Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth
Background Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean’s euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans. Methodology We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes. Results Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition. Conclusions Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.
Fuchsman et al. (2023) Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth. PeerJ 11:e14924 https://doi.org/10.7717/peerj.14924
The behavior of Broad-tailed hummingbirds is altered by cycles of human activity in a forested area converted into agricultural land
Background By changing the circumstances in which animals make their behavioral decisions, weekly cycles of human activity might cause changes in wildlife behavior. For example, when there is more human activity in a location, animals may become more vigilant, which can decrease the time they spend foraging, or roam farther from home, leading to increased home range size. Overall, there has been little exploration of how animal species living in locations that have undergone land use change are affected by the temporal dynamics of human activity levels. In this study, we aimed to analyze the effect of the weekend on agricultural activities and hummingbird territorial activity. We examined differences between weekdays and weekends in factors previously shown to follow weekly cyclical patterns, such as pedestrian presence, traffic, and the presence of domestic animals. We hypothesized that territorial hummingbirds would respond to these weekly cycles of human activity by altering their behavior. Methods We studied Broad-tailed hummingbird territories in forested areas that had been transformed to agriculture lands in central Mexico. We evaluated whether territorial individuals changed their behaviors (i.e., chases of intruders, foraging within their territory, number of intruders allowed to forage in the territory) in response to variation between weekdays and weekends in the number of pedestrians, cyclists, dogs, farm animals and vehicles. Results We found that the level of agriculture-related human activities showed a weekly cycle at our study site. On weekdays there was higher traffic of pedestrians, cyclists, dogs, farm animals and vehicles, compared to the weekends. Hummingbirds responded to these weekday-weekends differences by changing their territorial behavior. Compared to weekends, on weekdays hummingbirds showed a decrease in defense (number of chases) as well as the use of their territory (number of flowers visited), which allowed increased access to intruders (number of visited flowers by intruders). Conclusions Our findings suggest that variation in agriculture-related human activities between weekdays and weekends can alter the territorial behavior of hummingbirds. Behavioral shifts seem to be related to these human activity cycles, leading hummingbirds to reduce chases and feeding during weekdays when human activity is highest, but increasing both behaviors during times of minimal disturbance.
Mendiola-Islas et al. (2023) The behavior of Broad-tailed hummingbirds is altered by cycles of human activity in a forested area converted into agricultural land. PeerJ 11:e14953 https://doi.org/10.7717/peerj.14953
CircRNA expression profiles and functional analysis in a mouse model of chronic intermittent hypoxia-induced renal injury: new insight into pathogenesis
Increasing evidence has demonstrated that circular RNAs (circRNAs) play crucial roles in the pathogenesis of multiple diseases. However, the functions of circRNAs in renal injury induced by obstructive sleep apnea (OSA) are poorly understood. The aim of this current study is to identify the global changes of circRNAs expression in OSA-induced renal damage. The mouse model of OSA treated by chronic intermittent hypoxia (CIH) was established. We assessed the expression profiles of circRNAs in CIH caused renal injury by microarray analysis. Bioinformatic analyses were further performed by us to assess those differentially expressed circRNAs. Quantitative realtime PCR (qRT-PCR) were then conducted to assure the data of microarray. Finally, a circRNA-miRNA -mRNA competing endogenous RNA (ceRNA) regulatory network was constructed. We found 11 upregulated and 13 downregulated circRNAs in CIH-induced renal injury. The qRT-PCR validated that the six selected circRNAs were identical to the results of microarray. Both Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were further employed to annotate the potential functions of dysregulated circRNAs. Finally, we established a ceRNA network to predict the target genes of circRNAs. In general, our results first illustrate that circRNAs are aberrantly expressed in OSA-induced renal injury, which might aid in offering novel genetic insights into this disease and potential therapeutic targets for OSA-associated chronic kidney disease.
