A new approach for increasing graduate students’ science communication capacity and confidence
There is an increasing demand for emerging scientists to improve their ability to communicate with public audiences, yet little research investigates the effectiveness of science communication training for graduate students. We responded to this need by developing SciWrite@URI—an interdisciplinary model for science graduate students designed around three learning outcomes based on tenets from the field of writing and rhetoric—habitual writing, multiple genres, and frequent review. SciWrite students completed courses and a science communication internship, attended writing workshops, and became tutors at a newly established Graduate Writing Center. After 2 years of training, students more frequently wrote multiple drafts and engaged in peer review, increased their confidence as writers, and decreased their apprehension about writing. We conclude the tenets of the SciWrite program helped students improve as science communicators, and we make suggestions for effective ways graduate departments and training programs might implement and build on our model.
Harrington et al. (2024) A new approach for increasing graduate students’ science communication capacity and confidence. PeerJ 12:e18594 https://doi.org/10.7717/peerj.18594
Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina
Background The trematode parasite Fasciola hepatica (liver fluke) can infect livestock, wild mammals, and humans, generating serious economic losses worldwide. Aquatic or amphibious snails of the Lymnaeidae family are the intermediate host of this parasite. Both snail population dynamics and parasite development are closely associated with temperature, although most field studies have recorded air temperature rather than water temperature. Our aim was to statistically model the population dynamics of lymnaeid snails and their infection by F. hepatica under natural environmental conditions in Northwest Andean Patagonia. Methods For two years, we sampled snails monthly in four bodies of water, while registering water and air temperature hourly, and assessing F. hepatica infection in snails. Hierarchical Bayesian modeling allowed us to estimate the functional relationship between water temperature and population growth, the probability of detecting snails, and infection by F. hepatica. Results A total of 1,411 Galba viatrix snails were collected, identified, and analyzed for F. hepatica infection. All sites showed seasonal variation in the number of snails collected and in water temperature as well as sharp variations in snail counts between surveys adjacent in time. The hierarchical model revealed that water temperature acts, at least, at two different time scales: water temperature at the time of sampling determines snail detection probability, whereas the average water temperature between sampling dates affects lymnaeid population growth. We found maximum F. hepatica prevalences in snails of 40% (2/5 and 4/10), followed by 33% (65/197). These are the highest prevalences recorded in G. viatrix populations in Argentina to date. Our modeling evidenced that the positive effects of water temperature on infection probability increases with snail size and prevalence on the previous survey, while previous prevalence strongly enhances the effects of snail size. Conclusions Our results underscore the high temporal and spatial variability in the population of snails and the prevalence of F. hepatica, as well as the major impact temperature has on detecting snails. Our models provide quantifications of the effects of water temperature on the population growth of G. viatrix, its detection, and infection under natural field conditions. These are crucial steps towards generating mechanistic models of F. hepatica transmission that would facilitate the design and simulation of potential interventions based on treatments and on environmental and livestock management, taking into account the specific characteristics of each region.
Soler et al. (2024) Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina. PeerJ 12:e18648 https://doi.org/10.7717/peerj.18648
Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones
Background A grapevine crown gall tumor strain, Novosphingobium sp. strain Rr2-17 was previously reported to accumulate copious amounts of diverse quorum sensing signals during growth. Genome sequencing identified a single luxI homolog in strain Rr2-17, suggesting that it may encode for a AHL synthase with broad substrate range, pending functional validation. The exact identity of the complete suite of AHLs formed by novIspR1 is largely unknown. Methods This study validates the function of novIspR1 through inducible expression in Escherichia coli and in the wild-type parental strain Rr2-17. We further enhanced the capture of acyl homoserine lactone (AHL) signals produced by novIspR1 using polymeric resin XAD-16 and separated the AHLs by one- and two-dimensional thin layer chromatography followed by detection using AHL-dependent whole cell biosensor strains. Lastly, the complete number of AHLs produced by novIspR1 in our system was identified by LC-MS/MS analyses. Results The single LuxI homolog of N. sp. Rr2-17, NovIspR1, is able to produce up to eleven different AHL signals, including AHLs: C8-, C10-, C12-, C14-homoserine lactone (HSL) as well as AHLs with OH substitutions at the third carbon and includes 3-OH-C6-, 3-OH-C8-, 3-OH-C10-, 3-OH-C12- and 3-OH-C14-HSL. The most abundant AHL produced was identified as 3-OH-C8-HSL and isopropyl-D-1-thiogalactopyranoside (IPTG) induction of novIspR1 expression in wild type parental Rr2-17 strain increased its concentration by 6.8-fold when compared to the same strain with the vector only control plasmid. Similar increases were identified with the next two most abundant AHLs, 3-OH-C10- and unsubstituted C8-HSL. The presence of 2% w/v of XAD-16 resin in the growth culture bound 99.3 percent of the major AHL (3-OH-C8-HSL) produced by IPTG-induced overexpression of novIspR1 in Rr2-17 strain. This study significantly adds to our understanding of the AHL class of quorum sensing system in a grapevine crown gall tumor associated Novosphingobium sp. Rr2-17 strain. The identity of nine AHL signals produced by this bacterium will provide a framework to identify the specific function(s) of the AHL-mediated quorum-sensing associated genes in this bacterium.
