Optimization of extraction conditions and determination of purine content in marine fish during boiling
Background Gout is the second most common metabolic disease affecting human health. The disease of gout is closely related to the level of uric acid, which is the end-product of human purine metabolism. Moreover, food is the main way of external ingestion of purine. Method A simple and time-saving method was developed to extract purines like adenine, hypoxanthine, guanine, and xanthine from marine fish by single factor design combined with Box–Behnken. The contents of these purines in the edible parts and internal organs of marine fish, as well as Scophthalmus maximus, were determined by high-performance liquid chromatography to investigate the relationship between the boiling process and purine content. Result The mixed-acid method was chosen for the extraction of purine bases and the extraction conditions were as follows: mixture acid 90.00% TFA/80.00% FA (v/v, 1:1); hydrolysis temperature 90.00 °C; time 10.00 min; liquid-to-solid ratio 30:1. The total purine content of the edible parts (eyes, dorsal muscles, abdominal muscles, and skin) was the highest in Scophthalmus maximus, followed by sphyraena, Sardinella, Trichiurus lepturus, Scomberomorus niphonius, Pleuronectiformes, Sea catfish, Anguillidae, and Rajiformes. Moreover, boiling significantly reduced the purine content in the marine fish because of the transfer of the purines to the cooking liquid during boiling. Scophthalmus maximus, Sphyraena, and Sardinella were regard as high-purine marine fish, which we should eat less. We also confirmed that boiling significantly transferred purine bases from fish to cooking liquid. Thus, boiling could reduce the purine content of fish, thereby reducing the risk of hyperuricemia and gout.
Li et al. (2019) Optimization of extraction conditions and determination of purine content in marine fish during boiling. PeerJ 7:e6690 https://doi.org/10.7717/peerj.6690
Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States
Background Coagulase negative Staphylococcus (CNS) species are currently the most prevalent intra-mammary pathogens causing subclinical mastitis and occasional clinical mastitis or persistent infection in lactating dairy cattle. More than 10 CNS species have been identified, but they are generally managed as one group on most dairies in the United States. However, improved management decisions and treatment outcomes may be achieved with better understanding of the prevalent species, pathogenicity and strain diversity within and across dairies. Methodology A total of 604 CNS isolates were cultured from milk samples collected during a dry-cow treatment clinical trial conducted on 6 dairy herds in 4 states in the US. All the study cows were randomized to receive 1 of the 3 different intra-mammary antimicrobial infusions (Quatermaster, Spectramast DC or ToMorrow Dry Cow) at dry-off. Milk samples were collected at dry-off, calving (0–6 days in milk, DIM), post-calving (7–13 DIM) and at mastitis events within the first 100 DIM. The CNS isolates were identified to species level by partial sequencing of the rpoβ gene, and genetic relatedness within species was investigated by phylogenetic analysis of the pulse-field gel electrophoresis profiles of the isolates. Results The major CNS species identified were S. chromogenes (48.3%), S. haemolyticus (17.9%), S. simulans and S. epidermidis (each at 6.5%). Other CNS species identified at lower frequencies included S. hominis, S. auricularis, S. sciuri, S. spp KS-SP, S. capitis, S. cohnii, S. warneri, S. pasteuri, S. xylosus, S. hyicus, S. equorum, S. microti, S. rostri, S. gallinarum, S. saprophyticus and S. succinus. Phylogenetic analyses of the major species types demonstrated an association between genetic relatedness and epidemiological distributions of S. chromogenes, S. simulans, S. haemolyticus and S. auricularis. Additionally, identical strains of S. chromogenes and S. simulans were isolated from the same udder quarter of several cows at consecutive sample stages. The rest of the minor species had no deducible genetic-epidemiological link. Discussion The observed association between genetic and epidemiological distributions indicated animal-adapted nature of four CNS species, suggesting possible host-adapted and environmental transmission of these species. Multi-stage isolation of the same udder quarter strain was evidence for chronic intra-mammary infection. Conclusion The different CNS species and strains circulating on US dairy herds were genetically diverse. Four species identified were likely udder-adapted pathogens, 2 of which caused persistent infection. Our findings are important in guiding the design of effective mastitis control strategies.
Jenkins et al. (2019) Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States. PeerJ 7:e6749 https://doi.org/10.7717/peerj.6749
Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis
Introduction A hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis. Methods A total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population. Results In total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low FSTvalues obtained from pairwise FST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (all larvae populations in 2016, and R and H larvae populations in 2017), as demonstrated from the results of STRUCTURE and PCA analyses. Conclusion It was demonstrated that hatchery-reared fish are successful in producing the offspring in the natural environment during multiple years, which might assist in increasing the abundance of larvae. The hatchery-reared fish had variations in terms of the success rates on reproduction. Also, the hatchery-reared enhancement program had no significant effect on the genetic diversity or the genetic structure of wild populations. However, the genetic component of the W larvae population in 2017 was changed as compared to 2016, which was not due to the hatchery-reared enhancement program for silver carp. This could be due to flooding, but the specific causes need further studies. Our results clearly show the necessity to continuously inspect the genetic impact of the enhancement program so that historical information can be utilized for further research.