Chen et al. (2023) CircRNA expression profiles and functional analysis in a mouse model of chronic intermittent hypoxia-induced renal injury: new insight into pathogenesis. PeerJ 11:e14957 https://doi.org/10.7717/peerj.14957
Clinical characteristics and prognosis differences between isolated right and left ventricular myocardial infarction in the Chinese population: a retrospective study
Background and aims Acute myocardial infarction (AMI) is divided into left ventricular myocardial infarction (LVMI) and right ventricular myocardial infarction (RVMI) according to the regions of myocardial ischemic necrosis. Clinical characteristics, treatment strategies, and prognosis differences between isolated RVMI and LVMI have not been well characterized. This study aimed to explore this difference of patients with isolated RVMI and LVMI. Methods This retrospective cohort study included 3,506 patients hospitalized with coronary angiography diagnosed type 1 myocardial infarction (MI). Characteristics of admission and treatment strategies were compared in patients with isolated RVMI and LVMI. COX proportional hazards models with and without inverse probability of treatment weighting (IPTW) adjustment were performed to estimate the difference in all-cause and cardiovascular mortality between the two groups. Results In this retrospective study, we found the frequency of isolated RVMI was significantly lower in the population than that of isolated LVMI (406 (11.6%) vs 3,100 (88.4%)). Patients with isolated RVMI have similar age, sex, and comorbidities to the patients with isolated LVMI. However, patients with isolated RVMI have lower heart rate and blood pressure, but higher rates of cardiogenic shock and atrioventricular block. It is noteworthy that patients with isolated RVMI are more likely to be complicated with the multivessel lesion. Patients with isolated RVMI have lower risk of all-cause mortality (HR 0.36; 95% CI [0.24–0.54], p < 0.001) and cardiovascular mortality (HR 0.37; 95% CI [0.22–0.62], p < 0.001) than patients with isolated LVMI. Conclusions This study showed that patients with isolated RVMI and LVMI have similar baseline characteristics. However, the clinical manifestations were different in the isolated RVMI and LVMI patients. This study revealed a better prognosis of isolated RVMI patients compared to isolated LVMI, which indicates the ischemic region could be considered in AMI risk stratification models for better assessment of risk for adverse clinical events.
Chen et al. (2023) Clinical characteristics and prognosis differences between isolated right and left ventricular myocardial infarction in the Chinese population: a retrospective study. PeerJ 11:e14959 https://doi.org/10.7717/peerj.14959
Addressing the challenges of symbiont-mediated RNAi in aphids
Because aphids are global agricultural pests and models for bacterial endosymbiosis, there is a need for reliable methods to study and control their gene function. However, current methods available for aphid gene knockout and knockdown of gene expression are often unreliable and time consuming. Techniques like CRISPR-Cas genome editing can take several months to achieve a single gene knockout because they rely on aphids going through a cycle of sexual reproduction, and aphids often lack strong, consistent levels of knockdown when fed or injected with molecules that induce an RNA interference (RNAi) response. In the hopes of addressing these challenges, we attempted to adapt a new method called symbiont-mediated RNAi (smRNAi) for use in aphids. smRNAi involves engineering a bacterial symbiont of the insect to continuously supply double-stranded RNA (dsRNA) inside the insect body. This approach has been successful in thrips, kissing bugs, and honeybees. We engineered the laboratory Escherichia coli strain HT115 and the native aphid symbiont Serratia symbiotica CWBI-2.3T to produce dsRNA inside the gut of the pea aphid (Acyrthosiphon pisum) targeting salivary effector protein (C002) or ecdysone receptor genes. For C002 assays, we also tested co-knockdown with an aphid nuclease (Nuc1) to reduce RNA degradation. However, we found that smRNAi was not a reliable method for aphid gene knockdown under our conditions. We were unable to consistently achieve the expected phenotypic changes with either target. However, we did see indications that elements of the RNAi pathway were modestly upregulated, and expression of some targeted genes appeared to be somewhat reduced in some trials. We conclude with a discussion of the possible avenues through which smRNAi, and aphid RNAi in general, could be improved in the future.
