title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=986 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prebiotic supplementation effect on Escherichia coli and Salmonella species associated with experimentally induced intestinal coccidiosis in rabbits link: https://peerj.com/articles/10714 last-modified: 2021-01-22 description: BackgroundCoccidian infection may enhance the proliferation of gut Enterobacteriaceae. Bacterial infections in rabbits can negatively affect the body condition and cause high mortality, especially at young ages. Therefore, the effect of prebiotic supplementation on the presence of Escherichia coli and Salmonella species in rabbits experimentally infected with intestinal coccidiosis was investigated.MethodsThirty male rabbits aged 35–40 days were divided into three equal groups. These groups were; prebiotic supplemented (PS), positive control (PC), and negative control (NC) groups. The prebiotic group was supplemented with 2 g/L of Bio-Mos® until the end of the experiment. At day ten post prebiotic supplementation; the PS and PC groups were inoculated orally with 5.0 × 104 sporulated oocysts of mixed species of rabbit Eimeria. The daily fecal examination was carried out from the day 4 post-infection (PI) until the day 8 PI. At day 5 and day 8 PI, 5 rabbits from each group (PS, PC, and NC) were humanely slaughtered and parts of intestinal tissue were collected for microbiological analysis.ResultsThere was a significant decrease (P≤ 0.05) in the oocyst count in the PS group (25.12 × 104 ± 10.36) when compared with the PC group (43.43 × 104 ± 11.52) and this decrease was continued till the end of the experiment. Eleven E. coli isolates were detected in the collected samples with an overall prevalence of 24.4%. The highest prevalence of E. coli was in the PC group (13.33%) while the lowest one was in the PS group (4.44%). Meanwhile, four Salmonella serovars were isolated with an overall prevalence of 8.89%. The NC group showed one serovar (2.22%) and PC revealed three serovars (6.67%) while the prebiotic supplemented group didn’t show any salmonella isolate. Of E. coli isolates, five isolates (O78, O125, O152, O115 and O168) showed high resistance to florfenicol and neomycin (100%). Also, of salmonella serovars, thee serovars (Salmonella entrica subsp. enterica serovar Macclesfield, Salmonella entrica Subsp. enterica serovar Canada and Salmonella entrica Subsp. enterica serovar Kisangani) showed high resistance to sulphamazole, amoxicillin and flumequin (75%) while it was sensitive to levofloxacin and ciprofloxacine (75%). The bacterial colony in this study was the same results at days 5 and 8 PI.ConclusionThe use of prebiotic as prophylaxis in this experiment significantly reduced the prevalence of E. coli and salmonella associated with the intestinal coccidiosis in rabbits. creator: Shawky M. Aboelhadid creator: Shaymaa Hashem creator: El-Sayed Abdel-Kafy creator: Lilian N. Mahrous creator: Eman M. Farghly creator: Abdel-Azeem S. Abdel-Baki creator: Saleh Al-Quraishy creator: Asmaa A. Kamel uri: https://doi.org/10.7717/peerj.10714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Aboelhadid et al. title: Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes link: https://peerj.com/articles/10740 last-modified: 2021-01-22 description: BackgroundMelatonin is a hormone substance that exists in various living organisms. Since it was discovered in the pineal gland of cattle in 1956, the function of melatonin in animals has been roughly clarified. Nevertheless, in plants, the research on melatonin is still insufficient. Hulless barley (Hordeum vulgare L. var. nudum hook. f.) is a crop that originates from cultivated barley in the east, usually grown on the Qinghai-Tibet Plateau, becoming the most important food crop in this area. Although the genome and transcriptome research of highland barley has gradually increased recently years, there are still many problems about how hulless barley adapts to the cold climate of the Qinghai-Tibet Plateau.MethodsIn this study, we set three temperature conditions 25°C, 15°C, 5°C hulless barley seedlings, and at the same time soaked the hulless barley seeds with a 1 µM melatonin solution for 12 hours before the hulless barley seeds germinated. Afterwards, the growth and physiological indicators of hulless barley seedlings under different treatment conditions were determined. Meanwhile, the qRT-PCR method was used to determine the transcription level of the hulless barley circadian clock genes under different treatment conditions under continuous light conditions.ResultsThe results showed the possible mechanism by which melatonin pretreatment can promote the growth of hulless barley under cold stress conditions by studying the effect of melatonin on the rhythm of the circadian clock system and some physiological indicators. The results revealed that the application of 1 µM melatonin could alleviate the growth inhibition of hulless barley seedlings caused by cold stress. In addition, exogenous melatonin could also restore the circadian rhythmic oscillation of circadian clock genes, such as HvCCA1 and HvTOC1, whose circadian rhythmic phenotypes were lost due to environmental cold stress. Additionally, the results confirmed that exogenous melatonin even reduced the accumulation of key physiological indicators under cold stress, including malondialdehyde