Do the regular annual extreme water level changes affect the seasonal appearance of Anabaena in Poyang Lake?
Background Poyang Lake is an ecosystem experiencing annual variations in water level of up to 14 m. Water level changes were 8.03 and 11.22 m, respectively, in the years 2013 and 2014. The biomass and heterocyst frequency of Anabaena increased in the summers of recent years. Methods A weekly to bi-weekly monitoring from June to November 2013 and 2014 was set up to explain the variations of Anabaena appearance in different phases of the water level. Results Anabaena was present in the lake throughout the year. The average relative biomass of Anabaena in the present study was over 40%, being most abundant in summer. The average heterocyst frequency was 0.23% in 2013 and 0.76% in 2014. Correlation analysis indicated a positive trend of Anabaena biomass with water temperature and water level and a negative one with total nitrogen (TN), which is the reason for the increase of heterocyst frequency in 2013 and 2014. Heterocyst frequency of Anabaena was positively correlated with water temperature, water level and PO4-P, and negatively with dissolved inorganic nitrogen (DIN/DIP), NO3-N and TN. Moreover, water temperature and DIN/DIP were significantly correlated with water level, indicating that water level changes have a direct effect on Anabaena and heterocyst formation in Poyang Lake. Conclusions The results of this study support the hypothesis that increasing biomass and heterocyst formation of Anabaena can be primarily caused by seasonal changes of the water level in Poyang Lake.
Qian et al. (2019) Do the regular annual extreme water level changes affect the seasonal appearance of Anabaena in Poyang Lake?. PeerJ 7:e6608 https://doi.org/10.7717/peerj.6608
Comparison of long-term kidney functions after radical nephrectomy and simple nephrectomy
Objective To determine if there is a difference in proceeding to CKD between patients who had undergone radical nephrectomy (RN) and simple nephrectomy (SN) for different indications by comparing the short- and long-term renal function. Materials and Methods We retrospectively analyzed the records of all patients who underwent nephrectomy (either for malign or benign indications) in our clinic between January 2007 and September 2017. The patients were divided into 2 groups according the type of surgery: 1) Radical nephrectomy Group, 2) Simple Nephrectomy Group. Renal function was evaluated with Glomerular Filtration Rate (GFR) calculated using the MDRD formula. Results A total of 276 patients were included in the study. There were 202 patients in RN Group and 74 patients in SN Group. The mean age of the patients in RN Group and SN Group were age 59,2 ± 11,5 and 49,9 ± 15,1 years, respectively (p = 0.001). GFR levels of patients in RN Group versus SN Group were as follows: Preoperative period: 84.9 vs. 81 mL/min/1.73 m2; postoperative 1st day: 60.5 vs. 84.4 mL/min/1.73 m2, postoperative 1st month 58.9 vs. 76 mL/min/1.73 m2, postoperative 1st year: 59.5 vs. 74.1 mL/min/1.73 m2; at last control 60.3 and 76.1 mL/min/1.73 m2. While preoperative GFR was found to be similar in two groups (p = 0.26), postoperative GFR values were found to be significantly lower in Group RN (p < 0.001). In comparison of the decrease in GFR in two groups at last follow-up, significantly higher decrease was observed in RN Group, 29% vs. 6%, (p < 0.05). Conclusion The decrease in GFR exists more common and intensive after RN compared to SN. In long-term, compensation mechanisms that develop after sudden nephron loss like radical nephrectomy deteriorates kidney function more than gradual nephron loss as in benign etiologies which indicates simple nephrectomy.
Olcucuoglu et al. (2019) Comparison of long-term kidney functions after radical nephrectomy and simple nephrectomy. PeerJ 7:e6701 https://doi.org/10.7717/peerj.6701
The prevalence of Pseudomonas aeruginosa and multidrug resistant Pseudomonas aeruginosa in healthy captive ophidian
Background Snakes are globally considered as pet animals, and millions of ophidians are bred in captivity. Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium that can act as an opportunistic pathogen of man and animals and is frequently present in the oral and cloacal microbiota of healthy ophidians. It can cause severe clinical diseases and often shows antibiotic resistance. The aim of this study was to evaluate the prevalence and antibiotic resistance profiles of P. aeruginosa isolated from the cloacal microbiota of a large population sample of healthy captive ophidians and to evaluate the statistical associations with farming conditions. Methods A total of 419 cloacal swabs were collected from snakes belonging to the Boidae (n = 45), Colubridae (n = 48) and Pythonidae (n = 326) families and inoculated onto complete culture media. Food, water and bedding samples were also analyzed. The antimicrobial susceptibility of P. aeruginosa isolates was evaluated through the Kirby-Bauer agar diffusion test. Statistical analyses were performed with the chi-square test. Results The prevalence of P. aeruginosa was 59.9%, and 35.5% of these strains were multidrug resistant (MDR). The prevalence of MDR P. aeruginosa was significantly higher in adult samples than in young samples, and widespread resistance to Cephalosporins, Polymyxins and Sulfonamides was observed. Statistically significant differences in the prevalence of P. aeruginosa were observed depending on the farm size and snake family. Feeding thawed prey was associated with a higher P. aeruginosa and MDR P. aeruginosa prevalence. Moreover, snakes fed home-raised prey had a significantly higher MDR P. aeruginosa prevalence than snakes fed commercially available feed. Less frequent terrarium cleaning was associated with a higher MDR P. aeruginosa prevalence. On the other hand, snake reproductive status was not significantly associated with P. aeruginosa or MDR P. aeruginosa prevalence. All food, water and bedding samples were negative for P. aeruginosa presence. Discussion The overall P. aeruginosa prevalence found in this study was lower than that found by other authors, but a high proportion of the isolates were MDR. This study highlighted the presence of constitutive (such as age and taxonomic family) and managerial (farm size, cleaning cycle frequency and food type) factors associated with P. aeruginosa and/or MDR P. aeruginosa prevalence. Good breeding management and proper antibiotic treatment of P. aeruginosa infections could help reduce the presence of P. aeruginosa and MDR P. aeruginosa in the gut microbiota of snakes and consequently reduce the risk to public health.
