Contrasting patterns from two invasion fronts suggest a niche shift of an invasive predator of native bees
Background The accuracy of predictions of invasive species ranges is dependent on niche similarity between invasive and native populations and on our ability to identify the niche characteristics. With this work we aimed to compare the niche dynamics of two genetically related invasive populations of Vespa velutina (an effective predator of honeybees and wild pollinators), in two distinct climatic regions, one in central Europe and another one in the north-western Iberian Peninsula, and hence to identify uninvaded regions susceptible to invasion. Methods Niche dynamics and shifts of V. velutina were assessed by comparing the environmental niches of the native and of the two invasive populations, using climatic, topographic and land use variables. We also ran reciprocal distribution models using different algorithms and records from both native and invasive ranges to compare model predictions and estimate which regions are at a greater risk of being invaded. Results An apparent niche shift was detected in the population of the NW of Iberian Peninsula, where the species is living under environmental conditions different from the native niche. In central Europe, large suitable areas remain unoccupied. The fact that both invasive populations are well established, despite occupying environmentally distinct regions indicates that V. velutina has a high ability to successfully invade different environmental envelopes from those existing in its native range. For example, in north-western Iberian Peninsula the species is now thriving out of its native niche limits. Moreover, the large extent of still unoccupied environmental space with similar conditions to those used by the species in its native range suggests that there is still a large area of central and eastern Europe that can be potentially invaded by the species.
Spatial and Geographic Information Science
Verdasca et al. (2022) Contrasting patterns from two invasion fronts suggest a niche shift of an invasive predator of native bees. PeerJ 10:e13269 https://doi.org/10.7717/peerj.13269
Effects of fire disturbance on species and functional compositions vary with tree sizes in a tropical dry forest
Background Disturbances are crucial in determining forest biodiversity, dynamics, and ecosystem functions. Surface fire is a significant disturbance in tropical forests, but research on the effect of surface fire on structuring species and functional composition in a community through time remains scarce. Using a 20-year dataset of tree demography in a seasonal evergreen tropical forest in Thailand, we specifically addressed two essential questions: (1) What is the pattern of temporal turnover in species and functional composition in a community with frequent fire disturbance? (2) How did the temporal turnover vary with tree size? Methods We analyzed species compositional and functional temporal turnovers in four different tree size classes among five tree censuses. We quantified species turnover by calculating Bray-Curtis dissimilarity, and investigated its underlying mechanisms by comparing pairwise dissimilarity of functional traits with simulations from null models. If fire disturbances contribute more to a stochastic process, the functional composition would display a random pattern. However, if they contribute more towards a deterministic process, the functional composition should reveal a non-random pattern. Results Over 20 years (1994–2014), we observed changes in species composition, whereas functional composition remained relatively stable. The temporal turnover patterns of species and functional compositions varied with tree sizes. In particular, temporal functional turnover shifted very little for large trees, suggesting that changes in species composition of larger trees are contributed by species with similar functional traits through time. The temporal functional composition turnovers of smaller trees (DBH ≤ 5 cm) were mostly at random. We detected a higher functional turnover than expected by null models in some quadrats throughout the 50-ha study plot, and their observed turnover varied with diameter classes. Conclusions Species compositional changes were caused by changes in the abundance of species with similar functional traits through time. Temporal functional turnover in small trees was random in most quadrats, suggesting that the recruits came from the equal proportions of surviving trees and new individuals of fast-growing species, which increased rapidly after fires. On the other hand, functional composition in big trees was more likely determined by surviving trees which maintained higher functional similarities than small trees through time. Fire disturbance is important for ecosystem functions, as changing forest fire frequency may alter forest turnover, particularly in functional composition in the new recruits of this forest.
Kaewsong et al. (2022) Effects of fire disturbance on species and functional compositions vary with tree sizes in a tropical dry forest. PeerJ 10:e13270 https://doi.org/10.7717/peerj.13270
An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples
Importance The rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 (PSCS-CoV2). Objective To evaluate an affordable and convenient test for COVID-19. Methods The collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus. Results We show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method (n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 < 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%. Conclusion and Relevance We developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19.
Huang et al. (2022) An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples. PeerJ 10:e13277 https://doi.org/10.7717/peerj.13277
Evaluating acoustic signals to reduce avian collision risk
Collisions with human-made structures are responsible for billions of bird deaths each year, resulting in ecological damage as well as regulatory and financial burdens to many industries. Acoustic signals can alert birds to obstacles in their flight paths in order to mitigate collisions, but these signals should be tailored to the sensory ecology of birds in flight as the effectiveness of various acoustic signals potentially depends on the influence of background noise and the relative ability of various sound types to propagate within a landscape. We measured changes in flight behaviors from zebra finches released into a flight corridor containing a physical obstacle, either in no-additional-sound control conditions or when exposed to one of four acoustic signals. We selected signals to test two frequency ranges (4–6 kHz or 6–8 kHz) and two temporal modulation patterns (broadband or frequency-modulated oscillating) to determine whether any particular combination of sound attributes elicited the strongest collision avoidance behaviors. We found that, relative to control flights, all sound treatments caused birds to maintain a greater distance from hazards and to adjust their flight trajectories before coming close to obstacles. There were no statistical differences among different sound treatments, but consistent trends within the data suggest that the 4–6 kHz frequency-modulated oscillating signal elicited the strongest avoidance behaviors. We conclude that a variety of acoustic signals can be effective as avian collision deterrents, at least in the context in which we tested these birds. These results may be most directly applicable in scenarios when birds are at risk of collisions with solid structures, such as wind turbines and communication towers, as opposed to window collisions or collisions involving artificial lighting. We recommend the incorporation of acoustic signals into multimodal collision deterrents and demonstrate the value of using behavioral data to assess collision risk.