and soluble sugars.DiscussionOverall, these findings revealed an important mechanism that exogenous melatonin alleviated the inhibition of plant vegetative growths either by restoring the disrupted circadian rhythmic expression oscillations of clock genes, or by regulating the accumulation profiles of pivotal physiological indicators under cold stress. creator: Tianliang Chang creator: Yi Zhao creator: Hongyan He creator: Qianqian Xi creator: Jiayi Fu creator: Yuwei Zhao uri: https://doi.org/10.7717/peerj.10740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chang et al. title: Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii link: https://peerj.com/articles/10756 last-modified: 2021-01-22 description: BackgroundPseudomonas chlororaphis strain PA23 is a biocontrol agent that is able to protect canola against the pathogenic fungus Sclerotinia sclerotiorum. This bacterium secretes a number of metabolites that contribute to fungal antagonism, including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN) and degradative enzymes. In order to be successful, a biocontrol agent must be able to persist in the environment and avoid the threat of grazing predators. The focus of the current study was to investigate whether PA23 is able to resist grazing by the protozoan predator Acanthamoeba castellanii (Ac) and to define the role of bacterial metabolites in the PA23-Ac interaction.MethodsAc was co-cultured with PA23 WT and a panel of derivative strains for a period of 15 days, and bacteria and amoebae were enumerated on days 1, 5, 10 and 15. Ac was subsequently incubated in the presence of purified PRN, PHZ, and KCN and viability was assessed at 24, 48 and 72 h. Chemotactic assays were conducted to assess whether PA23 compounds exhibit repellent or attractant properties towards Ac. Finally, PA23 grown in the presence and absence of amoebae was subject to phenotypic characterization and gene expression analyses.ResultsPRN, PHZ and HCN were found to contribute to PA23 toxicity towards Ac trophozoites, either by killing or inducing cyst formation. This is the first report of PHZ-mediated toxicity towards amoebae. In chemotaxis assays, amoebae preferentially migrated towards regulatory mutants devoid of extracellular metabolite production as well as a PRN mutant, indicating this antibiotic has repellent properties. Co-culturing of bacteria with amoebae led to elevated expression of the PA23 phzI/phzR quorum-sensing (QS) genes and phzA and prnA, which are under QS control. PHZ and PRN levels were similarly increased in Ac co-cultures, suggesting that PA23 can respond to predator cues and upregulate expression of toxins accordingly.ConclusionsPA23 compounds including PRN, PHZ and HCN exhibited both toxic and repellent effects on Ac. Co-culturing of bacteria and amoebae lead to changes in bacterial gene expression and secondary metabolite production, suggesting that PA23 can sense the presence of these would-be predators and adjust its physiology in response. creator: Akrm Ghergab creator: Carrie Selin creator: Jennifer Tanner creator: Ann Karen Brassinga creator: Teresa Dekievit uri: https://doi.org/10.7717/peerj.10756 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ghergab et al. title: Estimating the average daily rainfall in Thailand using confidence intervals for the common mean of several delta-lognormal distributions link: https://peerj.com/articles/10758 last-modified: 2021-01-22 description: The daily average natural rainfall amounts in the five regions of Thailand can be estimated using the confidence intervals for the common mean of several delta-lognormal distributions based on the fiducial generalized confidence interval (FGCI), large sample (LS), method of variance estimates recovery (MOVER), parametric bootstrap (PB), and highest posterior density intervals based on Jeffreys’ rule (HPD-JR) and normal-gamma-beta (HPD-NGB) priors. Monte Carlo simulation was conducted to assess the performance in terms of the coverage probability and average length of the proposed methods. The numerical results indicate that MOVER and PB provided better performances than the other methods in a variety of situations, even when the sample case was large. The efficacies of the proposed methods were illustrated by applying them to real rainfall datasets from the five regions of Thailand. creator: Patcharee Maneerat creator: Sa-Aat Niwitpong uri: https://doi.org/10.7717/peerj.10758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Maneerat and Niwitpong title: Genome-wide identification, evolution, and expression of the SNARE gene family in wheat resistance to powdery mildew link: https://peerj.com/articles/10788 last-modified: 2021-01-22 description: SNARE proteins mediate eukaryotic cell membrane/transport vesicle fusion and act in plant resistance to fungi. Herein, 173 SNARE proteins were identified in wheat and divided into 5 subfamilies and 21 classes. The number of the SYP1 class type was largest in TaSNAREs. Phylogenetic tree analysis revealed that most of the SNAREs were distributed in 21 classes. Analysis of the genetic structure revealed large differences among the 21 classes, and the structures in the same group were similar, except across individual genes. Excluding the first homoeologous group, the number in the other homoeologous groups was similar. The 2,000 bp promoter region of the TaSNARE genes