Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme
Melatonin is a multifunctional nontoxic bio-stimulant or signaling molecule, generally distributing in different animal and plant organs for invigorating numerous physiological processes against abiotic stresses. In this study, we investigated the potential impact of melatonin on the cyanobacterium Nostoc flagelliforme when exposed to salt stress according to some biochemical and physiological parameters, such as relative electrolyte leakage, PSII activity, and photosynthetic pigments including chlorophyll a, phycocyanobilin, and phycoerythrobilin. We found that melatonin could also maintain K+ homeostasis in salt-stressed N. flagelliforme. These above results confirmed melatonin had multiple functions in hyperosmotic stress and ion stress caused by salinity. Notably, we observed melatonin could regulate the reactive oxygen species (ROS) signal and distinctly decrease the content of hydrogen peroxide and superoxide anion in salt-stressed cells, which were largely attributed to the increased antioxidant enzymes activities including catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase. Finally, qRT-PCR analysis showed that melatonin stimulated the expression of antioxidant genes (NfCAT, NfSOD, and NfGR). In general, our findings demonstrate melatonin has beneficial effects on N. flagelliforme under salt stress by intensively regulating antioxidant system.
Yuan et al. (2022) Exogenous melatonin improves salt tolerance mainly by regulating the antioxidant system in cyanobacterium Nostoc flagelliforme. PeerJ 10:e14479 https://doi.org/10.7717/peerj.14479
Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing?
Fish populations that bear considerable pressure levels tend to show a decline in the average size of individuals, with the small and unexploited species replacing the large and exploited ones. It is important to carry on with their characterization in areas where they are becoming an important source of food for local human populations. An example of such species are parrotfishes, whose responses to external factors such as fishing need to be understood and predicted. In this study, we used a diver-operated stereo-video to examine individual body size, sex ratios and proportion of species of the parrotfish assemblage and analyze them on a qualitative fishing pressure gradient at four oceanic islands in the Colombian Caribbean. We reported over 10,000 occurrences of eleven parrotfish species, of which we estimated the total length of over 90%, grouping them into three size categories (large, medium, and small). Our data showed a spatial variation of parrotfishes’ abundances, biomass, and individual body size. Observed differences are size-category-dependent throughout the qualitative fishing pressure. In general, the medium-bodied species had smaller sizes, lower abundances, and thus lower contribution to the total parrotfish biomass at the most heavily fished island. Unexpectedly, we found evidence of possible indirect effects over the small-bodied species Scarus iseri and Scarus taeniopterus with significantly greater abundances, and larger sizes of males of S. iseri, at the higher fishing pressure sites. Overall, our data highlights the extent of the spatial variation in the parrotfish communities at relatively short distances, and present new insights into the responses of parrotfish species on a spectrum of body sizes along a gradient of human pressure.
Rivas et al. (2022) Spatial variation of parrotfish assemblages at oceanic islands in the western Caribbean: evidence of indirect effects of fishing?. PeerJ 10:e14178 https://doi.org/10.7717/peerj.14178
Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression
Colorectal carcinoma (CRC) is the second most frequent cancer worldwide. MiR-491-3p, a tumor-suppressive microRNA (miRNA, miR), has been revealed to be abnormally expressed in CRC tissues. Meanwhile, up-regulated ubiquitous mitochondrial creatine kinase (uMtCK) contributes to CRC cell proliferation. Here we aim to explore whether aberrant miR-491-3p expression promotes CRC progression through regulating uMtCK. To this end, miR-491-3p and uMtCK levels were assessed in CRC tissues using quantitative real-time PCR (qRT-PCR). The biological roles of miR-491-3p and uMtCK in regulating CRC growth were evaluated using colony formation assay and mouse Xenograft tumour model. We found that miR-491-3p expression was decreased in CRC tissues compared with matched para-cancerous tissues, whereas uMtCK expression was increased. Functionally, miR-491-3p overexpression repressed SW480 cell growth, whereas miR-491-3p depletion accelerated SW620 cell proliferation and growth. Inversely, uMtCK positively regulated CRC cell proliferation. Mechanistically, miR-491-3p post-transcriptionally downregulated uMtCK expression by binding to 3’-UTR of uMtCK. Consequently, restoring uMtCK expression markedly eliminated the role of miR-491-3p in suppressing CRC growth. Collectively, miR-491-3p functions as a tumour suppressor gene by repressing uMtCK, and may be a potential target for CRC treatment.
Tang et al. (2022) Downregulated miRNA-491-3p accelerates colorectal cancer growth by increasing uMtCK expression. PeerJ 10:e14285 https://doi.org/10.7717/peerj.14285
A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors
Background Recent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted. Methods The potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration. Results Using the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. Moreover, as demonstrated by CCK-8 and Edu assays, RRM2 was an oncogene in liver cancer cells. We confirmed for the first time that RRM2 was significantly upregulated by HBx, suggesting that RRM2 may be a key regulator of LIHC induced by HBV. IHC analysis validated the upregulated expression of RRM2 protein and its correlation with immune infiltration makers in a LIHC patient cohort. Conclusion RRM2 may be a valuable molecular biomarker for predicting prognosis and immunotherapeutic efficacy in pan-cancer, particularly in LIHC.
