co-expression network, predicted the lncRNA TFs, and comprehensively analyzed lncRNA expression profiles in LD, providing a basis for future studies on LD clinical biomarkers and therapeutic targets. Further research is also needed to fully determine lncRNA’s role in LD development.
Zhang et al. (2021) Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders. PeerJ 9:e12485 https://doi.org/10.7717/peerj.12485
Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations
Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.
Aydemir et al. (2021) Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations. PeerJ 9:e11794 https://doi.org/10.7717/peerj.11794
MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla)
Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65–121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25–40% (Lacustris group), 50–87% (Reticulata group, Teleocichla), 68–168% (Saxatilis group), 125–200% (Wallacii group), and 158–241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.
Říčan et al. (2021) MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla). PeerJ 9:e12283 https://doi.org/10.7717/peerj.12283
Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey
Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome—the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick’s own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.
Price et al. (2021) Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey. PeerJ 9:e12313 https://doi.org/10.7717/peerj.12313
Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim
Juglans mandshurica Maxim is a hermaphroditic plant belonging to the genus Juglans in the family Juglandaceae. The pollination period of female flowers is different from the loose powder period of male flowers on the same tree. In several trees, female flowers bloom first, whereas in others, male flowers bloom first. In this study, male and female flower buds of J. mandshurica at the physiological differentiation stage were used. Illumina-based transcriptome sequencing was performed, and the quality of the sequencing results was evaluated and analyzed. A total of 138,138 unigenes with an average length of 788 bp were obtained. There were 8,116 differentially expressed genes (DEGs); 2,840 genes were upregulated, and 5,276 genes were downregulated. The DEGs were classified by Gene Ontology and analyzed by Kyoto Encyclopedia of Genes and Genomes. The signal transduction factors involved in phytohormone synthesis were selected. The results displayed that ARF and SAUR were expressed differently in the auxin signaling pathway. Additionally, DELLA protein (a negative regulator of gibberellin), the cytokinin synthesis pathway, and A-ARR were downregulated. On April 2nd, the contents of IAA, GA, CTK, ETH and SA in male and female flower buds of two types of J. mandshurica were opposite, and there were obvious genes regulating gender differentiation. Overall, we found that the sex differentiation of J. mandshurica was related to various hormone signal transduction pathways, and hormone signal transduction plays a leading role in regulation.
Qin et al. (2021) Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim. PeerJ 9:e12328 https://doi.org/10.7717/peerj.12328
Gene polymorphisms in ULK1 and PIK3CA are associated with the risk of microscopic polyangiitis in the Guangxi Zhuang Autonomous Region in China
Background Microscopic polyangiitis (MPA) is a systemic autoimmune disease characterized by inflammation of small- and medium-sized blood vessels. Autophagy-related protein polymorphisms are involved in autoimmune disease. The aim of this study was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the ULK1 and PIK3CA genes on the risk of MPA. Method A total of 208 patients with MPA and 211 controls in the Guangxi Zhuang Autonomous Region were recruited and analyzed. The SNPs selected were detected by polymerase chain reaction and high-throughput sequencing. The differences in allele and genotype frequency, various genetic models, and stratification analyses were evaluated, haplotype evaluation was performed after linkage disequilibrium analysis, and the interaction between gene alleles was analyzed. Results A statistically significant difference was detected in the genotypic distribution of two SNPs between the two groups: ULK1 rs4964879 (p = 0.019) and PIK3CA rs1607237 (p = 0.002). The results of the genetic models revealed that ULK1 rs4964879 and rs9481 were statistically significantly associated with an increased risk of MPA, whereas PIK3CA rs1607237 was associated with a reduced risk. The association between SNPs and MPA risk was affected by age, sex, and ethnicity. The ULK1 haplotype (G-T-A-C-G-A) and PIK3CA haplotype (T-G) were associated with a reduced risk of MPA, while the PIK3CA haplotype (C-G) was associated with an increased risk. Conclusion In this study, polymorphisms in the autophagy-related genes ULK1 and PIK3CA and their association with MPA were examined. The results showed that the polymorphisms in ULK1 (rs4964879 and rs9481) and PIK3CA (rs1607237) were significantly associated with MPA risk in the Guangxi population. However, the molecular mechanisms are still unclear; basic science research and studies with larger samples are needed to confirm our conclusions and explore the underlying mechanisms.
Zhu et al. (2021) Gene polymorphisms in ULK1 and PIK3CA are associated with the risk of microscopic polyangiitis in the Guangxi Zhuang Autonomous Region in China. PeerJ 9:e12377 https://doi.org/10.7717/peerj.12377
Population growth of microcrustaceans in water from habitats with differing salinities
Inland salt marshes are a rare habitat in North America. Little is known about the invertebrates in these habitats and their ability to cope with the brackish conditions of the marsh. We studied the population growth of ostracods found in an inland salt marsh (Maple River salt marsh) and of copepods found in the wetland habitat immediately adjacent to the freshwater Kalamazoo River. By studying these species in water from both habitats, we aimed to find out if they performed differently in the two habitats. We also tested Daphnia pulex in water from the two habitats due to the history of Daphnia spp. as model organisms. We found that copepods performed better in water taken from the Maple River salt marsh, and the ostracods and D. pulex performed equally well in either water. This was unexpected, since ostracods are found in the salt marsh and copepods in the freshwater area. As a second experiment, we tested the invertebrates in pairwise interactions. In water from the Kalamazoo River, ostracods outperformed the other two species, but there was no difference between D. pulex and copepods. No species outperformed the other in salt marsh water. Our results show no local adaptation to salinity, suggesting that ostracods and copepods may be limited in their respective distributions by dispersal limitation or habitat suitability.