Sala et al. (2019) The prevalence of Pseudomonas aeruginosa and multidrug resistant Pseudomonas aeruginosa in healthy captive ophidian. PeerJ 7:e6706 https://doi.org/10.7717/peerj.6706
Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii)
Objective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. In this study, we performed small RNA deep sequencing and microarray hybridization to identify potential sturgeon piRNAs. Methods Male and female sturgeon gonads were collected and used for small RNA sequencing on an Illumina HiSeq platform with the validation of piRNA expression by microarray chip. The program Bowtie and k-mer scheme were performed to filter small RNA reads and discover potential sturgeon piRNAs. A known piRNA database, the coding sequence (CDS), 5′ and 3′ untranslated region (UTR) database of the A. Schrenckii transcriptome, Gene Ontology (GO) database and KEGG pathway database were searched subsequently to analyze the potential bio-function of sturgeon piRNAs. Results A total of 875,679 putative sturgeon piRNAs were obtained, including 93 homologous to known piRNAs and hundreds showing sex-specific and sex-biased expression. Further analysis showed that they are predominant in both the ovaries and testes and those with a sex-specific expression pattern are nearly equally distribution between sexes. This may imply a relevant role in sturgeon gonadal development. KEGG pathway and GO annotation analyses indicated that they may be related to sturgeon reproductive processes. Conclusion Our study provides the first insights into the gonadal piRNAs in a sturgeon species and should serve as a useful resource for further elucidation of the gene regulation involved in the sex differentiation of vertebrates. These results should also facilitate the technological development of early sex identification in sturgeon aquaculture.
Yuan et al. (2019) Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii). PeerJ 7:e6709 https://doi.org/10.7717/peerj.6709
An experimental study on the early diagnosis of traumatic brain injury in rabbits based on a noncontact and portable system
Closed cerebral hemorrhage (CCH) is a common symptom in traumatic brain injury (TBI) patients who suffer intracranial hemorrhage with the dura mater remaining intact. The diagnosis of CCH patients prior to hospitalization and in the early stage of the disease can help patients get earlier treatments that improve outcomes. In this study, a noncontact, portable system for early TBI-induced CCH detection was constructed that measures the magnetic induction phase shift (MIPS), which is associated with the mean brain conductivity caused by the ratio between the liquid (blood/CSF and the intracranial tissues) change. To evaluate the performance of this system, a rabbit CCH model with two severity levels was established based on the horizontal biological impactor BIM-II, whose feasibility was verified by computed tomography images of three sections and three serial slices. There were two groups involved in the experiments (group 1 with 10 TBI rabbits were simulated by hammer hit with air pressure of 600 kPa by BIM-II and group 2 with 10 TBI rabbits were simulated with 650 kPa). The MIPS values of the two groups were obtained within 30 min before and after injury. In group 1, the MIPS values showed a constant downward trend with a minimum value of −11.17 ± 2.91° at the 30th min after 600 kPa impact by BIM-II. After the 650 kPa impact, the MIPS values in group 2 showed a constant downward trend until the 25th min, with a minimum value of −16.81 ± 2.10°. Unlike group 1, the MIPS values showed an upward trend after that point. Before the injury, the MIPS values in both group 1 and group 2 did not obviously change within the 30 min measurement. Using a support vector machine at the same time point after injury, the classification accuracy of the two types of severity was shown to be beyond 90%. Combined with CCH pathological mechanisms, this system can not only achieve the detection of early functional changes in CCH but can also distinguish different severities of CCH.
