Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in ...gene functional annotation, gene regulation analysis, and environmental factor verification. However, with increasing amounts of sequenced reads and reference model species, the selection of appropriate reference species for gene annotation has become a new challenge.
We proposed a novel approach for finding the most effective reference model species through taxonomic associations and ultra-conserved orthologous (UCO) gene comparisons among species. An online system for multiple species selection (MSS) for RNA-seq differential expression analysis was developed, and comprehensive genomic annotations from 291 reference model eukaryotic species were retrieved from the RefSeq, KEGG, and UniProt databases.
Using the proposed MSS pipeline, gene ontology and biological pathway enrichment analysis can be efficiently achieved, especially in the case of transcriptomic analysis of non-model organisms. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time, resulting in more accurate results than those of traditional approaches of using a single model reference species or the large non-redundant reference database.
Selection of appropriate reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. In addition, adequate model species selection reduces the computational time significantly while retaining the same order of accuracy. The proposed system indeed provides superior performance by selecting appropriate multiple species for transcriptomic analysis compared to traditional approaches.
Benzoapyrene (BaP) is a polycyclic aromatic hydrocarbon formed by the incomplete combustion of organic matter. Environmental BaP contamination poses a serious health risk to many organisms because ...the pollutant may negatively affect many physiological systems. As such, chronic exposure to BaP is known to lead to locomotor dysfunction and neurodegeneration in several organisms. In this study, we used the zebrafish model to delineate the acute toxic effects of BaP on the developing nervous system. We found that embryonic exposure of BaP downregulates shh and isl1, causing morphological hypoplasia in the telencephalon, ventral thalamus, hypothalamus, epiphysis and posterior commissure. Moreover, hypoxia-inducible factors (hif1a and hif2a) are repressed upon embryonic exposure of BaP, leading to reduced expression of the Hif-target genes, epo and survivin, which are associated with neural differentiation and maintenance. During normal embryogenesis, low-level oxidative stress regulates neuronal development and function. However, our experiments revealed that embryonic oxidative stress is greatly increased in BaP-treated embryos. The expression of catalase was decreased and sod1 expression increased in BaP-treated embryos. These transcriptional changes were coincident with increased embryonic levels of H2O2 and malondialdehyde, with the levels in BaP-treated fish similar to those in embryos treated with 120-μM H2O2. Together, our data suggest that reduced Hif signaling and increased oxidative stress are involved in BaP-induced acute neurotoxicity during embryogenesis.
Stratospheric ozone depletion has led to increasing levels of ultraviolet radiation (UVR) reaching the Earth’s surface. Elevated UVR, particularly in the high latitudes, potentially causes shifts in ...species composition and diversity in various ecosystems, consequently altering the biogeochemical cycles. Microalgae are not only ecologically important as primary producers, generating atmospheric oxygen and sequestering carbon dioxide; they are also economically important as sources of health supplement, pigments, biofuel and others. Changes to the size and composition of algal communities can lead to profound impacts to the fisheries productivity. There have been studies on the effects of UVR on the growth, photosynthesis and biochemical composition of microalgae, but limited information on the underlying molecular mechanisms involved in the response and adaptation of microalgae to UVR is available. We employed RNA-seq to quantitatively evaluate and compare the transcriptomes of an Antarctic freshwater
Chlorella
sp. grown at ambient versus elevated UVR conditions. Differentially expressed genes, relating to the fatty acid degradation, amino acid metabolism, starch and sucrose metabolism and peroxisome pathways, suggest conservation and remobilisation of energy resources, maintenance of newly synthesised protein and inhibition of protein degradation, ensuring membrane lipid homeostasis and regulating antioxidative mechanisms, as the acclimation strategies in response to UVR. These findings expand current knowledge of gene expression in polar
Chlorella
sp. in response to short-term UVR. Studies on stress tolerance mechanisms are important to understand and predict future impacts of climate change. Genes, proteins and pathways identified from these adaptable polar algae have potentially far-reaching biotechnological applications.
