Transcranial direct current stimulation over the right DLPFC selectively modulates subprocesses in working memory
Background Working memory, as a complex system, consists of two independent components: manipulation and maintenance process, which are defined as executive control and storage process. Previous studies mainly focused on the overall effect of transcranial direct current stimulation (tDCS) on working memory. However, little has been known about the segregative effects of tDCS on the sub-processes within working memory. Method Transcranial direct current stimulation, as one of the non-invasive brain stimulation techniques, is being widely used to modulate the cortical activation of local brain areas. This study modified a spatial n-back experiment with anodal and cathodal tDCS exertion on the right dorsolateral prefrontal cortex (DLPFC), aiming to investigate the effects of tDCS on the two sub-processes of working memory: manipulation (updating) and maintenance. Meanwhile, considering the separability of tDCS effects, we further reconfirmed the causal relationship between the right DLPFC and the sub-processes of working memory with different tDCS conditions. Results The present study showed that cathodal tDCS on the right DLPFC selectively improved the performance of the modified 2-back task in the difficult condition, whereas anodal tDCS significantly reduced the performance of subjects and showed an speeding-up tendency of response time. More precisely, the results of discriminability index and criterion showed that only cathodal tDCS enhanced the performance of maintenance in the difficult condition. Neither of the two tDCS conditions affected the performance of manipulation (updating). Conclusion These findings provide evidence that cathodal tDCS of the right DLPFC selectively affects maintenance capacity. Besides, cathodal tDCS also serves as an interference suppressor to reduce the irrelevant interference, thereby indirectly improving the working memory capacity. Moreover, the right DLPFC is not the unique brain regions for working memory manipulation (updating).
Wang et al. (2018) Transcranial direct current stimulation over the right DLPFC selectively modulates subprocesses in working memory. PeerJ 6:e4906 https://doi.org/10.7717/peerj.4906
Proteomics of Nasonia vitripennis and the effects of native Wolbachia infection on N. vitripennis
Background Nasonia vitripennis, a parasitic wasp, is a good model organism to study developmental and evolutionary genetics and to evaluate the interactions between insect hosts and their symbionts. Wolbachia may be the most prevalent endosymbiont among insect species due to their special ability to improve the fitness of the infected hosts. Transinfection of bacteria or fungi could substantially alter the expression of host immune system components. However, few studies have focused on the effects of native Wolbachia infection. Accordingly, in this study, we evaluated the proteomics of N. vitripennis following Wolbachia infection. Methods We studied the proteomics of N. vitripennis following native Wolbachia infection and in antibiotic-treated Wolbachia-free samples using isobaric tags for relative and absolute quantification-liquid chromatography tandem mass spectrometry, accompanying with some ecological experiments. Results In total, 3,096 proteins were found to be associated with a wide range of biological processes, molecular functions, and cellular components. Interestingly, there were few significant changes in immune or reproductive proteins between samples with and without Wolbachia infection. Differentially expressed proteins were involved in the binding process, catalytic activity, and the metabolic process, as confirmed by quantitative reverse transcription polymerase chain reaction. Discussion Invasion of any pathogen or bacterium within a short time can cause an immunoreaction in the host. Our results implied that during the long process of coexistence, the immune system of the host was not as sensitive as when the symbiont initially infected the host, implying that the organisms had gradually adjusted to cohabitation.