Chen et al. (2019) Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis. PeerJ 7:e6836 https://doi.org/10.7717/peerj.6836
Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis
Objectives This study aims to evaluate the changes of development trends and research hotspots of biomaterials research from 2013 to 2017, which can identify the general information of papers and explore the changes of research content, thus providing perspectives for the development of biomaterials in China and other countries. Methods Data of the paper were retrieved from the Web of Science Core Collection, and then analyzed by the bibliometric and CiteSpace visualization analysis. Results It was found that a total of 3,839 related papers had been published from the year 2013 to 2017. The analysis of the articles showed that the annual quantity and quality of the articles in the biomaterials research have been increasing since 2013, and the Wang L / Chinese Academy of Sciences were the most productive author/institution. Meanwhile, the keywords “in vitro”, “scaffold”, “nanoparticle” , “mechanical property”, and “biocompatibility” have the relatively higher frequency, and the keywords “apatite”, “deposition”, and “surface modification” have the strongest burst citation. Conclusions After statistics and analysis, we found that biomaterials is a promising research field. The study may be helpful in understanding research trends in this field.
Hou et al. (2019) Biomaterials research of China from 2013 to 2017 based on bibliometrics and visualization analysis. PeerJ 7:e6859 https://doi.org/10.7717/peerj.6859
Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway
The limb-bud and heart development (LBH) gene is a highly conserved, tissue-specific transcription cofactor in vertebrates that regulates multiple key genes in embryonic development. The role of LBH in various cancer types is still controversial, and its specific role and molecular mechanism in the oncogenesis of gastric cancer (GC) remains largely unexplored. In the present study, the prognostic significance and clinicopathological characteristics of LBH in GC was determined. The LBH mRNA expression was first investigated in four independent public datasets (TCGA-STAD, GSE15459, GSE29272, and GSE62254) and then validated with our samples at the protein level. LBH was overexpressed at both the mRNA and protein levels in cancer compared with normal tissues. High LBH expression was correlated with advanced T, N, and M stages. Kaplan–Meier analysis and log-rank test indicated that higher LBH expression was statistically correlated with shorter overall survival (OS) in the public datasets and our study samples. Univariate and multivariate Cox regression analysis showed that LBH was an independent prognostic biomarker for survival in TCGA-STAD, GSE15459, GSE62254 cohorts, and our GC patients. In vitro experiments showed that knockdown of LBH can significantly inhibit the proliferation and invasion of HGC-27 cells, while overexpression of LBH can significantly enhance the proliferation and invasion of BGC-823 cells. Gene Set Enrichment Analysis (GSEA), Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) indicated that high LBH expression is associated with the PI3K-Akt pathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction. Western blot analysis showed that knockdown of LBH significantly inhibited the expression of integrin α5, integrin β1, p-FAK, and p-Akt. Therefore, results from the present study indicate that LBH is a potential independent prognostic biomarker and promotes proliferation and invasion of GC cells by activating the integrin/FAK/Akt pathway.
Yu et al. (2019) Elevated limb-bud and heart development (LBH) expression indicates poor prognosis and promotes gastric cancer cell proliferation and invasion via upregulating Integrin/FAK/Akt pathway. PeerJ 7:e6885 https://doi.org/10.7717/peerj.6885
Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem
Background Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. Methods We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. Results Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. Conclusions There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.
McGlinn et al. (2019) Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem. PeerJ 7:e6738 https://doi.org/10.7717/peerj.6738
Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation
Ultraviolet radiation can cause many serious problems for all living organisms. With a growing population, the UV sensitivity of crop plants presents a particular problem. To evaluate the suitability of growing in areas under UV irradiance, the influence of different doses of UV-B (3.042, 6.084 and 9.126 kJm−2d−1) on the sugar beet (Beta vulgaris L) plants was studied. UV-B induced a significant decrease in growth displayed as reduced height and fresh and dry weight. This reduction is not dose dependent and was associated with diminishing photosynthetic O2 evolution, relative chlorophyll content, photosynthetic pigments and chlorophyll fluorescence. On the other hand, antioxidant enzyme activities, total protein content, compatible solutes, total free amino acids and total betalain content were increased under 9.126 kJm−2d−1 UV-B treatments, representing mechanisms by which the plants coped with the stress. The oxidative stress upon UV-B treatment was evident by increased malondialdehyde (MDA) content, however, hydrogen peroxide (H2O2) was not affected in UV-B exposed plants. Thus, the studied sugar beet variety BR1seems to be suitable particularly for areas with high doses of UV-B irradiation.
Rahimzadeh Karvansara et al. (2019) Physiological and biochemical responses of sugar beet (Beta vulgaris L) to ultraviolet-B radiation. PeerJ 7:e6790 https://doi.org/10.7717/peerj.6790
Gene drives as a new quality in GMO releases—a comparative technology characterization
Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits—the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
Frieß et al. (2019) Gene drives as a new quality in GMO releases—a comparative technology characterization. PeerJ 7:e6793 https://doi.org/10.7717/peerj.6793
Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids
Background Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama. Methods Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents. Results We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.
Symes et al. (2019) Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids. PeerJ 7:e6808 https://doi.org/10.7717/peerj.6808
Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize
Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
Gonzalez-Segovia et al. (2019) Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize. PeerJ 7:e6815 https://doi.org/10.7717/peerj.6815