Multiple sound source separation in a reverberant environment has become popular in recent years. To improve the quality of the separated signal in a reverberant environment, a separation method ...based on a DOA cue and a deep neural network (DNN) is proposed in this paper. Firstly, a pre-processing model based on non-negative matrix factorization (NMF) is utilized for recorded signal dereverberation, which makes source separation more efficient. Then, we propose a multi-source separation algorithm combining sparse and non-sparse component points recovery to obtain each sound source signal from the dereverberated signal. For sparse component points, the dominant sound source for each sparse component point is determined by a DOA cue. For non-sparse component points, a DNN is used to recover each sound source signal. Finally, the signals separated from the sparse and non-sparse component points are well matched by temporal correlation to obtain each sound source signal. Both objective and subjective evaluation results indicate that compared with the existing method, the proposed separation approach shows a better performance in the case of a high-reverberation environment.
Gracilaria salicornia is an agar-producing red macroalga commonly found growing in the intertidal and upper subtidal on various substrates with distribution across the Indo-Pacific. The ability of G. ...salicornia to survive under harsh conditions suggests potential use as a candidate for sustainable farming and alternative source of livelihood for the local coastal communities under future climate conditions. An earlier study investigated the effects of future predicted pCO2 level on the photosynthesis and respiration of G. salicornia but studies on the metabolomic responses of this alga to constant elevated pCO2 level is lacking. Here, elevated pCO2 level was simulated on G. salicornia for 14 days to compare its growth, photosynthetic efficiency, pigment content, agar properties and metabolite composition under current pCO2 level (∼pH 8.1) and end-of-century future-predicted (∼pH 7.8) pCO2 level. The observed biomass growth, coupled with unaffected photosynthetic parameters and agar-related properties underscore G. salicornia’s ability to adapt to higher pCO2 levels. The modulation of metabolites showcases the alga’s adaptive strategies at elevated pCO2 whereby stress-mediating compounds such as gallic acid and oxalic acid were increased while stress-indicating metabolites such as serine, glycine, and ascorbic acid did not show significant changes. Interestingly, the metabolome profile imply that the alga regulates its metabolism according to culture duration rather than the pCO2 level.
•This study observed the effects of elevated pCO2 level on metabolite composition and agar yield and quality of Gracilaria species.•G.salicornia is a potential candidate for sustainable aquaculture given its non-negative responses to predicted future pCO2 level.•The metabolome profile suggests that G. salicornia regulates its metabolite production according to the culture duration.
Differential gene expression analysis using RNA-seq data is a popular approach for discovering specific regulation mechanisms under certain environmental settings. Both gene ontology (GO) and KEGG ...pathway enrichment analysis are major processes for investigating gene groups that participate in common biological responses or possess related functions. However, traditional approaches based on differentially expressed genes only detect a few significant GO terms and pathways, which are frequently insufficient to explain all-inclusive gene regulation mechanisms.
Transcriptomes of survivin (birc5) gene knock-down experimental and wild-type control zebrafish embryos were sequenced and assembled, and a differential expression (DE) gene list was obtained for traditional functional enrichment analysis. In addition to including DE genes with significant fold-change levels, we considered additional associated genes near or overlapped with differentially expressed long noncoding RNAs (DE lncRNAs), which may directly or indirectly activate or inhibit target genes and play important roles in regulation networks. Both the original DE gene list and the additional DE lncRNA-associated genes were combined to perform a comprehensive overrepresentation analysis.
In this study, a total of 638 DE genes and 616 DE lncRNA-associated genes (lncGenes) were leveraged simultaneously in searching for significant GO terms and KEGG pathways. Compared to the traditional approach of only using a differential expression gene list, the proposed method of employing DE lncRNA-associated genes identified several additional important GO terms and KEGG pathways. In GO enrichment analysis, 60% more GO terms were obtained, and several neuron development functional terms were retrieved as complete annotations. We also observed that additional important pathways such as the FoxO and MAPK signaling pathways were retrieved, which were shown in previous reports to play important roles in apoptosis and neuron development functions regulated by the survivin gene.
We demonstrated that incorporating genes near or overlapped with DE lncRNAs into the DE gene list outperformed the traditional enrichment analysis method for effective biological functional interpretations. These hidden interactions between lncRNAs and target genes could facilitate more comprehensive analyses.