Li et al. (2018) Proteomics of Nasonia vitripennis and the effects of native Wolbachia infection on N. vitripennis. PeerJ 6:e4905 https://doi.org/10.7717/peerj.4905
Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China
Objectives The prognosis of people with pancreatic cancer is extremely unfavorable. However, the prognostic factors remain largely undefined. We aimed to perform comprehensive analyses of clinicopathologic characteristics, laboratory parameters, and treatment protocols for exploring their role as prognostic factors of pancreatic cancer. Methods Patients diagnosed with pancreatic cancer and hospitalized at the China National Cancer Center between April 2006 and May 2016 were enrolled in this retrospective cohort study. Clinicopathologic characteristics, laboratory parameters, and treatment protocols were compared among patients at different stages of the disease. The association between these factors and overall survival (OS) was analyzed using the Kaplan–Meier method and Cox proportional hazards model. Results The present study included 1,433 consecutive patients with pancreatic cancer. Median OS was 10.6 months (95% confidence interval [CI] 9.8–11.3 months), with 1-, 3-, and 5-year survival rates of 43.7%, 14.8%, and 8.8%, respectively. Cox multivariate analysis findings identified the following factors as independent predictors of OS: gender (female vs male, hazard ratio 0.72, 95% CI [0.54–0.95]); elevated total bilirubin (TBil; 1.82, 1.34–2.47); elevated carbohydrate antigen 19-9 (CA19-9; 1.72, 1.17–2.54); tumor being located in pancreatic body and tail (1.52, 1.10–2.10); advanced T stage (T3-4 vs T1-2, 1.62, 1.15–2.27); lymph node metastasis (1.57, 1.20–2.07); distant metastasis (1.59, 1.12–2.27); the presence of surgical resection (0.53, 0.34–0.81); and the presence of systemic chemotherapy (0.62, 0.45–0.82). Conclusions Being male, elevated TBil and carcinoembryonic antigen, tumor being located in pancreatic body and tail, advanced T stage, lymph node and distant metastasis, the absence of surgical resection, and the absence of systematic chemotherapy were associated with worse OS in patients with pancreatic cancer.
Zhang et al. (2018) Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China. PeerJ 6:e4893 https://doi.org/10.7717/peerj.4893
BLAST-based validation of metagenomic sequence assignments
When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.
Bazinet et al. (2018) BLAST-based validation of metagenomic sequence assignments. PeerJ 6:e4892 https://doi.org/10.7717/peerj.4892
Predicting New Zealand riverine fish reference assemblages
Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites.
Canning (2018) Predicting New Zealand riverine fish reference assemblages. PeerJ 6:e4890 https://doi.org/10.7717/peerj.4890
Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta)
Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses, and to other ant species that lay trophic eggs, S. invicta workers completely lack ovaries or the ability to lay eggs. This provides a unique model to investigate whether Vg duplication in S. invicta was followed by subfunctionalization to acquire non-reproductive functions and whether Vg was co-opted to regulate behavior within the worker caste. To investigate these questions, we compared the expression patterns of S. invicta Vg genes among workers from different morphological subcastes or performing different tasks. RT-qPCRs revealed higher relative expression of Vg1 in major workers compared to both medium and minor workers, and of Vg2 in major workers when compared to minor workers. Relative expression of Vg1 was also higher in carbohydrate foragers when compared to nurses and protein foragers. By contrast, the level of expression of Vg2, Vg3, and Vg4 were not significantly different among the workers performing the specific tasks. Additionally, we analyzed the relationship between the expression of the Vg genes and S-hydroprene, a juvenile hormone analog. No changes in Vg expression were recorded in workers 12 h after application of the analog. Our results suggest that in S. invicta the Vg gene underwent subfunctionalization after duplication to new functions based on the expression bias observed in these data. This may suggest an alternative and still unknown function for Vg in the workers that needs to be investigated further.
Hawkings et al. (2018) Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta). PeerJ 6:e4875 https://doi.org/10.7717/peerj.4875
Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia
Hulsanpes perlei is an enigmatic theropod dinosaur from the Baruungoyot Formation (?mid- to upper Campanian, Upper Cretaceous) of Mongolia. It was discovered in 1970, during the third Polish-Mongolian paleontological expedition to the Nemegt Basin. The taxon is known based on a partial braincase and an incomplete right hindlimb. However, the braincase fragment has never been described nor illustrated. We redescribe all elements that form the holotype of Hulsanpes and discuss the affinities of this taxon. The braincase fragment is interpreted as belonging to the inner ear region, and includes the floccular recess and part of the labyrinth. Hulsanpes perlei is confirmed as a valid taxon, diagnosed by a unique combination of metatarsal characters, including two autapomorphies. Historically, it represents the oldest record of the recently-established clade Halszkaraptorinae. Our findings identify subcursorial adaptations for Hulsanpes, shared with Mahakala, and differentiating them from Halszkaraptor. As such, appendicular disparity in the potentially sympatric halszkaraptorines suggest a reduced ecological overlap among these taxa, which may explain the co-occurrence of multiple species of this clade during the latest Cretaceous in what is now the Nemegt Basin.