Gan et al. (2024) Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones. PeerJ 12:e18657 https://doi.org/10.7717/peerj.18657
Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis
Background Growing evidence indicates a significant correlation between polycystic ovary syndrome (PCOS) and endometrial carcinoma (EC); nevertheless, the fundamental molecular mechanisms involved continue to be unclear. Methods Initially, differential analysis, the least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms were employed to identify candidate genes associated with ferroptosis in PCOS. Subsequently, the TCGA-UCEC data were utilized to pinpoint the core gene. Then, the expression of ENPP2 in granulosa cells and endometrium of PCOS was validated using real-time PCR (RT-qPCR). Additionally, we investigated the role of ENPP2 in the progression from PCOS to EC through western blotting (WB), colony formation assay, cell scratch assay, transwell assay, and immunofluorescence (IF). Subsequently, ENPP2 gene set enrichment analysis (GSEA) analyses were conducted to identify common pathways involved in PCOS and EC, which were then verified by RT-qPCR. Finally, immune infiltration and the tumor microenvironment (TME) were explored to examine the involvement of ENPP2 in EC progression. Results The datasets TCGA-UCEC (pertaining to EC), GSE34526, GSE137684, and GSE6798 (related to PCOS) were procured and subjected to analysis. The gene ENPP2 has been recognized as the shared element connecting PCOS and EC. Next, we observed a significant downregulation of ENPP2 expression in the granulosa cells in PCOS compared to the normal patients, while an upregulation of ENPP2 expression was observed in the endometrium of hyperandrogenic PCOS patients relative to the normal. In vitro, the WB revealed that 5-dihydrotestosterone (DHT) upregulated ENPP2 expression in Ishikawa and HEC-1-A cells. Additionally, we found that ENPP2 promoted the proliferation, migration, and invasion of Ishikawa and HEC-1-A cells. Subsequently, we discovered that overexpressed ENPP2 may lead to an increase in CYP19A1 (aromatase) and AR mRNA level. IF demonstrated that ENPP2 increased the expression of AR, suggesting a regulatory role for ENPP2 in hormonal response within PCOS and EC. Our findings indicated a significant correlation between ENPP2 expression and the modulation of immune responses.
Zhang et al. (2024) Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis. PeerJ 12:e18666 https://doi.org/10.7717/peerj.18666
Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia
Contamination of seafood products with multi-drug-resistant (MDR) bacteria is considered to be a potential source for the spread of MDR bacteria in communities. However, little is known about the extent of the contamination of seafood, in particular shrimp, with MDR bacteria in Saudi Arabia. In this study, imported frozen shrimp in retail markets were examined for the antimicrobial susceptibility patterns of Escherichia coli. Escherichia coli was isolated from 40 frozen shrimp samples; a total of 25 and 15 shrimp samples were imported from China and Vietnam, respectively. Of the 40 examined frozen shrimp samples, 30 tested positive for E. coli, resulting in an overall isolation rate of 75%, with a total of 180 isolates being identified. The largest number of positive samples for E. coli isolates (n = 140) were found in 22 out of 25 samples from frozen shrimp imported from China. Additionally, eight out of 15 samples from frozen shrimp imported from Vietnam were positive for E. coli, leading to the recovery of 40 isolates. Overall, the susceptibilities among E. coli isolates were observed against 99.4% for amikacin, augmentin and kanamycin, 95% for cefoxitin and 92.7% for ceftazidime and nitrofurantoin. High percentage of the isolates exhibited resistance to cephalothin (174/180, 96.6%), ampicillin (167/180, 92.7%), Cephalexin (163/180. 90.5%), piperacillin (156/180, 86.6%), ceftriaxone (123/180, 68.3%), nalidixic acid (95/180, 52.7%), trimethoprim sulphamethoxazole (90/180, 50%), and tetracycline (88/180, 48.8%). Additionally, the MDR (resistant to ≥3 different class of antimicrobials) rate among E. coli isolates was 94.4% (170/180). A relatively high intermediate resistance of 60% (108/180) was exhibited for aztreonam. Notably, E. coli showed 71 different antibiotic resistance patterns with the multiple antibiotic resistant (MAR) index ranging from 0.04 to 0.66 and 89.4% of E. coli isolates recorded very significant MAR indexes above the range of 0.2. In this study, we recorded highest antimicrobial co-resistance patterns of 162 (90%) isolates between cephalothin and ampicillin, followed by 158 (87.7%) isolates between cephalothin and cephalexin. Furthermore, and interestingly, the segregation of antimicrobial resistance patterns based on the source of country origin of frozen shrimp revealed few inter-country resistant patterns found interconnecting and this influenced 44 (24.4%) isolates overlapping between isolates origin from frozen shrimp imported from China and Vietnam. This study documents the antimicrobial resistance in E. coli isolated from imported frozen shrimp and the presence of MDR E. coli in shrimp consuming communities, which may pose a risk to public health and the transfer of resistant bacteria to the food chain and environment.
