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Historical and current distribution ranges and loss of mega-herbivores and carnivores of Asia Ecosystem functioning is dependent a lot on large mammals, which are, however, vulnerable and facing extinction risks due to human impacts mainly. Megafauna of Asia has been declining for a long, not only in numbers but also in their distribution ranges. In the current study, we collected information on past and current occurrence and distribution records of Asia’s megafauna species. We reconstructed the historical distribution ranges of the six herbivores and four carnivores for comparison with their present ranges, to quantify spatially explicit levels of mega-defaunation. Results revealed that historically the selected megafauna species were more widely distributed than at current. Severe range contraction was observed for the Asiatic lion, three rhino species, Asian elephant, tigers, and tapirs. Defaunation maps generated have revealed the vanishing of megafauna from parts of the East, Southeast, and Southwest Asia, even some protected Areas losing up to eight out of ten megafaunal species. These defaunation maps can help develop future conservation policies, to save the remaining distribution ranges of large mammals.
PeerJ - Tập 9 - Trang e10738
Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer
Background
The hepatic microenvironment, which may include chronic inflammation and fibrosis, is considered to contribute to the development of liver metastases. Hepatic steatosis (HS) might cause liver inflammation and fibrosis. However, to date, no studies have investigated the impact of HS on liver metastasis in patients with non-small cell lung cancer (NSCLC).
Methods
A retrospective cohort study was performed on patients who received NSCLC treatment at two hospitals affiliated with the Southern Medical University from January 2005 to December 2015. The patients were grouped according to the presence of HS. The clinicopathological features of patients between the two groups were compared. The effect of HS on liver metastasis and overall metastasis was evaluated, adjusting for other confounders using Cox regression analyses.
Results
In total, 1,873 patients with NSCLC with no distant metastases were included in this study, and 408 (21.8%) patients were diagnosed with HS (at the time of diagnosis or before diagnosis). Liver metastases occurred in 166 (8.9%) patients. Liver metastasis-free survival was significantly worse in the study (HS) group (hazard ratio (HR) 1.42; (95% CI [1.03–1.96]); P = 0.031). Multivariate regression analysis demonstrated that HS was an independent risk factor for liver metastasis (HR 1.43; 95% CI [1.02–2.01]; P = 0.039). However, HS was not associated with overall metastasis of NSCLC (HR 0.99; 95% CI [0.84–1.17]; P = 0.895).
Conclusion
Hepatic steatosis was an independent predictor of liver metastasis from in patients with NSCLC.
PeerJ - Tập 7 - Trang e6612
Evolutionary origins of the emergent ST796 clone of vancomycin resistant<i>Enterococcus faecium</i> From early 2012, a novel clone of vancomycin resistantEnterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to otherE. faecium genomes shows Ef_aus0233 is a member of the epidemic hospital-adapted lineage and has evolved from an ST555-like ancestral progenitor by the accumulation or modification of five mosaic plasmids and five putative prophage, acquisition of two cryptic genomic islands, accrued chromosomal single nucleotide polymorphisms and a 80 kb region of recombination, also gaining Tn1549 and Tn916 , transposons conferring resistance to vancomycin and tetracycline respectively. The genomic dissection of this new clone presented here underscores the propensity of the hospitalE. faecium lineage to change, presumably in response to the specific conditions of hospital and healthcare environments.
PeerJ - Tập 5 - Trang e2916
The behavioral effects of antibiotic treatment on the snail<i>Biomphalaria glabrata</i> Schistosomiasis is a detrimental neglected tropical disease that is transmitted by Planorbid snails. Understanding the transmission and control of this disease requires an extensive understanding of these intermediate hosts, which is only achieved by the effective rearing and study of species such asBiomphalaria glabrata . This species is the intermediate host forSchistosoma mansoni in the New World, and is also the main model for studying schistosomes in mollusks. Antibiotics are used routinely inB. glabrata tissue culture, and occasionally on live snails. Here we show that standard doses of three common antibiotics (penicillin, streptomycin and gentamicin) drastically diminish the activity of healthyB. glabrata , but that treated snails recover rapidly when placed in fresh water. Ampicillin treated snails did not show altered activity. We suggest that researchers keep these apparent toxicities in mind if a need for antibiotic treatment of live Planorbid snails arises.
PeerJ - Tập 5 - Trang e4171
Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance
PeerJ - Tập 8 - Trang e9646 - 2020
#Microbiota; Transcriptome; Metabolites; Shrimp intestine; Black tiger shrimp; Growth performance; Penaeus monodon
Reef fish communities are spooked by scuba surveys and may take hours to recover Ecological monitoring programs typically aim to detect changes in the abundance of species of conservation concern or which reflect system status. Coral reef fish assemblages are functionally important for reef health and these are most commonly monitored using underwater visual surveys (UVS) by divers. In addition to estimating numbers, most programs also collect estimates of fish lengths to allow calculation of biomass, an important determinant of a fish’s functional impact. However, diver surveys may be biased because fishes may either avoid or are attracted to divers and the process of estimating fish length could result in fish counts that differ from those made without length estimations. Here we investigated whether (1) general diver disturbance and (2) the additional task of estimating fish lengths affected estimates of reef fish abundance and species richness during UVS, and for how long. Initial estimates of abundance and species richness were significantly higher than those made on the same section of reef after diver disturbance. However, there was no evidence that estimating fish lengths at the same time as abundance resulted in counts different from those made when estimating abundance alone. Similarly, there was little consistent bias among observers. Estimates of the time for fish taxa that avoided divers after initial contact to return to initial levels of abundance varied from three to 17 h, with one group of exploited fishes showing initial attraction to divers that declined over the study period. Our finding that many reef fishes may disperse for such long periods after initial contact with divers suggests that monitoring programs should take great care to minimise diver disturbance prior to surveys.