Thady et al. (2022) Evaluating acoustic signals to reduce avian collision risk. PeerJ 10:e13313 https://doi.org/10.7717/peerj.13313
ESR2 gene variants (rs1256049, rs4986938, and rs1256030) and their association with breast cancer risk
Background Variants of the estrogen receptor b (ESR2) gene have been associated with different types of cancer. However, these associations have been inconsistent. We genotyped the ESR2 variants (rs1256049, rs4986938, and rs1256030) in breast cancer (BC) patients and in healthy women. Results The variants rs1256049 and rs4986938 in the ESR2 gene were not associated with risk susceptibility in BC patients. However, the rs1256030 variant had an association as a risk factor for BC patients when compared with controls and BC patients for the TT genotype (odds ratio (OR) 1.86, 95% confidence intervals (CI) [1.05–3.28], p = 0.042). In addition, differences were observed in patients and controls carrying the TT genotype under 50 years of age (OR 1.85, 95% CI [1.05–3.27], p = 0.043). Thus, evident differences showed the rs1256030 variant in patients with TT, TC, and TC+TT genotypes with: (1) Stage IV (OR 1.60, 95% CI [1.06–2.54], p = 0.033), and (2) Luminal A (OR 1.60, 95% CI [0.47–0.21], p = 0.041), as well as in BC carriers of the TT genotype with indices of cellular proliferative (Ki-67) elevated (>20%) and overweight (OR 1.67, 95% CI [0.85–3.28], p = 0.041), respectively. In BC HER2 with lymph node metastasis, the TT genotype was a protective factor (OR 0.38, 95% CI [0.18–0.78], p = 0.005). The identification of haplotypes included two common GAT as risk factors (OR 3.1, 95% CI [1.31–7.72], p = 0.011) and GGC as a protective factor (OR 0.7, 95% CI [0.60–0.97], p = 0.034). The haplogenotype GGGATC was a risk factor (OR 2.5, 95% CI [1.28–5.0], p = 0.008). Conclusion The variant rs1256030 (TT) of the ESR2 gene and haplotype GAT were associated with susceptibility to BC as risk factors in this sample from the Mexican population.
Gallegos-Arreola et al. (2022) ESR2 gene variants (rs1256049, rs4986938, and rs1256030) and their association with breast cancer risk. PeerJ 10:e13379 https://doi.org/10.7717/peerj.13379
Different pruning level effects on flowering period and chlorophyll fluorescence parameters of Loropetalum chinense var. rubrum
“Pruning” is a simple and efficient way to control the flowering period, but it is rarely used in perennial woody ornamental plants. In this paper, Loropetalum chinense var. rubrum was pruned in different degrees, and the relationship between pruning intensity and flowering number, and flowering time and chlorophyll fluorescence parameters were compared. After statistics, it was found that pruning could advance blossoms of L. chinense var. rubrum; also, light and heavy cutting could both obtain a larger number of flowers. In addition, through correlation analysis, it was found that during the flowering period, the Rfd parameter of the unpruned treatment had a very significant positive correlation with the number of flowers FN, which was 0.81. In other pruning treatment groups, Rfd and FN also presented a certain positive correlation, indicating that the Rfd parameter can be used to predict the number of flowers during the flowering process of L. chinense var. rubrum. The research results provided a new idea for the regulation of the flowering period of L. chinense var. rubrum and other woody ornamental plants and laid the foundation for the diversified application of L. chinense var. rubrum.