were analyzed, and many W-box, MYB and disease-related cis-acting elements were identified. The qRT-PCR-based analysis of the SNARE genes revealed similar expression patterns of the same subfamily in one wheat variety. The expression patterns of the same gene in resistant/sensitive varieties largely differed at 6 h after infection, suggesting that SNARE proteins play an important role in early pathogen infection. Here, the identification and expression analysis of SNARE proteins provide a theoretical basis for studies of SNARE protein function and wheat resistance to powdery mildew. creator: Guanghao Wang creator: Deyu Long creator: Fagang Yu creator: Hong Zhang creator: Chunhuan Chen creator: Yajuan Wang creator: Wanquan Ji uri: https://doi.org/10.7717/peerj.10788 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: A review of the carotid artery and facial nerve canal systems in extant turtles link: https://peerj.com/articles/10475 last-modified: 2021-01-21 description: The cranial circulation and innervation systems of turtles have been studied for more than two centuries and extensively used to understand turtle systematics. Although a significant number of studies related to these structures exists, a broader comprehension of variation across the tree has been hindered by poor sampling and a lack of synthetic studies that addressed both systems together. We here provide new insights regarding the carotid circulation and facial nerve innervation systems in a broad set of extant turtles using CT (computed tomography) scans, which allow us to trace the canals these structures form in bone and understand the interaction between both systems. We document that the palatine artery, including the lateral carotid canal, is absent in all pleurodires and carettochelyids and was likely reduced or lost several times independently within Testudinoidea. We also highlight osteological correlates for the location of the mandibular artery. We finally summarize variation regarding the placement of the mandibular artery, location of the geniculate ganglion, placement of the hyomandibular and vidian nerves, and situations where we recommend caution when assessing canals in fossils. A morphometric study confirms that the relative sizes of the carotid canals are correlated with one another. Our results have the potential for building new phylogenetic characters and investigating the circulation systems of fossil taxa, which are expected to shed light on the evolution of the circulation system of turtles and clarify some unresolved relationships between fossil turtle clades. creator: Yann Rollot creator: Serjoscha W. Evers creator: Walter G. Joyce uri: https://doi.org/10.7717/peerj.10475 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Rollot et al. title: COVID-19 mortality in cancer patients: a report from a tertiary cancer centre in India link: https://peerj.com/articles/10599 last-modified: 2021-01-21 description: BackgroundCancer patients, especially those receiving cytotoxic therapy, are assumed to have a higher probability of death from COVID-19. We have conducted this study to identify the Case Fatality Rate (CFR) in cancer patients with COVID-19 and have explored the relationship of various clinical factors to mortality in our patient cohort.MethodsAll confirmed cancer cases presented to the hospital from June 8 to August 20, 2020, and developed symptoms/radiological features suspicious of COVID-19 were tested by Real-time polymerase chain reaction assay and/or cartridge-based nucleic acid amplification test from a combination of naso-oropharyngeal swab for SARS-CoV-2. Clinical data, treatment details, and outcomes were assessed from the medical records.ResultsOf the total 3,101 cancer patients admitted to the hospital, 1,088 patients were tested and 186 patients were positive for SARS-CoV-2. The CFR in the cohort was 27/186 (14.52%). Univariate analysis showed that the risk of death was significantly associated with the presence of any comorbidity (OR: 2.68; (95% CI [1.13–6.32]); P = 0.025), multiple comorbidities (OR: 3.01; (95% CI [1.02–9.07]); P = 0.047 for multiple vs. single), and the severity of COVID-19 presentation (OR: 27.48; (95% CI [5.34–141.49]); P < 0.001 for severe vs. not severe symptoms). Among all comorbidities, diabetes (OR: 3.31; (95% CI [1.35–8.09]); P = 0.009) and cardiovascular diseases (OR: 3.77; (95% CI [1.02–13.91]); P = 0.046) were significant risk factors for death. Anticancer treatments including chemotherapy, surgery, radiotherapy, targeted therapy, and immunotherapy administered within a month before the onset of COVID-19 symptoms had no significant effect on mortality.ConclusionTo the best of our knowledge, this is the first study from India reporting the CFR, clinical associations, and risk factors for mortality in SARS-CoV-2 infected cancer patients. Our study shows that the frequency of COVID-19 in cancer patients is high. Recent anticancer therapies are not associated with mortality. Pre-existing comorbidities, especially diabetes, multiple comorbidities, and severe symptoms at presentation are significantly linked with COVID-19 related death in the cohort. creator: Anurag Mehta creator: Smreti Vasudevan creator: Anuj Parkash creator: Anurag Sharma creator: Tanu Vashist creator: Vidya Krishna uri: https://doi.org/10.7717/peerj.10599 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mehta