Breen et al. (2021) Population growth of microcrustaceans in water from habitats with differing salinities. PeerJ 9:e12378 https://doi.org/10.7717/peerj.12378
Studying suicide using proxy-based data: reliability and validity of a short version scale for measuring quality of life in rural China
Background To evaluate the reliability and validity of the short version six-item Quality of Life Scale (QOLS-6) and the consistency of subject-proxy data in a case-control psychological autopsy study on elderly suicide in rural China. Methods A two-stage stratified cluster sampling method was used to select research sites. We used self-administered questionnaires to collect proxy-based information from informants and subject-based information from living comparisons. Results A total of 242 pairs of suicide cases and living comparisons were selected in our research. Subject-proxy consistency for QOLS-6 was good (Intraclass correlation coefficient (ICC) was 0.688) in living controls. Good internal consistency of QOLS-6 was validated by Cronbach’s α being greater than 0.6 among suicide cases and living comparisons. The mean scores of quality of life were lower among suicide cases than living controls. Quality of life was negatively correlated with depression, loneliness, hopelessness, impulsiveness and stressful life events, while it was positively correlated with activities of daily living and family function. Conclusions QOLS-6 has good reliability and validity, which can be used for assessing quality of life among Chinese rural older adults. It is shorter and easier than any other scale for measuring quality of life and can be used as a screening tool in future studies.
He et al. (2021) Studying suicide using proxy-based data: reliability and validity of a short version scale for measuring quality of life in rural China. PeerJ 9:e12396 https://doi.org/10.7717/peerj.12396
Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis
Background In the past decade, RNA sequencing and mass spectrometry based quantitative approaches are being used commonly to identify the differentially expressed biomarkers in different biological conditions. Data generated from these approaches come in different sizes (e.g., count matrix, normalized list of differentially expressed biomarkers, etc.) and shapes (e.g., sequences, spectral data, etc.). The list of differentially expressed biomarkers is used for functional interpretation and retrieve biological meaning, however, it requires moderate computational skills. Thus, researchers with no programming expertise find difficulty in data interpretation. Several bioinformatics tools are available to analyze such data; however, they are less flexible for performing the multiple steps of visualization and functional interpretation. Implementation We developed an easy-to-use Shiny based web application (named as OMnalysis) that provides users with a single platform to analyze and visualize the differentially expressed data. The OMnalysis accepts the data in tabular form from edgeR, DESeq2, MaxQuant Perseus, R packages, and other similar software, which typically contains the list of differentially expressed genes or proteins, log of the fold change, log of the count per million, the P value, q-value, etc. The key features of the OMnalysis are multiple image type visualization and their dimension customization options, seven multiple hypothesis testing correction methods to get more significant gene ontology, network topology-based pathway analysis, and multiple databases support (KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database PharmGKB and STRINGdb) for extensive pathway enrichment analysis. OMnalysis also fetches the literature information from PubMed to provide supportive evidence to the biomarkers identified in the analysis. In a nutshell, we present the OMnalysis as a well-organized user interface, supported by peer-reviewed R packages with updated databases for quick interpretation of the differential transcriptomics and proteomics data to biological meaning. Availability The OMnalysis codes are entirely written in R language and freely available at https://github.com/Punit201016/OMnalysis. OMnalysis can also be accessed from - http://lbmi.uvlf.sk/omnalysis.html. OMnalysis is hosted on a Shiny server at https://omnalysis.shinyapps.io/OMnalysis/. The minimum system requirements are: 4 gigabytes of RAM, i3 processor (or equivalent). It is compatible with any operating system (windows, Linux or Mac). The OMnalysis is heavily tested on Chrome web browsers; thus, Chrome is the preferred browser. OMnalysis works on Firefox and Safari.
Tyagi et al. (2021) Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis. PeerJ 9:e12415 https://doi.org/10.7717/peerj.12415
Locomotor behavior of Neocaridina palmata: a study with leachates from UV-weathered microplastics
Weathering of plastics leads to the formation of increasingly smaller particles with the release of chemical compounds. The latter occurs with currently unknown environmental impacts. Leachate-induced effects of weathered microplastics (MPs) are therefore of increasing concern. To investigate the toxicity of the chemical mixtures from such plastics, we exposed the freshwater shrimp Neocaridina palmata to enriched leachates from unweathered and artificially weathered (UV-A/B light) MPs (≤1 mm) from recycled low-density polyethylene (LDPE-R) pellets and from a biodegradable, not fully bio-based starch blend (SB) foil. We analyzed the individual locomotor activity (moved distance and frozen events) on day 1, 3, 7 and 14 of exposure to five leachate concentrations equivalent to 0.40–15.6 g MPs L−1, representing the upper scale of MPs that have been found in the environment. The median moved distance did not change as a function of concentration, except for the unweathered SB treatment on day 14 that indicated hyperactivity with increasing concentrations. Significant impacts were solely detected for few concentrations and exposure days. Generally, no consistent trend was observed across the experiments. We further assessed the baseline toxicity of the samples in the Microtox assay and detected high bioluminescence inhibitions of the bacterium Aliivibrio fischeri. This study demonstrates that neither the recycled nor the biodegradable material are without impacts on test parameters and therefore cannot be seen as safe alternative for conventional plastics regarding the toxicity. However, the observed in vitro toxicity did not result in substantial effects on the behavior of shrimps. Overall, we assume that the two endpoints examined in the atyid shrimp N. palmata were not sensitive to chemicals leaching from plastics or that effects on the in vivo level affect other toxic endpoints which were not considered in this study.
Klein et al. (2021) Locomotor behavior of Neocaridina palmata: a study with leachates from UV-weathered microplastics. PeerJ 9:e12442 https://doi.org/10.7717/peerj.12442