Elston et al. (2023) Addressing the challenges of symbiont-mediated RNAi in aphids. PeerJ 11:e14961 https://doi.org/10.7717/peerj.14961
Determination of drought tolerance of different strawberry genotypes
Strawberry production future depends on productive, high quality and drought tolerant varieties. The goal of this study was to determine the most suitable variety by determining the yield and photosynthetic responses (net photosynthesis (Pn), stomatal conductance (gs), and transpiration rate (E)) of four strawberry genotypes with different characteristics (Rubygem, Festival; 33, and 59) at two different irrigation levels (IR50: water stress (WS), IR100: well-watered (WW)). It was also aimed to prepare the irrigation program by making use of the crop water stress index (CWSI). The trial was conducted at the Agronomic Research Area, University of Çukurova, Turkey during 2019–2020 experimental year. The trial was implemented as a 4 × 2 factorial scheme of genotypes and irrigation levels, in a split-plot design. Genotype Rubygem had the highest canopy temperature (Tc)–air temperature (Ta), whereas genotype 59 had the lowest, indicating that genotype 59 has better ability to thermoregulate leaf temperatures. Moreover, yield, Pn, and E were found to have a substantial negative relationship with Tc–Ta. WS reduced yield, Pn, gs, and E by 36%, 37%, 39%, and 43%, respectively, whereas it increased CWSI (22%) and irrigation water use efficiency (IWUE) (6%). Besides, the optimal time to measure leaf surface temperature of strawberries is around 1:00 pm and strawberry irrigation management might be maintained under the high tunnel in Mediterranean utilizing CWSI values between 0.49 and 0.63. Although genotypes had varying drought tolerance, the genotype 59 had the strongest yield and photosynthetic performances under both WW and WS conditions. Furthermore, 59 had highest IWUE and lowest CWSI in the WS conditions, proving to be the most drought tolerant genotype in this research.
Celiktopuz (2023) Determination of drought tolerance of different strawberry genotypes. PeerJ 11:e14972 https://doi.org/10.7717/peerj.14972
Is Xenopus laevis introduction linked with Ranavirus incursion, persistence and spread in Chile?
Ranaviruses have been associated with amphibian, fish and reptile mortality events worldwide and with amphibian population declines in parts of Europe. Xenopus laevis is a widespread invasive amphibian species in Chile. Recently, Frog virus 3 (FV3), the type species of the Ranavirus genus, was detected in two wild populations of this frog near Santiago in Chile, however, the extent of ranavirus infection in this country remains unknown. To obtain more information about the origin of ranavirus in Chile, its distribution, species affected, and the role of invasive amphibians and freshwater fish in the epidemiology of ranavirus, a surveillance study comprising wild and farmed amphibians and wild fish over a large latitudinal gradient (2,500 km) was carried out in 2015–2017. In total, 1,752 amphibians and 496 fish were tested using a ranavirus-specific qPCR assay, and positive samples were analyzed for virus characterization through whole genome sequencing of viral DNA obtained from infected tissue. Ranavirus was detected at low viral loads in nine of 1,011 X. laevis from four populations in central Chile. No other amphibian or fish species tested were positive for ranavirus, suggesting ranavirus is not threatening native Chilean species yet. Phylogenetic analysis of partial ranavirus sequences showed 100% similarity with FV3. Our results show a restricted range of ranavirus infection in central Chile, coinciding with X. laevis presence, and suggest that FV3 may have entered the country through infected X. laevis, which appears to act as a competent reservoir host, and may contribute to the spread the virus locally as it invades new areas, and globally through the pet trade.
Peñafiel-Ricaurte et al. (2023) Is Xenopus laevis introduction linked with Ranavirus incursion, persistence and spread in Chile?. PeerJ 11:e14497 https://doi.org/10.7717/peerj.14497
Stress-induced immunosuppression affecting immune response to Newcastle disease virus vaccine through “miR-155-CTLA-4” pathway in chickens
MiR-155 and CTLA-4 are important factors involved in the regulation of immune function. However, there is no report about their involvement in function regulation of stress-induced immunosuppression affecting immune response. In this study, the chicken model of stress-induced immunosuppression affecting immune response (simulation with dexamethasone and immunization with Newcastle disease virus (NDV) attenuated vaccine) was established, then the expression characteristics of miR-155 and CTLA-4 gene were analyzed at several key time points during the processes of stress-induced immunosuppression affecting NDV vaccine immune response at serum and tissue levels. The results showed that miR-155 and CTLA-4 were the key factors involved in stress-induced immunosuppression and NDV immune response, whose functions involved in the regulation of immune function were different in different tissues and time points, and 2 day post immunization (dpi), 5dpi and 21dpi were the possible key regulatory time points. CTLA-4, the target gene of miR-155, had significant game regulation relationships between them in various tissues, such as bursa of Fabricius, thymus and liver, indicating that miR-155-CTLA-4 pathway was one of the main mechanisms of their involvement in the regulations of stress-induced immunosuppression affecting NDV immune response. This study can lay the foundation for in-depth exploration of miR-155-CTLA-4 pathway involved in the regulation of immune function.
