DLFF-ACP: prediction of ACPs based on deep learning and multi-view features fusion
An emerging type of therapeutic agent, anticancer peptides (ACPs), has attracted attention because of its lower risk of toxic side effects. However process of identifying ACPs using experimental methods is both time-consuming and laborious. In this study, we developed a new and efficient algorithm that predicts ACPs by fusing multi-view features based on dual-channel deep neural network ensemble model. In the model, one channel used the convolutional neural network CNN to automatically extract the potential spatial features of a sequence. Another channel was used to process and extract more effective features from handcrafted features. Additionally, an effective feature fusion method was explored for the mutual fusion of different features. Finally, we adopted the neural network to predict ACPs based on the fusion features. The performance comparisons across the single and fusion features showed that the fusion of multi-view features could effectively improve the model’s predictive ability. Among these, the fusion of the features extracted by the CNN and composition of k-spaced amino acid group pairs achieved the best performance. To further validate the performance of our model, we compared it with other existing methods using two independent test sets. The results showed that our model’s area under curve was 0.90, which was higher than that of the other existing methods on the first test set and higher than most of the other existing methods on the second test set. The source code and datasets are available at https://github.com/wame-ng/DLFF-ACP.
Cao et al. (2021) DLFF-ACP: prediction of ACPs based on deep learning and multi-view features fusion. PeerJ 9:e11906 https://doi.org/10.7717/peerj.11906
Impact of the the COVID-19 pandemic on a queen conch (Aliger gigas) fishery in The Bahamas
The onset of the coronavirus (COVID-19) pandemic in early 2020 led to a dramatic rise in unemployment and fears about food-security throughout the Caribbean region. Subsistence fisheries were one of the few activities permitted during emergency lockdown in The Bahamas, leading many to turn to the sea for food. Detailed monitoring of a small-scale subsistence fishery for queen conch was undertaken during the implementation of coronavirus emergency control measures over a period of twelve weeks. Weekly landings data showed a surge in fishing during the first three weeks where landings were 3.4 times higher than subsequent weeks. Overall 90% of the catch was below the minimum legal-size threshold and individual yield declined by 22% during the lockdown period. This study highlights the role of small-scale fisheries as a ‘natural insurance’ against socio-economic shocks and a source of resilience for small island communities at times of crisis. It also underscores the risks to food security and long-term sustainability of fishery stocks posed by overexploitation of natural resources.
Higgs (2021) Impact of the the COVID-19 pandemic on a queen conch (Aliger gigas) fishery in The Bahamas. PeerJ 9:e11924 https://doi.org/10.7717/peerj.11924
DUSP12 regulates the tumorigenesis and prognosis of hepatocellular carcinoma
Background Dual specificity protein phosphatase (DUSP)12 is an atypical member of the protein tyrosine phosphatase family, which are overexpressed in multiple types of malignant tumors. This protein family protect cells from apoptosis and promotes the proliferation and motility of cells. However, the pathological role of DUSP12 in hepatocellular carcinoma (HCC) is incompletely understood. Methods We analyzed mRNA expression of DUSP12 between HCC and normal liver tissues using multiple online databases, and explored the status of DUSP12 mutants using the cBioPortal database. The correlation between DUSP12 expression and tumor-infiltrating immune cells was demonstrated using the Tumor Immune Estimation Resource database and the Tumor and Immune System Interaction Database. Loss of function assay was utilized to evaluate the role of DUSP12 in HCC progression. Results DUSP12 had higher expression along with mRNA amplification in HCC tissues compared with those in normal liver tissues, which suggested that higher DUSP12 expression predicted shorter overall survival. Analyses of functional enrichment of differentially expressed genes suggested that DUSP12 regulated HCC tumorigenesis, and that knockdown of DUSP12 expression by short hairpin (sh)RNA decreased the proliferation and migration of HCC cells. Besides, DUSP12 expression was positively associated with the infiltration of cluster of differentiation (CD)4+ T cells (especially CD4+ regulatory T cells), macrophages, neutrophils and dendritic cells. DUSP12 expression was positively associated with immune-checkpoint moieties, and was downregulated in a C3 immune-subgroup of HCC (which had the longest survival). Conclusion These data suggest that DUSP12 may have a critical role in the tumorigenesis, infiltration of immune cells, and prognosis of HCC.