In the cloud age, it is quite easy to collect sensory data from smartphones. With these sensory data, it is desired to provide various kinds of applications to serve the user. In this research, we ...aim at developing an indoor navigation system on smartphone using solely smartphone sensory data. There are many researches on indoor localization and navigation in the literature. Nevertheless, environmental sensors and/or wearable sensors are usually needed. This can be costly and inconvenient. In this paper, we propose a smartphone indoor localization system using only accelerometer and gyroscope data from the smartphone. The Pedestrian Dead Reckoning (PDR) approach is used to build this system. The PDR approach is simple and efficient though seems traditional. The major weakness of the PDR is that the estimation error would accumulate over time. Thus we propose to add so-called calibration marks which look like short arrows and are placed on both the floor plan and the ground. To use the system, the user first finds a calibration mark on the ground, stands on it and faces the right direction. He/she then moves the android icon (representing the user) on top of the calibration mark on the floor plan on the smartphone. When the user starts to move, the android icon also moves on the floor plan following the real-time estimation of step length and moving direction change for each step from accelerometer and gyroscope data. This is a prototype of an indoor navigation system that can become fully functional after an optimal path planning module is included. Experimental results of estimated walking trace tests show high accuracy. The system is promising and useful as long as a floor plan and calibration marks are built in advance.
The current outlook on mitigation of global warming does not appear promising, with figures in the reduction of anthropogenic greenhouse gas emissions lagging far behind climate goals. A recent ...environmental report even postulated a high possibility of temperature increase of at least 3 °C by 2100. Despite the low number of human inhabitants in Antarctica, the Antarctic Peninsula was reported as one of the most rapidly warming locations on earth. Many studies have shown that heat stress modulates physiological performance in many species of microalgae; however, studies to elucidate the molecular mechanisms of high-temperature thermotolerance are generally focused on the model species, i.e.
Chlamydomonas reinhardtii
. Furthermore, previous transcriptomic work in this aspect generally employed the microarray technique and/or involved the tropical or temperate strains, and few were conducted on the polar strains. In this study, RNA-Seq-mediated transcriptomic analysis was undertaken to compare the whole transcriptome profile of an Antarctic
Chlorella
sp. grown at ambient (4 °C) versus stress-inducing high (33 °C) temperatures and harvested at the 120-h time point. The findings of this study indicated a coordinated response to fine tune balance between energy production and utilisation for biosynthesis by redirecting carbon provision, and the arrest of cell division as a coping mechanism for an intense and relatively long period of stress. The strategies undertaken by this alga in acclimation to heat stress are somewhat similar to the heat stress response of the model species.
The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect ...vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily RESULTS: The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of antigenicity and cross antigenicity. The conserved LEs for Iridoviridae family reflected high antigenicity responses for the two subfamilies, while exclusive LEs reflected high antigenicity responses only for the host-specific subfamily CONCLUSIONS: Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
The liver plays a vital role in metabolism, detoxification, digestion, and the maintenance of homeostasis. During development, the vertebrate embryonic liver undergoes a series of morphogenic ...processes known as hepatogenesis. Hepatogenesis can be separated into three interrelated processes: endoderm specification, hepatoblast differentiation, and hepatic outgrowth. Throughout this process, signaling molecules and transcription factors initiate and regulate the coordination of cell proliferation, apoptosis, differentiation, intercellular adhesion, and cell migration. Hifs are already recognized to be essential in embryonic development, but their role in hepatogenesis remains unknown. Using the zebrafish embryo as a model organism, we report that the lack of Hif2-alpha but not Hif1-alpha blocks hepatic outgrowth. While Hif2-alpha is not involved in hepatoblast specification, this transcription factor regulates hepatocyte cell proliferation during hepatic outgrowth. Furthermore, we demonstrated that the lack of Hif2-alpha can reduce the expression of liver-enriched gene 1 (leg1), which encodes a secretory protein essential for hepatic outgrowth. Additionally, exogenous mRNA expression of leg1 can rescue the small liver phenotype of hif2-alpha morphants. We also showed that Hif2-alpha directly binds to the promoter region of leg1 to control leg1 expression. Interestingly, we discovered overrepresented, high-density Hif-binding sites in the potential upstream regulatory sequences of leg1 in teleosts but not in terrestrial mammals. We concluded that hif2-alpha is a key factor required for hepatic outgrowth and regulates leg1 expression in zebrafish embryos. We also proposed that the hif2-alpha-leg1 axis in liver development may have resulted from the adaptation of teleosts to their environment.
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