Wen et al. (2023) Stress-induced immunosuppression affecting immune response to Newcastle disease virus vaccine through “miR-155-CTLA-4” pathway in chickens. PeerJ 11:e14529 https://doi.org/10.7717/peerj.14529
Benthic biogeographic patterns on the deep Brazilian margin
The Brazilian continental margin (BCM) extends from the Tropical to the Subtropical Atlantic Ocean, with much of its seafloor within deep waters, supporting rich geomorphological features and under wide productivity gradients. Deep-sea biogeographic boundaries on the BCM have been limited to studies that used water mass and salinity properties of deep-water masses, partly as a result of historical under sampling and a lack of consolidation of available biological and ecological datasets. The aim of this study was to consolidate benthic assemblage datasets and test current oceanographic biogeographical deep-sea boundaries (200–5,000 m) using available faunal distributions. We retrieved over 4,000 benthic data records from open-access databases and used cluster analysis to examine assemblage distributions against the deep-sea biogeographical classification scheme from Watling et al. (2013). Starting from the assumption that vertical and horizontal distribution patterns can vary regionally, we test other schemes incorporating latitudinal and water masses stratification within the Brazilian margin. As expected, the classification scheme based on benthic biodiversity is in overall agreement with the general boundaries proposed by Watling et al. (2013). However, our analysis allowed much refinement in the former boundaries, and here we propose the use of two biogeographic realms, two provinces and seven bathyal ecoregions (200–3,500 m), and three abyssal provinces (>3,500 m) along the BCM. The main driver for these units seems to be latitudinal gradients as well as water mass characteristics such as temperature. Our study provides a significant improvement of benthic biogeographic ranges along the Brazilian continental margin allowing a more detailed recognition of its biodiversity and ecological value, and also supports the needed spatial management for industrial activities occurring in its deep waters.
Gaurisas et al. (2023) Benthic biogeographic patterns on the deep Brazilian margin. PeerJ 11:e14585 https://doi.org/10.7717/peerj.14585
Some fundamental elements for studying social-ecological co-existence in forest common pool resources
For millennia, societies have tried to find ways to sustain people’s livelihoods by setting rules to equitably and sustainably access, harvest and manage common pools of resources (CPR) that are productive and rich in species. But what are the elements that explain historical successes and failures? Elinor Ostrom suggested that it depends on at least eight axiomatic principles of good governance, whereas empirical results suggest that these principles are not sufficient to describe them, especially when applied to CPRs that possess great social and ecological diversity. The aim of this article is to explore the behavior of a mathematical model of multi-species forest dynamics that respects the foundations of ecology and Ostrom’s governance theory, in order to detect possible constraints inherent to the functioning of these complex systems. The model reveals that fundamental structural laws of compatibilities between species life-history traits are indeed constraining the level of co-existence (average and variance) between a diversity of co-vulnerable timber resource users (RU) and of competing tree species. These structural constraints can also lead to unexpected outcomes. For instance in wetter forest commons, opening up the access to as many diverse RUs as there are competing tree species, produces a diversity of independently-controlled disturbances on species, collectively improving the chances of coexistence between species with different life-history traits. Similar benefits are observed on forest carbon and on profits from timber harvesting. However in drier forest commons, the same benefits cannot be observed, as predicted on the basis of the constraining laws. The results show that the successes and failures of certain management strategies can be reasonably explained by simple mechanistic theories from ecology and the social-ecological sciences, which are themselves constrained by fundamental ecological invariants. If corroborated, the results could be used, in conjunction with Ostrom’s CPR theory, to understand and solve various human-nature coexistence dilemmas in complex social-ecological systems.
Pichancourt (2023) Some fundamental elements for studying social-ecological co-existence in forest common pool resources. PeerJ 11:e14731 https://doi.org/10.7717/peerj.14731