Alhabib et al. (2024) Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia. PeerJ 12:e18689 https://doi.org/10.7717/peerj.18689
Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer
Background Colorectal cancer (CRC) shows a high incidence in developed countries. This study established a prognosis signature based on N6-methyladenosine (m6A) regulators involved in CRC progression. Method The bulk RNA-seq data from the Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM) and GSE33113 CRC datasets were obtained from the cBioportal and GEO databases, and a total of 21 m6A regulators genes were collected from a previous study. The scRNA-seq analysis of the GSE146771 cohort was conducted applying the Seurat and harmony R packages. Consensus clustering based on the expressions of m6A regulators was performed with the ConsensusClusterPlus package. The ggGSEA package was used for the Gene Set Enrichment Analysis (GSEA). The un/multivariate and LASSO Cox analysis were performed applying the “survival” and “glmnet” packages for developing a risk model. The pRRophetic and GSVA packages were utilized to analyze potential drugs for CRC and immune infiltration in different risk groups, followed by the Kaplan–Meier (KM) survival and ROC analysis with the “survival” and “timeROC” packages. In vitro assays included the quantitative polymerase chain reaction (qPCR), wound healing and transwell were performed. Results CRC patients in the AC-ICAM cohort were assigned into three molecular subtypes (S1, 2 and 3) based on nine m6A regulator genes. Specifically, the prognostic outcome of the S3 was the most favorable, while that of the S1 was the worst and this subtype was associated with the activation of NF-kB, TNF-α and hypoxia pathways. Three key genes, namely, methyltransferase-like 3 (METTL3), insulinolike Growth Factor2 mRNA-Binding Protein 3 (IGF2BP3) and YTH domain-containing protein 2 (YTHDC2), selected from the 9 m6A regulator genes were combined into a RiskScore, which showed a high classification effectiveness in dividing the patients into high- and low-risk groups. Inhibition of the expression of METTL3A or that of IGF2BP3 suppressed the invasion and migration of CRC cells. Notably, the high-risk patients had higher immune cell infiltration to support the activation of multiple immune responses and exhibited significantly poor prognosis. Meanwhile, a nomogram with practical clinical value was developed based on the RiskScore and other clinical features. Finally, eight potential drugs associated with the RiskScore were identified, and CD4+ cells and Tregs were found to be closely associated with CRC progression. Conclusion The RiskScore model developed based on m6A regulators played a critical role in CRC development and can be considered as a prognosis predictor for patients with the cancer. The present discoveries will facilitate the diagnosis and clinical management of CRC patients.
Zhu et al. (2024) Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer. PeerJ 12:e18719 https://doi.org/10.7717/peerj.18719
Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China
Alfalfa (Medicago sativa L.) establishment is an effective strategy for grassland reconstruction in degraded ecosystems. However, the mechanisms underlying vegetation succession in reconstructed grasslands following alfalfa establishment remain elusive. In this study, we investigated vegetation community, soil quality and rhizosphere microbiota dynamics across a reconstructed grassland chronosequence in the loess region of Northwest China. A space-for-time substitution method was used to evaluate grassland vegetation coverage and alfalfa production performance in nine stands of different ages (1–50 years old). High-throughput sequencing was conducted to characterise rhizosphere microbial communities associated with alfalfa. The plant heights, yields and stem-to-leaf ratios of alfalfa all peaked in the 7-year-old stand and then decreased in older stands, with Stipa bungeana replacing alfalfa as the dominant species in the 50-year-old stand. Soil bulk density and major nutrient contents were highest in the artificial grassland (1–10 years). Soil enzyme activities (e.g., urease and sucrase) were enhanced in the transitional grassland (10–30 years), accompanied by enrichment of potentially beneficial microbial taxa (e.g., Actinobacteria and Mortierella) and functional fungi (e.g., saprotrophs and symbiotrophs) in the rhizosphere. Soil water content, total porosity and rhizosphere microbial diversity reached their maximum levels in the natural grassland (>30 years). The results indicate that alfalfa establishment alters soil structure and nutrient status in the short term, creating an optimal rhizosphere micro-environment. The improved soil conditions and rhizosphere microbiota are favourable for subsequent establishment of native grass species, leading to the formation of a stable semi-natural grasslands.
