Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma
Background Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous malignancy with varied outcomes. However, the fundamental mechanisms remain to be fully defined. Aim We aimed to identify core differentially co-expressed hub genes and perturbed pathways relevant to the pathogenesis and prognosis of DLBCL. Methods We retrieved the raw gene expression profile and clinical information of GSE12453 from the Gene Expression Omnibus (GEO) database. We used integrated bioinformatics analysis to identify differentially co-expressed genes. The CIBERSORT analysis was also applied to predict tumor-infiltrating immune cells (TIICs) in the GSE12453 dataset. We performed survival and ssGSEA (single-sample Gene Set Enrichment Analysis) (for TIICs) analyses and validated the hub genes using GEPIA2 and an independent GSE31312 dataset. Results We identified 46 differentially co-expressed hub genes in the GSE12453 dataset. Gene expression levels and survival analysis found 15 differentially co-expressed core hub genes. The core genes prognostic values and expression levels were further validated in the GEPIA2 database and GSE31312 dataset to be reliable (p < 0.01). The core genes’ main KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichments were Ribosome and Coronavirus disease-COVID-19. High expressions of the 15 core hub genes had prognostic value in DLBCL. The core genes showed significant predictive accuracy in distinguishing DLBCL cases from non-tumor controls, with the area under the curve (AUC) ranging from 0.992 to 1.00. Finally, CIBERSORT analysis on GSE12453 revealed immune cells, including activated memory CD4+ T cells and M0, M1, and M2-macrophages as the infiltrates in the DLBCL microenvironment. Conclusion Our study found differentially co-expressed core hub genes and relevant pathways involved in ribosome and COVID-19 disease that may be potential targets for prognosis and novel therapeutic intervention in DLBCL.
Charwudzi et al. (2021) Integrated bioinformatics analysis reveals dynamic candidate genes and signaling pathways involved in the progression and prognosis of diffuse large B-cell lymphoma. PeerJ 9:e12394 https://doi.org/10.7717/peerj.12394
Going rogue: what scientists can learn about Twitter communication from “alt” government accounts
The inauguration of President Trump in the United States led to the active restriction of science communication from federal agencies, resulting in the creation of many unofficial “alt” Twitter accounts to maintain communication. Alt accounts had many followers (e.g., 15 accounts had > 100,000) and received a large amount of media attention, making them ideal for better understanding how differences in messaging can affect public engagement with science on microblogging platforms. We analyzed tweets produced by alt and corresponding official agency accounts to compare the two groups and determine if specific features of a tweet made them more likely to be retweeted or liked to help the average scientist potentially reach a broader audience on Twitter. We found adding links, images, hashtags, and mentions, as well as expressing angry and annoying sentiments all increased retweets and likes. Evidence-based terms such as “peer-review” had high retweet rates but linking directly to peer-reviewed publications decreased attention compared to popular science websites. Word choice and attention did not reflect official or alt account types, indicating topic is more important than source. The number of tweets generated and attention received by alt accounts has decreased since their creation, demonstrating the importance of timeliness in science communication on social media. Together our results show potential pathways for scientists to increase efficacy in Twitter communications.
Wilson et al. (2021) Going rogue: what scientists can learn about Twitter communication from “alt” government accounts. PeerJ 9:e12407 https://doi.org/10.7717/peerj.12407
Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery
This study aims to understand the spatial distribution of coral reefs in the central region of Viet Nam. We classified live coral cover in Son Tra Peninsula (ST) and Cu Lao Cham Island (CLC) in the South-Central Coast Region of Viet Nam using the Maximum Likelihood Classifier on 3 m Planetscope imagery. Confusion matrices and the accuracy of the classifier were assessed using field data (1,543 and 1,560 photographs in ST and CLC, respectively). The results showed that the reef’s width ranged from 30 to 300 m across the study site, and we were able to detect live coral cover across a depth gradient of 2 to 6 m below the sea surface. The overall accuracies of the classifier (the Kappa coefficient) were 76.78% (0.76) and 78.08% (0.78) for ST and CLC, respectively. We found that 60.25% of coral reefs in ST were unhealthy and the live coral cover was less than 50%, while 25.75% and 11.46% of those in CLC were in good and excellent conditions, respectively. This study demonstrates the feasibility of utilizing Planetscope imagery to monitor shallow coral reefs of small islands at a high spatial resolution of 3 m. The results of this study provide valuable information for coral reef protection and conservation.