Zhang et al. (2022) Different pruning level effects on flowering period and chlorophyll fluorescence parameters of Loropetalum chinense var. rubrum. PeerJ 10:e13406 https://doi.org/10.7717/peerj.13406
The impacts of bovine milk, soy beverage, or almond beverage on the growing rat microbiome
Background Milk, the first food of mammals, helps to establish a baseline gut microbiota. In humans, milk and milk products are consumed beyond infancy, providing comprehensive nutritional value. Non-dairy beverages, produced from plant, are increasingly popular as alternatives to dairy milk. The nutritive value of some plant-based products continues to be debated, whilst investigations into impacts on the microbiome are rare. The aim of this study was to compare the impact of bovine milk, soy and almond beverages on the rat gut microbiome. We previously showed soy and milk supplemented rats had similar bone density whereas the almond supplemented group had compromised bone health. There is an established link between bone health and the microbiota, leading us to hypothesise that the microbiota of groups supplemented with soy and milk would be somewhat similar, whilst almond supplementation would be different. Methods Three-week-old male Sprague Dawley rats were randomly assigned to five groups (n = 10/group) and fed ad libitum for four weeks. Two control groups were fed either standard diet (AIN-93G food) or AIN-93G amino acids (AA, containing amino acids equivalent to casein but with no intact protein) and with water provided ad libitum. Three treatment groups were fed AIN-93G AA and supplemented with either bovine ultra-heat treatment (UHT) milk or soy or almond UHT beverages as their sole liquid source. At trial end, DNA was extracted from caecum contents, and microbial abundance and diversity assessed using high throughput sequencing of the V3 to V4 variable regions of the 16S ribosomal RNA gene. Results Almost all phyla (91%) differed significantly (FDR < 0.05) in relative abundance according to treatment and there were distinct differences seen in community structure between treatment groups at this level. At family level, forty taxa showed significantly different relative abundance (FDR < 0.05). Bacteroidetes (Bacteroidaceae) and Firmicutes populations (Lactobacillaceae, Clostridiaceae and Peptostreptococcaceae) increased in relative abundance in the AA almond supplemented group. Supplementation with milk resulted in increased abundance of Actinobacteria (Coriobacteriaceae and Bifidobacteriaceae) compared with other groups. Soy supplementation increased abundance of some Firmicutes (Lactobacilliaceae) but not Actinobacteria, as previously reported by others. Conclusion Supplementation with milk or plant-based drinks has broad impacts on the intestinal microbiome of young rats. Changes induced by cow milk were generally in line with previous reports showing increased relative abundance of Bifidobacteriacea, whilst soy and almond beverage did not. Changes induced by soy and almond drink supplementation were in taxa commonly associated with carbohydrate utilisation. This research provides new insight into effects on the microbiome of three commercially available products marketed for similar uses.
Cakebread et al. (2022) The impacts of bovine milk, soy beverage, or almond beverage on the growing rat microbiome. PeerJ 10:e13415 https://doi.org/10.7717/peerj.13415
Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem
Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.
Ghosh et al. (2022) Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem. PeerJ 10:e13169 https://doi.org/10.7717/peerj.13169
Continuous video capture, and pollinia tracking, in Platanthera (Orchidaceae) reveal new insect visitors and potential pollinators
Orchids often have specific pollinators, which should provide reproductive isolation, yet many produce natural hybrids. Platanthera dilatata and P. stricta differ in floral morphology but often co-occur, overlap in flowering, and are reputed parents of P. xestesii. We used motion-triggered video detection units to monitor floral visitors of P. dilatata and P. stricta on Vancouver Island, Canada. Pollinia removal in P. dilatata was observed using histochemical staining, and cross-pollinations were performed to determine compatibility. From 1,152 h, 753 videos were recorded; 655 contained insects and 91 contained arachnids. Bumblebees, butterflies, and moths removed pollinia from P. dilatata. No pollinia removal was observed from P. stricta. Five videos showed insects moving between Platanthera species. Pollinia removal rates were low. Hand-pollinations resulted in capsule development and seed production. This study adds to the known diversity of insects interacting with these orchids, and highlights regional differences in floral visitors.
van der Voort et al. (2022) Continuous video capture, and pollinia tracking, in Platanthera (Orchidaceae) reveal new insect visitors and potential pollinators. PeerJ 10:e13191 https://doi.org/10.7717/peerj.13191
Effect of napping on a bean bag chair on sleep stage, muscle activity, and heart rate variability
Background Although ample evidence has demonstrated that daytime napping is beneficial for health and cognitive performance, bedding for napping has not yet been scientifically investigated. Objectives To explore the effect of a bean bag chair on daytime napping and physiological parameters related to sleep. Methods Fourteen healthy participants were enrolled within the context of a randomized, single-blind, crossover study to evaluate the effects of a bean bag chair in comparison with those of a urethane chair manufactured to have a similar shape. Electroencephalogram, electromyogram, and heart rate variability were recorded and compared between wakefulness and napping. Results Electroencephalogram analyses revealed no significant differences in sleep architecture or frequency components; however, a significant decrease was found in electromyogram recordings in the trapezius muscle, which represents the neck region (p = 0.019). Additionally, a significant main effect of bedding in the low-frequency/high-frequency ratio (F[1,20] = 4.314, p = 0.037) was revealed. Conclusions These results suggest that napping in a bean bag chair may provide a comfortable napping environment involving muscle relaxation and proper regulation of the autonomic nervous function.
Nishida et al. (2022) Effect of napping on a bean bag chair on sleep stage, muscle activity, and heart rate variability. PeerJ 10:e13284 https://doi.org/10.7717/peerj.13284