Cau et al. (2018) Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia. PeerJ 6:e4868 https://doi.org/10.7717/peerj.4868
Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles
Background Selenium is an essential element; however, at higher doses, it can be toxic. Therefore, alternative nanotechnological solutions are required to overcome toxicological issues, rather than conventional alternatives. Nanoparticles show new and promising properties that may be able to suppress toxicity while maintaining the positive effects of selenium on an organism. The aim of the experiment was to determine the influence of sodium selenite and selenium nanoparticles (SeNPs) on the antioxidant status of rats. Methods The males of the outbreed rat strain Wistar albino were selected as a model organism. Animals were fed different forms of selenium. The control group was given a mixture without selenium addition, whereas other groups were fed a mixture containing sodium selenite, Se-49, and Se-100 SeNPs respectively. The duration of the trial was 30 days. Results Analysis of blood and liver was performed where the concentration of reduced (GSH) and oxidised (GSSG) glutathione, and total selenium content were measured. In the liver, a significant reduction in GSSG was found for all experiment groups. Blood samples showed a significant reduction in GSH and an increase in GSSG. Discussion These results show that SeNPs may be an alternative to dietary selenium for animal organisms.
Urbankova et al. (2018) Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles. PeerJ 6:e4862 https://doi.org/10.7717/peerj.4862
Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells
Background The Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA. Methods In order to approach the natural conditions of infection and possible integration, we generated linear JcDV-gfp based molecules which were transfected into non permissive Spodoptera frugiperda (Sf9) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed. Results We show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear “scrambled” whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter. Conclusion Altogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequences were extensively rearranged with cellular DNA during or after random integration in the host cell genome. Lastly, the non-structural proteins seem to participate in the regulation of p9 promoter activity rather than to the integration of viral sequences.
Rizk et al. (2018) Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells. PeerJ 6:e4860 https://doi.org/10.7717/peerj.4860
Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV
It is generally feasible to classify different species of vegetation based on remotely sensed images, but identification of different sub-species or even cultivars is uncommon. Tea trees (Camellia sinensis L.) have been proven to show great differences in taste and quality between cultivars. We hypothesize that hyperspectral remote sensing would make it possibly to classify cultivars of plants and even to estimate their taste-related biochemical components. In this study, hyperspectral data of the canopies of tea trees were collected by hyperspectral camera mounted on an unmanned aerial vehicle (UAV). Tea cultivars were classified according to the spectral characteristics of the tea canopies. Furthermore, two major components influencing the taste of tea, tea polyphenols (TP) and amino acids (AA), were predicted. The results showed that the overall accuracy of tea cultivar classification achieved by support vector machine is higher than 95% with proper spectral pre-processing method. The best results to predict the TP and AA were achieved by partial least squares regression with standard normal variant normalized spectra, and the ratio of TP to AA—which is one proven index for tea taste—achieved the highest accuracy (RCV = 0.66, RMSECV = 13.27) followed by AA (RCV = 0.62, RMSECV = 1.16) and TP (RCV = 0.58, RMSECV = 10.01). The results indicated that classification of tea cultivars using the hyperspectral remote sensing from UAV was successful, and there is a potential to map the taste-related chemical components in tea plantations from UAV platform; however, further exploration is needed to increase the accuracy.
Tu et al. (2018) Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV. PeerJ 6:e4858 https://doi.org/10.7717/peerj.4858