et al. title: Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench) link: https://peerj.com/articles/10617 last-modified: 2021-01-21 description: To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions. creator: Jie Li creator: Xinhao Liu creator: Qingmei Wang creator: Junyan Sun creator: Dexian He uri: https://doi.org/10.7717/peerj.10617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: The influence of rare birds on observer effort and subsequent rarity discovery in the American birdwatching community link: https://peerj.com/articles/10713 last-modified: 2021-01-21 description: Birdwatching is a rapidly growing pastime, increasingly involving the pursuit of rare birds as birders build lists of species they encounter. We expected reports of rare bird discoveries to quickly draw birders to locations, and that the increased attention at those locations would decay over time. We hypothesized that magnitude of draw and rates of decay would vary depending on characteristics of the species and the geographic locations where rarities were discovered. Discoveries of additional rarities might affect both the draw and decay, so we also quantified empirical evidence for the Patagonia Picnic Table Effect (PPTE), a social feedback loop where rarity discoveries are presumed to lead to additional rarity discoveries because of the elevated levels of birder activity once an initial rarity is reported. Although commonly invoked, supporting evidence for the PPTE hypothesis is anecdotal. We used 10 years of eBird data (2008–2017) in the United States to (1) understand birding activity when rarities were reported and the factors associated with draw and decay, and (2) assess the frequency at which initial rarity discoveries lead to reports of additional rarities. Across 273 rarity events, birder effort, as indexed by numbers of eBird checklists, increased above the pre-event baseline level, with the magnitude of draw varying geographically. We found no indication that draw was influenced by species identity or rarity-level, but latitude and distance to small airport proved important in drawing additional eBirders to rare bird discoveries. Mean draw of rarities and mean number of checklists from the same locations prior to each rarity discovery grew through the ten years, suggesting an increased influence of eBird on birder behavior in general. Decay rates in birder effort were more gradual in rare bird events with longer durations. Effort declined below baseline-levels after rarities went undetected, suggesting, “location-fatigue” following rarity events. Results did not support the PPTE hypothesis. Controlling for site-specific circumstances, birders had no better chance of finding additional rarities during events than at times outside events. Our results emphasize that eBird checklist quantity at rarity events follows a predictable but variable pattern of draw and decay influenced by location and time since rarity discovery; that birders have statistically similar chances of finding rarities during normal “baseline” birding activities as they do when known rarities are present; and that eBird represents a largely untapped resource for studying factors that influence levels of birding activity. creator: Jesse A. Laney creator: Tyler A. Hallman creator: Jenna R. Curtis creator: W. Douglas Robinson uri: https://doi.org/10.7717/peerj.10713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Laney et al. title: Evaluation of two fluorescence immunoassays for the rapid detection of SARS-CoV-2 antigen—new tool to detect infective COVID-19 patients link: https://peerj.com/articles/10801 last-modified: 2021-01-21 description: BackgroundReal-Time Reverse-Transcription Polymerase Chain Reaction (RT-PCR) is currently the only recommended diagnostic method for SARS-CoV-2. However, rapid immunoassays for SARS-CoV-2 antigen could significantly reduce the COVID-19 burden currently weighing on laboratories around the world.MethodsWe evaluated the performance of two rapid fluorescence immunoassays (FIAs), SOFIA SARS Antigen FIA (Quidel Corporation, San Diego, CA, USA) and STANDARD F COVID-19 Ag FIA (SD Biosensor Inc., Gyeonggi-do, Republic of Korea), which use an automated reader. The study used 64 RT-PCR characterized clinical samples (32 positive; 32 negative), which consisted of nasopharyngeal swabs in universal transport medium.ResultsOf the 32 positive specimens, all from patients within 5 days of symptom onset, the Quidel and SD Biosensor assays detected 30 (93.8%) and 29 (90.6%) samples, respectively. Among the 27 samples with high viral loads (Ct ≤ 25), the two tests had a sensitivity of 100%. Specificity was 96.9% for both kits.ConclusionThe high performance of the evaluated FIAs indicates a potential use as rapid and PCR-independent tools for COVID-19 diagnosis in early stages of infection. The excellent sensitivity to detect cases with viral loads above ~106 copies/mL (Ct values ≤ 25), the estimated threshold of contagiousness, suggests that the assays might serve to rapidly identify infective individuals. creator: Lorena Porte creator: Paulette Legarraga creator: Mirentxu Iruretagoyena creator: Valeska Vollrath creator: Gabriel Pizarro creator: Jose Munita creator: Rafael Araos creator: Thomas Weitzel uri: https://doi.org/10.7717/peerj.10801 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Porte et al.