Spatial and Geographic Information Science
Nguyen et al. (2021) Characterizing the spatial distribution of coral reefs in the South-Central Coast region of Viet Nam using Planetscope imagery. PeerJ 9:e12413 https://doi.org/10.7717/peerj.12413
Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea
In this study, size selectivity and exploitation pattern of six diamond-mesh codends with different mesh sizes, ranging from 25 to 54 mm, for Southern velvet shrimp (Metapenaeopsis palmensis) were tested and compared in a shrimp trawl fishery of the South China Sea (SCS). We used a codend with a mesh size of 25 mm (D25) as a starting point, which is the minimum mesh size (MMS) currently regulated in the studied area. Four different fishing population scenarios were applied to quantify and compare how mesh sizes of codends used would impact the size selectivity and exploitation pattern for the target shrimp species. The results demonstrated that the D25 codend was not proper for protecting juvenile shrimp at the studied area. By applying this legal codend, L50 (50% retention length) of the target shrimp species was below its minimum conservation reference size (MCRS, 7.0 cm total length), the retention probability of shrimp with a length of MCRS was above 95% CI [91–99] and more than 43% of undersized shrimp was retained. To mitigate the bycatch issue of undersized shrimp, increasing the mesh size in the diamond mesh codend is a simple and effective option. However, the loss of catch efficiency for marketable shrimp is a major concern while increasing the mesh size. A good compromise between releasing undersized shrimp and maintaining the legal individuals is manifested by using the codend with 35 mm mesh size (D35). Our study will be beneficial for the management of shrimp trawl fisheries in the SCS.
Yang et al. (2021) Comparing size selectivity and exploitation pattern of diamond-mesh codends for Southern velvet shrimp (Metapenaeopsis palmensis) in shrimp trawl fishery of the South China Sea. PeerJ 9:e12436 https://doi.org/10.7717/peerj.12436
Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics
In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.
Höhna et al. (2021) Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics. PeerJ 9:e12438 https://doi.org/10.7717/peerj.12438
Genetic structure of marine and lake forms of Pacific herring Clupea pallasii
The Pacific herring (Clupea pallasii) is one of the most important species in the commercial fisheries distributed in the North Pacific Ocean and the northeastern European seas. This teleost has marine and lake ecological forms a long its distribution in the Holarctic. However, the level of genetic differentiation between these two forms is not well known. In the present study, we used ddRAD-sequencing to genotype 54 specimens from twelve wild Pacific herring populations from the Kara Sea and the Russian part of the northwestern Pacific Ocean for unveiling the genetic structure of Pacific herring. We found that the Kara Sea population is significantly distinct from Pacific Ocean populations. It was demonstrated that lake populations of Pacific herring differ from one another as well as from marine specimens. Our results show that fresh and brackish water Pacific herring, which inhabit lakes, can be distinguished as a separate lake ecological form. Moreover, we demonstrate that each observed lake Pacific herring population has its own and unique genetic legacy.
Orlova et al. (2021) Genetic structure of marine and lake forms of Pacific herring Clupea pallasii. PeerJ 9:e12444 https://doi.org/10.7717/peerj.12444
Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum
Background Malaria parasites reproduce asexually, leading to the production of large numbers of genetically identical parasites, here termed a clonal line or clone. Infected hosts may harbor one or more clones, and the number of clones in a host is termed multiplicity of infection (MOI). Understanding the distribution of parasite clones among hosts can shed light on the processes shaping this distribution and is important for modeling MOI. Here, I determine whether the distribution of clones of the lizard malaria parasite Plasmodium mexicanum differ significantly from statistical distributions commonly used to model MOI and logical extensions of these models. Methods The number of clones per infection was assessed using four microsatellite loci with the maximum number of alleles at any one locus used as a simple estimate of MOI for each infection. I fit statistical models (Poisson, negative binomial, zero-inflated models) to data from four individual sites to determine a best fit model. I also simulated the number of alleles per locus using an unbiased estimate of MOI to determine whether the simple (but potentially biased) method I used to estimate MOI influenced model fit. Results The distribution of clones among hosts at individual sites differed significantly from traditional Poisson and negative binomial distributions, but not from zero-inflated modifications of these distributions. A consistent excess of two-clone infections and shortage of one-clone infections relative to all fit distributions was also observed. Any bias introduced by the simple method for estimating of MOI did not appear to qualitatively alter the results. Conclusions The statistical distributions used to model MOI are typically zero-truncated; truncating the Poisson or zero-inflated Poisson yield the same distribution, so the reasonable fit of the zero-inflated Poisson to the data suggests that the use of the zero-truncated Poisson in modeling is adequate. The improved fit of zero-inflated distributions relative to standard distributions may suggest that only a portion of the host population is located in areas suitable for transmission even at small sites (<1 ha). Collective transmission of clones and premunition may also contribute to deviations from standard distributions.