Li et al. (2022) A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors. PeerJ 10:e14432 https://doi.org/10.7717/peerj.14432
A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study
Background Anastomotic leakage remains one of the most common serious complications after rectal cancer surgery. How to predict its occurrence and prevent it remains largely elusive. Objective This study aimed to identify the risk factors of anastomotic leakage and construct a nomogram for predicting postoperative anastomotic leakage in patients with rectal cancer. Methods The data of 406 patients with rectal cancer after gastrointestinal surgery in the Third Affiliated Hospital of Sun Yat-sen University from January 2011 to May 2020 were collected (243 in the training set and 163 in the testing set). Logistic regression was applied to determine the risk factors of postoperative anastomotic leakage of rectal cancer, and a nomogram prediction model was thus established. Predictive performance of the nomogram was evaluated by C-index and area under the receiver-operating characteristic (ROC) curve. Results Logistic regression analysis showed that preoperative bowel obstruction (odds ratio [OR] = 12.846, 95% confidence interval CI [1.441–114.54], p = 0.022) and early first defecation after surgery (OR = 0.501, 95% CI [0.31–0.812], p = 0.005) were independent risk factors, which could be used to develop a nomogram to predict the occurrence of anastomotic leakage accurately. The evaluation of the prediction model shows that the C-index value of the model was 0.955, the area under the ROC curve (AUC) of the training set was 0.820, and the testing set was 0.747, whereas the optimal cut-off point based on the nomogram score was 174.6. Conclusion This nomogram had a good prediction ability for postoperative anastomotic leakage in patients with rectal cancer. It can provide a reference for perioperative treatment and the selection of surgical methods to promote individualized and accurate treatment.
Li et al. (2022) A novel nomogram for anastomotic leakage after surgery for rectal cancer: a retrospective study. PeerJ 10:e14437 https://doi.org/10.7717/peerj.14437
Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule
Background Suitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution. Methodology We integrated climate-based ecological niche models with information about topography and rivers’ network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85). Results Current weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a ‘belt’ connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe. Conclusions The outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats.
Iannella et al. (2022) Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule. PeerJ 10:e14446 https://doi.org/10.7717/peerj.14446
Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer
Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is responsible for producing one protein. Therefore, there is always an immense need to find promising and novel anti-cancer drug targets. Furthermore, proteases have an integral role in cell proliferation and growth because the proteolysis mechanism is an irreversible process that aids in regulating cellular growth during tumorigenesis. Therefore, an inactive rhomboid protease known as iRhom2 encoded by the gene RHBDF2 can be considered an important target for cancer treatment. Speculatively, previous studies on gene expression analysis of RHBDF2 showed heterogenous behaviour during tumorigenesis. Consistent with this, several studies have reported the antagonistic role of iRhom2 in tumorigenesis, i.e., either they are involved in negative regulation of EGFR ligands via the ERAD pathway or positively regulate EGFR ligands via the EGFR signalling pathway. Additionally, different opinions suggest iRhom2 mediated cleavage of EGFR ligands takes place TACE dependently or TACE independently. However, reconciling these seemingly opposing roles is still unclear and might be attributed to more than one transcript isoform of iRhom2. Methods To observe the differences at isoform resolution, the current strategy identified isoform switching in RHBDF2 via differential transcript usage using RNA-seq data during breast cancer initiation and progression. Furthermore, interacting partners were found via correlation and enriched to explain their antagonistic role. Results Isoform switching was observed at DCIS, grade 2 and grade 3, from canonical to the cub isoform. Neither EGFR nor ERAD was found enriched. However, pathways leading to TACE-dependent EGFR signalling pathways were more observant, specifically MAPK signalling pathways, GPCR signalling pathways, and toll-like receptor pathways. Nevertheless, it was noteworthy that during CTCs, the cub isoform switches back to the canonical isoform, and the proteasomal degradation pathway and cytoplasmic ribosomal protein pathways were significantly enriched. Therefore, it could be inferred that cub isoform functions during cancer initiation in EGFR signalling. In contrast, during metastasis, where invasion is the primary task, the isoform switches back to the canonical isoform.