PeerJ - Tập 6 - Trang e4886
Comparative study of gut microbiota in Tibetan wild asses (<i>Equus kiang</i>) and domestic donkeys (<i>Equus asinus</i>) on the Qinghai-Tibet plateau Tibetan wild asses (Equus Kiang ) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P < 0.05). No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla Bacteroidetes and Firmicutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214 , Phascolarctobacterium , Coprostanoligenes_group , Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than in domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses have advantages over domestic donkeys in dry matter digestion, gut microbial community composition and function, and wild asses have their unique intestinal flora to adapt high altitudes on the Qinghai-Tibet plateau.
PeerJ - Tập 8 - Trang e9032
Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics) with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial composition, concentrations of caecal short-chain fatty acids (SCFAs) and biomarkers of gut health using an in vivo model of obesity. Obese diabetic (db/db) mice received a supplemented diet with 10% cherry powder (supplemented mice, n = 12) for 12 weeks; obese (n = 10) and lean (n = 10) mice served as controls and received a standard diet without cherry. High-throughput sequencing of the 16S rRNA gene and quantitative real-time PCR (qPCR) were used to analyze the gut microbiota; SCFAs and biomarkers of gut health were also measured using standard techniques. According to 16S sequencing, supplemented mice harbored a distinct colonic microbiota characterized by a higher abundance of mucin-degraders (i.e., Akkermansia ) and fiber-degraders (the S24-7 family) as well as lower abundances of Lactobacillus and Enterobacteriaceae. Overall this particular cherry-associated colonic microbiota did not resemble the microbiota in obese or lean controls based on the analysis of weighted and unweighted UniFrac distance metrics. qPCR confirmed some of the results observed in sequencing, thus supporting the notion that cherry supplementation can change the colonic microbiota. Moreover, the SCFAs detected in supplemented mice (caproate, methyl butyrate, propionate, acetate and valerate) exceeded those concentrations detected in obese and lean controls except for butyrate. Despite the changes in microbial composition and SCFAs, most of the assessed biomarkers of inflammation, oxidative stress, and intestinal health in colon tissues and mucosal cells were similar in all obese mice with and without supplementation. This paper shows that dietary supplementation with cherry powder for 12 weeks affects the microbiota and the concentrations of SCFAs in the lower intestinal tract of obese db/db diabetic mice. These effects occurred in absence of differences in most biomarkers of inflammation and other parameters of gut health. Our study prompts more research into the potential clinical implications of cherry consumption as a dietary supplement in diabetic and obese human patients.
PeerJ - Tập 6 - Trang e4195
CTLA-4 polymorphisms associate with breast cancer susceptibility in Asians: a meta-analysis Previous studies have investigated the association between cytotoxic T-lymphocyte antigen-4 (CTLA-4 ) polymorphisms and breast cancer susceptibility, but the results remained inconsistent. Therefore, we evaluated the relationship between four common CTLA-4 polymorphisms and breast cancer risk by a meta-analysis, aiming to derive a comprehensive and precise conclusion. We searched EMBASE, Pubmed, Web of Science, CNKI, and Wanfang databases until July 18th, 2016. Finally, ten eligible studies involving 4,544 breast cancer patients and 4,515 cancer-free controls were included; all these studies were from Asia. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the breast cancer risk in five genetic models. The results indicated that the CTLA-4 +49A>G (rs231775 ) polymorphism had a significant association with decreased breast cancer risk in allelic, homozygous, dominant and recessive models. Also, the +6230G>A (rs3087243 ) polymorphism reduced breast cancer risk especially in the Chinese population under homozygous and recessive models. In contrast, the −1661A>G (rs4553808 ) polymorphism increased breast cancer risk in allelic, heterozygous and dominant models, whereas −1722 T>C (rs733618 ) did not relate to breast cancer risk. In conclusion, CTLA-4 polymorphisms significantly associate with breast cancer susceptibility in Asian populations, and different gene loci may have different effects on breast cancer development. Further large-scale studies including multi-racial populations are required to confirm our findings.
PeerJ - Tập 5 - Trang e2815
Baseline scenarios of heat-related ambulance transportations under climate change in Tokyo, Japan
Background
Predictive scenarios of heatstroke over the long-term future have yet to be formulated. The purpose of the present study was to generate baseline scenarios of heat-related ambulance transportations using climate change scenario datasets in Tokyo, Japan.
Methods
Data on the number of heat-related ambulance transportations in Tokyo from 2015 to 2019 were examined, and the relationship between the risk of heat-related ambulance transportations and the daily maximum wet-bulb globe temperature (WBGT) was modeled using three simple dose–response models. To quantify the risk of heatstroke, future climatological variables were then retrieved to compute the WBGT up to the year 2100 from climate change scenarios (i.e. , RCP2.6, RCP4.5, and RCP8.5) using two scenario models. The predicted risk of heat-related ambulance transportations was embedded onto the future age-specific projected population.
Results
The proportion of the number of days with a WBGT above 28°C is predicted to increase every five years by 0.16% for RCP2.6, 0.31% for RCP4.5, and 0.68% for RCP8.5. In 2100, compared with 2000, the number of heat-related ambulance transportations is predicted to be more than three times greater among people aged 0–64 years and six times greater among people aged 65 years or older. The variance of the heatstroke risk becomes greater as the WBGT increases.
Conclusions
The increased risk of heatstroke for the long-term future was demonstrated using a simple statistical approach. Even with the RCP2.6 scenario, with the mildest impact of global warming, the risk of heatstroke is expected to increase. The future course of heatstroke predicted by our approach acts as a baseline for future studies.
PeerJ - Tập 10 - Trang e13838
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