Ju et al. (2021) DUSP12 regulates the tumorigenesis and prognosis of hepatocellular carcinoma. PeerJ 9:e11929 https://doi.org/10.7717/peerj.11929
Aspirin inhibits tumor progression and enhances cisplatin sensitivity in epithelial ovarian cancer
Background Ovarian cancer is the most common gynecological malignancy and is difficult to manage due to the emergence of resistance to various chemotherapeutic drugs. New efforts are urgently awaited. Aspirin, which is traditionally considered a nonsteroidal anti-inflammatory drug (NSAID), has been reported to exert potential chemopreventive effects. Therefore, we aimed to investigate the anticancer effect and explore the underlying molecular mechanisms of aspirin on epithelial ovarian cancer (EOC) cells. Methods We conducted wound healing, transwell migration, EdU cell proliferation, colony formation and apoptosis detection assays to observe the effects of aspirin on the migration, proliferation and apoptosis of EOC cells (A2870, Caov-3, and SK-OV-3). EOC cells were treated with a combination of aspirin and cisplatin (CDDP) to observe the effect of aspirin on enhancing CDDP sensitivity. Orthotopic xenograft models of ovarian cancer established with A2780-Luciferase-GFP cells were applied to compare tumor growth inhibition in the control, CDDP and CDDP plus aspirin groups through in vivo imaging, which can be used to continuously monitor tumor growth. The expression and acetylation levels of p53 in EOC cells treated with aspirin were determined using western blotting, and p53 acetylation levels were examined in tumors harvested from the transplanted mice. Quantitative real-time PCR was used to assess the mRNA expression of p53 target genes. Results Aspirin inhibited migration and proliferation and induced apoptosis in EOC cell lines in a concentration-dependent manner. In vitro, aspirin enhanced the sensitivity of EOC cells to CDDP by increasing its inhibitory effect on proliferation and its effect on inducing apoptosis. In vivo, the differences in the tumor growth inhibition rates among the different CDDP experimental groups were statistically significant (p < 0.05). Aspirin did not affect p53 protein expression but increased the p53 acetylation level in a concentration-dependent manner. In addition, the mRNA levels of CDKN1A, BAX, FOXF1, PUMA, and RRAD in EOC cells were significantly increased by the aspirin treatment. Conclusions Aspirin inhibits tumor progression and enhances the CDDP sensitivity of EOC cells. These antitumor effects of aspirin might be mediated by p53 acetylation and subsequent activation of p53 target genes.
Guo et al. (2021) Aspirin inhibits tumor progression and enhances cisplatin sensitivity in epithelial ovarian cancer. PeerJ 9:e11591 https://doi.org/10.7717/peerj.11591
Embryo and larval biology of the deep-sea octocoral Dentomuricea aff. meteor under different temperature regimes
Deep-sea octocorals are common habitat-formers in deep-sea ecosystems, however, our knowledge on their early life history stages is extremely limited. The present study focuses on the early life history of the species Dentomuricea aff. meteor, a common deep-sea octocoral in the Azores. The objective was to describe the embryo and larval biology of the target species under two temperature regimes, corresponding to the minimum and maximum temperatures in its natural environment during the spawning season. At temperature of 13 ±0.5 °C, embryos of the species reached the planula stage after 96h and displayed a median survival of 11 days. Planulae displayed swimming only after stimulation, swimming speed was 0.24 ±0.16 mm s−1 and increased slightly but significantly with time. Under a higher temperature (15 °C ±0.5 °C) embryos reached the planula stage 24 h earlier (after 72 h), displayed a median survival of 16 days and had significantly higher swimming speed (0.3 ±0.27 mm s−1). Although the differences in survival were not statistically significant, our results highlight how small changes in temperature can affect embryo and larval characteristics with potential cascading effects in larval dispersal and success. In both temperatures, settlement rates were low and metamorphosis occurred even without settlement. Such information is rarely available for deep-sea corals, although essential to achieve a better understanding of dispersal, connectivity and biogeographical patterns of benthic species.
Rakka et al. (2021) Embryo and larval biology of the deep-sea octocoral Dentomuricea aff. meteor under different temperature regimes. PeerJ 9:e11604 https://doi.org/10.7717/peerj.11604
High genetic diversity and mixing of coastal horseshoe crabs (Tachypleus gigas) across major habitats in Sundaland, Indonesia
Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (FST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p < 0.05). Additionally, the 34 analysis of molecular variance (AMOVA) showed the most variation within populations (95.23%) compared to less among populations (4.77%). The haplotype network showed evidence of shared haplotypes between populations. Tajima’s D and Fu’s FS test values indicated a population expansion. Our results showed a low level of differentiation, suggesting a single stock and high connectivity. Therefore, a regionally-based conservation strategy is recommended for the coastal horseshoe crab in Indonesia.