Neal (2021) Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum. PeerJ 9:e12448 https://doi.org/10.7717/peerj.12448
Concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in adults with chronic heart failure
Background The study investigated the relationship between the concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in the blood serum of patients with heart failure (HF) and the potential influence on the development and progression of HF. Material & methods The study included 214 patients (155 men and 59 women), aged 40–87 years, presenting symptoms or signs typical of HF (according to the NYHA functional classification). Serum concentrations were determined for Mg, Ca, Fe, Cu, Zn, P, C-reactive protein (CRP), creatinine, urea, triglyceride levels (TG), total cholesterol (CH), high density protein (HDL), low density protein (LDL). The levels of macro-and microminerals were analysed using inductively coupled serum optical emission spectrometry (ICP-OES). Results Our study confirmed the role of known risk factors in the development of heart failure, including: overweight, diabetes, hypertension, high triglycerides (TG), high total cholesterol (CH), high levels of low density protein (LDL) and reduced levels of high density protein (HDL), high CRP, high creatinine. Moreover, deficient serum concentrations of Mg (47% of the studied men and 54% of the women) and Cu (in 44% of men and more than 30% of women) were observed, as well as subnormal serum Fe (2% of women) and Zn (1% of men). Elevated serum Ca was found in 50% of men and 49% of women. In 44% of the studied men and 52% of the studied women, P levels in serum were also above-average. The study revealed a significant positive correlation between serum levels of Ca and Mg, and also Ca and Cu in women. In men, serum Cu was positively correlated with Mg and Ca concentrations. In patients from group 1 (NYHA I–II), Mg content was positively correlated with Ca and Cu. In this patient group, Ca was also positively associated with Cu content in serum. In group 2 (NYHA III-IV), serum Mg concentration was significantly positively correlated with that of Cu and Ca. Conclusions Changes in the serum concentrations of macro-and microminerals may significantly affect the severity of HF in Polish patients.
Gorący et al. (2021) Concentrations of Mg, Ca, Fe, Cu, Zn, P and anthropometric and biochemical parameters in adults with chronic heart failure. PeerJ 9:e12207 https://doi.org/10.7717/peerj.12207
PLGA-PEG-PLGA hydrogel with NEP1-40 promotes the functional recovery of brachial plexus root avulsion in adult rats
Adult brachial plexus root avulsion can cause serious damage to nerve tissue and impair axonal regeneration, making the recovery of nerve function difficult. Nogo-A extracellular peptide residues 1-40 (NEP1-40) promote axonal regeneration by inhibiting the Nogo-66 receptor (NgR1), and poly (D, L-lactide-co-glycolide)-poly (ethylene glycol)-poly (D, L-lactide-co-glycolide) (PLGA-PEG-PLGA) hydrogel can be used to fill in tissue defects and concurrently function to sustain the release of NEP1-40. In this study, we established an adult rat model of brachial plexus nerve root avulsion injury and conducted nerve root replantation. PLGA-PEG-PLGA hydrogel combined with NEP1-40 was used to promote nerve regeneration and functional recovery in this rat model. Our results demonstrated that functional recovery was enhanced, and the survival rate of spinal anterior horn motoneurons was higher in rats that received a combination of PLGA-PEG-PLGA hydrogel and NEP1-40 than in those receiving other treatments. The combined therapy also significantly increased the number of fluorescent retrogradely labeled neurons, muscle fiber diameter, and motor endplate area of the biceps brachii. In conclusion, this study demonstrates that the effects of PLGA-PEG-PLGA hydrogel combined with NEP1-40 are superior to those of other therapies used to treat brachial plexus nerve root avulsion injury. Therefore, future studies should investigate the potential of PLGA-PEG-PLGA hydrogel as a primary treatment for brachial plexus root avulsion.
Guo et al. (2021) PLGA-PEG-PLGA hydrogel with NEP1-40 promotes the functional recovery of brachial plexus root avulsion in adult rats. PeerJ 9:e12269 https://doi.org/10.7717/peerj.12269
Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes
Infection with Helicobacter pylori is one of the most important risk factors for developing gastric cancer (GC). The type IV secretion system (T4SS) encoded in the cag pathogenicity island is the main virulence factor of H. pylori associated with GC. Additionally, other virulence factors have been shown to play a role in the H. pylori virulence, such as vacuolizing cytotoxin (VacA), urease, flagella, and adhesins. Long-chain fatty acids (LCFAs) are signaling molecules that affect the transcription of virulence genes in several pathogenic bacteria such as Salmonella enterica, Vibrio cholerae, Pseudomonas aeruginosa and Mycobacterium tuberculosis. However, the effect of LCFAs on the transcription of H. pylori virulence and regulatory genes remains unknown. Here we analyzed whether the transcription of virulence genes that encode T4SS and cellular envelope components, flagellins, adhesins, toxins, urease, as well as the transcription of different regulatory genes of the H. pylori strain 26695, are altered by the presence of five distinct LCFAs: palmitic, stearic, oleic, linoleic, and linolenic acids. Palmitic and oleic acids up-regulated the transcription of most of the virulence genes tested, including cagL, cagM, flaB, sabA, mraY and vacA, as well as that of the genes encoding the transcriptional regulators NikR, Fur, CheY, ArsR, FlgR, HspR, HsrA, Hup, and CrdR. In contrast, the other LCFAs differentially affected the transcription of the virulence and regulatory genes assessed. Our data show that LCFAs can act as signaling molecules that control the transcription of the H. pylori virulome.
Valdez-Salazar et al. (2021) Long-chain fatty acids alter transcription of Helicobacter pylori virulence and regulatory genes. PeerJ 9:e12270 https://doi.org/10.7717/peerj.12270