Yang et al. (2019) An experimental study on the early diagnosis of traumatic brain injury in rabbits based on a noncontact and portable system. PeerJ 7:e6717 https://doi.org/10.7717/peerj.6717
Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis
The anthrax toxin is a virulence factor produced by the bacterium Bacillus anthracis. Transcription of anthrax toxin genes is controlled by the transcription factor AtxA. Thus, AtxA is thought to be a key factor for the pathogenicity of B. anthracis. Despite its important role in B. anthracis infection, the molecular mechanism by which AtxA controls expression of anthrax toxin remains unclear. This study aimed to characterize the molecular mechanism of AtxA-mediated regulation of protective antigen (PA), a component of anthrax toxin encoded by the pagA gene. First, the interaction between the upstream region of pagA and AtxA was evaluated in vivo by constructing a transcriptional fusion of the upstream region with an auxotrophic marker. The results showed that (i) the upstream region of pagA suppressed transcription of the downstream gene and (ii) AtxA recovered suppressed transcription. Second, in vitro analysis using a gel mobility shift assay was performed to evaluate binding specificity of the AtxA–DNA interaction. The result showed sequence-independent binding of AtxA to DNA. Taken together, our findings suggest that the expression of PA was suppressed by the upstream region of pagA and that an interaction of AtxA and the upstream region releases the suppression.
Toyomane et al. (2019) Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis. PeerJ 7:e6718 https://doi.org/10.7717/peerj.6718
Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana
Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed Arabidopsis Skp1-Like (ASK) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in ASK genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the ASK2 coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of ASK1 yield high levels of expression implied negative expression regulation of ASK1 by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.
Hua et al. (2019) Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana. PeerJ 7:e6740 https://doi.org/10.7717/peerj.6740
Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods
Background The application of an appropriate extraction method is a relevant factor for the success of all molecular studies. Methods Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated. Results Although low DNA concentrations were measured for all methods, the results showed that—with the exception of two methods—the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results. Discussion In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.
Lienhard et al. (2019) Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ 7:e6753 https://doi.org/10.7717/peerj.6753
Crowdsourcing in medical research: concepts and applications
Crowdsourcing shifts medical research from a closed environment to an open collaboration between the public and researchers. We define crowdsourcing as an approach to problem solving which involves an organization having a large group attempt to solve a problem or part of a problem, then sharing solutions. Crowdsourcing allows large groups of individuals to participate in medical research through innovation challenges, hackathons, and related activities. The purpose of this literature review is to examine the definition, concepts, and applications of crowdsourcing in medicine. This multi-disciplinary review defines crowdsourcing for medicine, identifies conceptual antecedents (collective intelligence and open source models), and explores implications of the approach. Several critiques of crowdsourcing are also examined. Although several crowdsourcing definitions exist, there are two essential elements: (1) having a large group of individuals, including those with skills and those without skills, propose potential solutions; (2) sharing solutions through implementation or open access materials. The public can be a central force in contributing to formative, pre-clinical, and clinical research. A growing evidence base suggests that crowdsourcing in medicine can result in high-quality outcomes, broad community engagement, and more open science.
Tucker et al. (2019) Crowdsourcing in medical research: concepts and applications. PeerJ 7:e6762 https://doi.org/10.7717/peerj.6762
Age, growth, mortality and recruitment of thin sharpbelly Toxabramis swinhonis Günther, 1873 in three shallow lakes along the middle and lower reaches of the Yangtze River basin, China
Despite being the most dominant and widespread small fish species in the lakes along the middle and lower reaches of the Yangtze River basin, Toxabramis swinhonis has been paid little attention by fisheries scientists and little is known about its population characteristics. For this reason, we estimated age, growth, mortality and recruitment of this species based on three shallow lakes, Biandantang Lake, Shengjin Lake and Kuilei Lake (BDT, SJH and KLH, respectively) in this region. A total of 13,585 (8,818 in BDT, 2,207 in SJH and 2,560 in KLH) individuals were collected during monthly sampling from July 2016 to September 2017. The results revealed that the age structures of T. swinhonis consisted of four age groups (0+–3+), with 0+–1+ year old fish comprising more than 98% of the samples. Allometric growth patterns were displayed by fish from all sampling sites and the von Bertalanffy growth functions estimated were Lt = 173.25 (1 – e−1.20 (t + 1.09)): BDT; Lt = 162.75 (1 – e−1.20 (t + 1.08)): SJH and Lt = 215.25 (1 – e−1.20 (t + 1.12)): KLH, respectively. The rates of total mortality (Z), natural mortality (M) and fishing mortality (F) at BDT, SJH and KLH were computed as 5.82, 5.50 and 4.55 year−1; 1.89, 1.87 and 1.75 year−1; 3.93, 3.63 and 2.80 year−1, respectively. Meanwhile, growth performance indices (φ′) were 0.68 (in BDT), 0.66 (in SJH) and 0.62 (in KLH), which indicated that T. swinhonis were overfished slightly in all study areas. Area-specific recruitment patterns were similar to each other, displaying evidence of batch spawning, with major peaks in April and August, accounting for 92.21% (BDT), 88.21% (SJH) and 88.73% (KLH) of total recruitment, respectively. These results showed that brief generation-time, fast growth rate, relatively high natural mortality rate and strong reproductive capacity (r-strategies) are reasons why this species became the most dominant species in many lakes of China.
Dong et al. (2019) Age, growth, mortality and recruitment of thin sharpbelly Toxabramis swinhonis Günther, 1873 in three shallow lakes along the middle and lower reaches of the Yangtze River basin, China. PeerJ 7:e6772 https://doi.org/10.7717/peerj.6772