Ma et al. (2024) Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China. PeerJ 12:e18723 https://doi.org/10.7717/peerj.18723
Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids
Background Seedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species Pinus arizonica, P. durangensis, P. engelmannii, P. leiophylla, and P. teocote and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico. Methods Spearman’s coefficient (rs) and the unbiased conditional pseudo coefficient of determination (R2c) between each specific predictor and each response variable and their 95% confidence interval (CI95%) were determined using Random Forest, generalized linear model, and bootstrapping. By bootstrapping, the potential environmental heterogeneity inside the trial fields and its impact on the results were also quantified. Results Among the studied species and their hybrids moderate correlations were observed between the nursery seedling dimensions and the plant dimensions 44 months after planting. However, only weak significant correlations were found between survival rate (SR) and height (H) (rs = 0.10) and between SR and robustness index (HRCD) both before planting (rs = 0.06). Also, weak significant R2c values of the seedlings RCD, H and HRCD were detected with respect to the corresponding RCD, H and SR 44 months after planting, respectively. Furthermore, the predictor variable “seed provenance” (with 23 provenances) significantly explained the variation in the post-planting RCD, H and SR of the seedlings, with R2c values ranging from 0.10 to 0.15. The low width of the CI95% shows that the environmental conditions in the trial fields were quite homogeneous. Discussion The results also show that the inclusion of “confounding” variables in the statistical analysis of the study was crucial. Important factors to explain this low association could be the strong damage observed caused by pocket gopher, the typically low winter-spring precipitation in both field trials and adaptation factors. The study findings provide preliminary insights and information aimed at helping to design more appropriate standards for nurseries.
Ponce-Figueroa et al. (2024) Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids. PeerJ 12:e18725 https://doi.org/10.7717/peerj.18725
The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa
The spotted ragged-tooth shark, Carcharias taurus, is widely distributed in subtropical continental coastal seas. In South Africa, it is commonly found along the entire south and east coasts, including the iSimangaliso Wetland Park (IWP) in the far north, which is the largest Marine Protected Area on the South African coast. Pregnant females occur there for much of the year, with the largest aggregations in summer. It is here we used remote underwater photography (RUP), supplemented with in-situ surveys to photo-identify individuals, using unique spot patterns. Three known aggregation sites (Raggie Reef, Quarter-Mile Reef and Mushroom Rocks) were monitored over a 5-year period between 2018 and 2023. We photo-identified 574 individuals (569 females and five males) and registered 1,200 sightings, using images of the right flank. The identification of new individuals persisted throughout the study, with the discovery curve showing no signs of reaching an asymptote. A total of 97% (n = 550) of females observed were noticeably pregnant. Individuals were consistently identified across all sample years and at all three reefs, exhibiting movements among the three monitored sites. The reproductive cycle is generally regarded as 2 years, but some females appeared to have a 2-year rest between pregnancies. Raggie Reef, which lies in the sanctuary zone, emerged as the reef with the highest index of popularity, as individuals were present almost constantly (90% of the sampling days). The findings of this study confirm the crucial role that the IWP plays in the conservation of a species that is globally Critically Endangered.
Cerqueira et al. (2024) The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa. PeerJ 12:e18736 https://doi.org/10.7717/peerj.18736
Visual codon: a user-friendly Python program for viewing and optimizing gene GC content
Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of Escherichia coli as default and can work with other species as well. It provides a Graphical User Interface (GUI) interface, which allows users to change codons and intuitively see the effect of codon changes on local GC content. Our program brings convenience for the optimization of gene GC content and the subsequent gene cloning experiments.
Lin et al. (2024) Visual codon: a user-friendly Python program for viewing and optimizing gene GC content. PeerJ 12:e18755 https://doi.org/10.7717/peerj.18755