Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor
Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.
Baeza et al. (2017) Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor. PeerJ 5:e3004 https://doi.org/10.7717/peerj.3004
Risk analysis of colorectal cancer incidence by gene expression analysis
Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis.
Shangkuan et al. (2017) Risk analysis of colorectal cancer incidence by gene expression analysis. PeerJ 5:e3003 https://doi.org/10.7717/peerj.3003
Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells
Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
Okada et al. (2017) Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells. PeerJ 5:e2999 https://doi.org/10.7717/peerj.2999
ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium
Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort.
Kulik et al. (2017) ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium. PeerJ 5:e2992 https://doi.org/10.7717/peerj.2992
Opportunities drive the global distribution of protected areas
Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize the predominant opportunistic nature that the establishment of protected areas has had until present times.
Baldi et al. (2017) Opportunities drive the global distribution of protected areas. PeerJ 5:e2989 https://doi.org/10.7717/peerj.2989
The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study
Background Paroxysmal sympathetic hyperactivity (PSH) results and aggravates in secondary brain injury, which seriously affects the prognosis of severe traumatic brain injury patients. Although several studies have focused on the treatment of PSH, few have concentrated on its prevention. Methods Ninety post-operation (post-op) severe traumatic brain injury (sTBI) patients admitted from October 2014 to April 2016 were chosen to participate in this study. Fifty of the post-op sTBI patients were sedated with dexmedetomidine and were referred as the “dexmedetomidine group” (admitted from May 2015 to April 2016). The other 40 patients (admitted from October 2014 to May 2015) received other sedations and were referred as the “control group.” The two groups were then compared based on their PSH scores and the scores and ratios of those patients who met the criteria of “probable,” “possible” and “unlikely” using the PSH assessment measure (PSH-AM) designed by Baguley et al. (2014). The durations of the neurosurgery intensive care unit (NICU) and hospital stays and the Glasgow outcome scale (GOS) values for the two groups were also compared to evaluate the therapeutic effects and the patients’ prognosis. Results The overall PSH score for the dexmedetomidine group was 5.26 ± 4.66, compared with 8.58 ± 8.09 for the control group. The difference between the two groups’ PSH scores was significant (P = 0.017). The score of the patients who met the criterion of “probable” was 18.33 ± 1.53 in the dexmedetomidine group and 22.63 ± 2.97 in the control group, and the difference was statistically significant (P = 0.045). The ratio of patients who were classified as “unlikely” between the two groups was statistically significant (P = 0.028); that is, 42 (84%) in the dexmedetomidine group and 25 (62.5%) in the control group. The differences in NICU, hospital stays and GOS values between the two groups were not significant. Conclusion Dexmedetomidine has a preventive effect on PSH in sTBI patients who have undergone surgery.
Tang et al. (2017) The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study. PeerJ 5:e2986 https://doi.org/10.7717/peerj.2986
Is there a relation between dental anxiety, fear and general psychological status?
Background Dental anxiety is a widespread problem in many populations. This problem can be a barrier to dental care and may lead to poor oral health. Dental anxiety may be related to psychological status. Aims The aim of the present study was to assess the levels of dental anxiety, dental fear, Beck Depression, and state-trait anxiety according to age, gender and education level in patients at the periodontology clinic in the Diyarbakır Mouth and Dental Health Center. Study Design A total of 231 patients (115 males, 116 females) filled out dental fear scale (DFS), dental anxiety scale (DAS), Beck Depression Inventory (BDI), state-trait anxiety inventory-state (STAI-S), and state-trait anxiety inventory–trait (STAI-T) questionnaires, and evaluations of DFS, DAS, BDI, STAI-S, and STAI-T were conducted according to age, gender, and education level. Results The mean DFS, DAS, BDI, STAI-T, and STAI –S were 45.64, 9.15, 13.16, 38.90, and 40.18, respectively. There was a significant association among DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). These surveys scores were significantly higher in females than males (p < 0.05). The results of this study indicated that gender age and education level have important effects on DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). Conclusion Dental anxiety and dental fear were found to be related to psychological status (BDI, STAI-S, and STAI-T) over time. There are some patients with unaddressed psychological distress.
Talo Yildirim et al. (2017) Is there a relation between dental anxiety, fear and general psychological status?. PeerJ 5:e2978 https://doi.org/10.7717/peerj.2978
Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground
White-streaked grouper (Epinephelus ongus) is an important fisheries target and forms spawning aggregations at particular spawning grounds. The aims of the present study were to investigate the ecological characteristics of annual spawning aggregations such as (1) spatial variations in the density of E. ongus at the spawning ground, (2) the relationship between fish density and environmental variables, (3) inter-annual variations in the spawning aggregation, (4) the proportion of males to females at the spawning ground for several days pre—and post-spawning and (5) the relationship between male density and female density at the protected spawning ground, based on observations over five years at an Okinawan coral reef. Although the protected spawning ground area was large (ca. 2,500 m × 700 m), high density of E. ongus (over 25 individuals per 100 m2) was found in a limited area (within c.a. 750 m × 50 m). Current velocity and coverage of rocks had significant positive effects on the spatial distribution of E. ongus at the spawning ground. Inter-annual variation in the degree of aggregation was found and this variation was explained by the annual variation of mean seawater temperature during 40 days before the spawning day. The male–female ratio (male:female) at the spawning ground was ca. 3:1 for three years (May 2012, May 2014 and May 2015) whereas >13:1 for one year (May 2013). Significant positive relationships between male density and female density were found at the aggregation sites. It is suggested that E. ongus use aggregation sites with greater current velocity to reduce the risk of egg predation and seawater temperature is one of the main factors that is responsible for determining the degree of aggregation. It is also suggested that females possibly select sites with a greater density of males and this selection behavior might be the reason why females arrived at the spawning ground after the arrival of the males. For effective management of spawning grounds, precise site selection as well as the duration of the protection period are suggested to be key aspects to protect the spawning aggregations of E. ongus, which have been currently achieved at the spawning ground.
Nanami et al. (2017) Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground. PeerJ 5:e3000 https://doi.org/10.7717/peerj.3000
Modafinil decreases anxiety-like behaviour in zebrafish
Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish.
Johnson et al. (2017) Modafinil decreases anxiety-like behaviour in zebrafish. PeerJ 5:e2994 https://doi.org/10.7717/peerj.2994
An open source device for operant licking in rats
We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.
Longley et al. (2017) An open source device for operant licking in rats. PeerJ 5:e2981 https://doi.org/10.7717/peerj.2981