Masood et al. (2022) Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer. PeerJ 10:e14124 https://doi.org/10.7717/peerj.14124
Trends and biases in African large carnivore population assessments: identifying priorities and opportunities from a systematic review of two decades of research
African large carnivores have undergone significant range and population declines over recent decades. Although conservation planning and the management of threatened species requires accurate assessments of population status and monitoring of trends, there is evidence that biodiversity monitoring may not be evenly distributed or occurring where most needed. Here, we provide the first systematic review of African large carnivore population assessments published over the last two decades (2000–2020), to investigate trends in research effort and identify knowledge gaps. We used generalised linear models (GLMs) and generalised linear mixed models (GLMMs) to identify taxonomic and geographical biases, and investigated biases associated with land use type and author nationality. Research effort was significantly biased towards lion (Panthera leo) and against striped hyaena (Hyaena hyaena), despite the latter being the species with the widest continental range. African wild dog (Lycaon pictus) also exhibited a negative bias in research attention, although this was partly explained by its relatively restricted distribution. The number of country assessments for a species was significantly positively associated with its geographic range in that country. Population assessments were biased towards southern and eastern Africa, particularly South Africa and Kenya. Northern, western, and central Africa were generally under-represented. Most studies were carried out in photographic tourism protected areas under government management, while non-protected and trophy hunting areas received less attention. Outside South Africa, almost half of studies (41%) did not include authors from the study country, suggesting that significant opportunities exist for capacity building in range states. Overall, large parts of Africa remain under-represented in the literature, and opportunities exist for further research on most species and in most countries. We develop recommendations for actions aimed at overcoming the identified biases and provide researchers, practitioners, and policymakers with priorities to help inform future research and monitoring agendas.
Strampelli et al. (2022) Trends and biases in African large carnivore population assessments: identifying priorities and opportunities from a systematic review of two decades of research. PeerJ 10:e14354 https://doi.org/10.7717/peerj.14354
Combined transcriptome and proteome analysis of yak PASMCs under hypoxic and normoxic conditions
Background Yaks are animals that have lived in plateau environments for generations. Yaks can adapt to the hypoxic plateau environment and also pass this adaptability on to the next generation. The lungs are the most important respiratory organs for mammals to adapt to their environment. Pulmonary artery smooth muscle cells play an important role in vascular remodeling under hypoxia, but the genetic mechanism underpinning the yak’s ability to adapt to challenging plateau conditions is still unknown. Methods A tandem mass tag (TMT) proteomics study together with an RNA-seq transcriptome analysis were carried out on pulmonary artery smooth muscle cells (PASMCs) that had been grown for 72 hours in both normoxic (20% O2) and hypoxic (1% O2) environments. RNA and TP (total protein) were collected from the hypoxic and normoxic groups for RNA-seq transcriptome sequencing and TMT marker protein quantification, and RT-qPCR validation was performed. Results A total of 17,711 genes and 6,859 proteins were identified. Further, 5,969 differentially expressed genes (DEGs) and 531 differentially expressed proteins (DEPs) were identified in the comparison group, including 2,924 and 186 upregulated genes and proteins and 3,045 and 345 down-regulated genes and proteins, respectively. The transcriptomic and proteomic analyses revealed that 109 DEGs and DEPs were highly positively correlated, with 77 genes showing the same expression trend. Nine overlapping genes were identified in the HIF-1 signaling pathway, glycolysis / gluconeogenesis, central carbon metabolism in cancer, PPAR signaling pathway, AMPK signaling pathway, and cholesterol metabolism (PGAM1, PGK1, TPI1, HMOX1, IGF1R, OLR1, SCD, FABP4 and LDLR), suggesting that these differentially expressed genes and protein functional classifications are related to the hypoxia-adaptive pathways. Overall, our study offers abundant data for further analysis of the molecular mechanisms in yak PASMCs and their adaptability to different oxygen concentrations.
Zhang et al. (2022) Combined transcriptome and proteome analysis of yak PASMCs under hypoxic and normoxic conditions. PeerJ 10:e14369 https://doi.org/10.7717/peerj.14369
Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal
Background Intertidal rocky shore surveys along the South African coastline (∼3,000 km) have demonstrated the presence and abundance of the encrusting orange sponge Hymeniacidon perlevis (Montagu, 1814), a well-known globally distributed species. After analysing the southern African populations, we gained a better understanding of the genetic structure of this now-accepted global species. Apart from confirming the presence of a single population of H. perlevis, we also determined its distribution in the southern African intertidal rocky shore ecosystem, compared its genetic diversity to congeners, predict its global distribution via environmental niche modelling, and discussed possible underlying mechanisms controlling the species’ global distribution. Methods We surveyed the South African coastline and sampled sponges at 53 rocky shore sites spanning over 3,000 km, from Grosse Bucht south of Lüderitz (Namibia) to Kosi Bay on the east coast of South Africa. DNA sequences of the nuclear rDNA internal transcribed spacer (ITS1) and the COI mitochondrial gene were obtained from 61 samples and compared them to a world-wide sample of other H. perlevis sequences. Using environmental predictor variables from the global dataset BIO-ORACLE, we predicted the probability of global occurrence of the species using an ensemble of eight distribution models. Results South African specimens were found to be 99–100% identical to other populations of H. perlevis (=H. sinapium) from other world-wide regions. The presence of a single population of H. perlevis in southern Africa is supported by genetic data, extending its distribution to a relatively wide geographical range spanning more than 4,000 km along the temperate southern African coast. The predicted global occurrence by ensemble model matched well with the observed distribution. Surface temperature mean and range were the most important predictor variables. Conclusion While H. perlevis appears to have been introduced in many parts of the world, its origins in Europe and southern Africa are unclear.
Samaai et al. (2022) Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal. PeerJ 10:e14388 https://doi.org/10.7717/peerj.14388