Aini et al. (2021) High genetic diversity and mixing of coastal horseshoe crabs (Tachypleus gigas) across major habitats in Sundaland, Indonesia. PeerJ 9:e11739 https://doi.org/10.7717/peerj.11739
What’s for dinner this time?: DNA authentication of “wild mushrooms” in food products sold in the USA
Mushrooms have been consumed by humans for thousands of years, and while some have gastronomic and nutritional value, it has long been recognized that only select species of mushrooms are suitable for consumption. Adverse health effects of consuming poisonous mushrooms range from mild illness to death. Many valuable edible mushrooms are either impractical or unable to be grown commercially, requiring them to be harvested from the wild. In the U.S., products containing these wild-collected mushrooms are often sold with the nonspecific and undefined label “wild mushrooms,” although in some cases particular species are listed in the ingredients. However, the ambiguity of the definition of “wild mushrooms” in foods makes it impossible to know which species are involved or whether they are truly wild-collected or cultivated varieties. As a consequence, any individual adverse reactions to consuming the mushrooms in these products cannot be traced to the source due to the minimal regulations around the harvest and sale of wild mushrooms. For this study, we set out to shed light on what species of fungi are being sold as “wild mushrooms” using DNA metabarcoding to identify fungal contents of various food products acquired from locally sourced grocers and a large online retail site. Twenty-eight species of mushroom were identified across 16 food products, ranging from commonly cultivated species to wild species not represented in global DNA databases. Our results demonstrate that “wild mushroom” ingredients often consist entirely or in part of cultivated species such as the ubiquitous white and brown “button” mushrooms and portabella (Agaricus bisporus), oyster (Pleurotus spp.) and shiitake (Lentinula edodes). In other cases truly wild mushrooms were detected but they were not always consistent with the species on the label. More alarmingly, a few products with large distribution potential contained species whose edibility is at best dubious, and at worst potentially toxic.
Cutler II et al. (2021) What’s for dinner this time?: DNA authentication of “wild mushrooms” in food products sold in the USA. PeerJ 9:e11747 https://doi.org/10.7717/peerj.11747
Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning
Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5–10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
Osathanunkul et al. (2021) Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning. PeerJ 9:e11753 https://doi.org/10.7717/peerj.11753
Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Background Cytochrome P450s play crucial roles in various biosynthetic reactions. Ginger (Zingiber officinale), which is often threatened by Ralstonia solanacearum, is the most economically important crop in the family Zingiberaceae. Whether the cytochrome P450 complement (CYPome) significantly responds to this pathogen has remained unclear. Methods Transcriptomic responses to R. solanacearum and soil moisture were analyzed in ginger, and expression profiles of the CYPome were determined based on transcriptome data. Results A total of 821 P450 unigenes with ORFs ≥ 300 bp were identified. Forty percent soil moisture suppressed several key P450 unigenes involved in the biosynthesis of flavonoids, gingerols, and jasmonates, including unigenes encoding flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase, steroid 22-alpha-hydroxylase, cytochrome P450 family 724 subfamily B polypeptide 1, and allene oxide synthase. Conversely, the expression of P450 unigenes involved in gibberellin biosynthesis and abscisic acid catabolism, encoding ent-kaurene oxidase and abscisic acid 8′-hydroxylase, respectively, were promoted by 40% soil moisture. Under R. solanacearum infection, the expression of P450 unigenes involved in the biosynthesis of the above secondary metabolites were changed, but divergent expression patterns were observed under different soil moisture treatments. High moisture repressed expression of genes involved in flavonoid, brassinosteroid, gingerol, and jasmonate biosynthesis, but promoted expression of genes involved in GA anabolism and ABA catabolism. These results suggest possible mechanisms for how high moisture causes elevated susceptibility to R. solanacearum infection.
Huang et al. (2021) Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale). PeerJ 9:e11755 https://doi.org/10.7717/peerj.11755
Neural correlates of tactile hardness intensity perception during active grasping
While tactile sensation plays an essential role in interactions with the surroundings, relatively little is known about the neural processes involved in the perception of tactile information. In particular, it remains unclear how different intensities of tactile hardness are represented in the human brain during object manipulation. This study aims to investigate neural responses to various levels of tactile hardness using functional magnetic resonance imaging while people grasp objects to perceive hardness intensity. We used four items with different hardness levels but otherwise identical in shape and texture. A total of Twenty-five healthy volunteers participated in this study. Before scanning, participants performed a behavioral task in which they received a pair of stimuli and they were to report the perceived difference of hardness between them. During scanning, without any visual information, they were randomly given one of the four objects and asked to grasp it. We found significant blood oxygen-level-dependent (BOLD) responses in the posterior insula in the right hemisphere (rpIns) and the right posterior lobe of the cerebellum (rpCerebellum), which parametrically tracked hardness intensity. These responses were supported by BOLD signal changes in the rpCerebellum and rpIns correlating with tactile hardness intensity. Multidimensional scaling analysis showed similar representations of hardness intensity among physical, perceptual, and neural information. Our findings demonstrate the engagement of the rpCerebellum and rpIns in perceiving tactile hardness intensity during active object manipulation.
Kim et al. (2021) Neural correlates of tactile hardness intensity perception during active grasping. PeerJ 9:e11760 https://doi.org/10.7717/peerj.11760