Search

Studies on large-sample gut microbial sequencing data indicate that gut microbiota can be divided into multiple community types; different community types may influence the community function and ecosystem service. However, the knowledge on the classification, diversity, interaction, and assembling of microbial community types in the gut of wild animals is still insufficient. Here, we used pika gut microbiota data as an example to study the microbial community types in large-sample sequencing dataset. Cecal microbial communities from 118 wild plateau pika (Ochotona curzoniae) individuals at 5 elevational regions on the Qinghai-Tibet Plateau were analyzed. Our results show that pika gut microbiota can be separated into 2 community types (Cluster I and Cluster II). Cluster I was mainly distributed on the high-elevation regions with more than 3694 m and was most dominated by Firmicutes. Cluster II was from the low-elevation areas (lower than 3580 m), and was predominated by Bacteroidetes. Cluster I had a higher community alpha-diversity and predicted functional diversity than Cluster II, and the beta-diversity and predicted functional profiles of these 2 clusters were significantly different. Network analysis revealed that there were more complex interactions between Cluster I, which had enhanced influence on the co-occurrences of other microbes in the bacterial community when compared to Cluster II. Phylogenetic analysis found that the environmental filtering in the Cluster I was stronger than Cluster II. The assemblages of pika gut bacterial communities were determined mainly by deterministic processes, while the relative importance of deterministic processes accounted for more percentages in the Cluster I than Cluster II. Our results demonstrated that 2 gut microbial community types in pikas had distinct diversity patterns and ecological functions. Current methods are also helpful for identifying gut community types and the related mechanisms behind gut microbiota types in large-sample sequencing data of wild animals.

Contamination of antibiotic resistomes due to animal carcass decay has become a serious environmental concern. However, the relationship between main metabolite compounds of corpse decomposition (i.e., putrescine and cadaverine) and antibiotic resistomes remains unclear. To tackle this issue, the response of antibiotic resistance genes (ARGs) and microbiome in aquatic environment to excess putrescine, cadaverine and a mixture of both based on laboratory simulation experiment was investigated by high-throughput quantitative PCR and amplicon sequencing methods. Our results showed putrescine and cadaverine led to the increasing of TC (total carbon) and TN (total nitrogen) both in water and sediment. Under the exposure of putrescine and cadaverine, the total abundance of mobile genetic elements (MGEs) and most ARGs in water was higher than in sediment. In particular, putrescine and cadaverine caused significantly different decreases in alpha diversity of microbial community in water and sediment compared with the control group. Microbial community structures both in water and sediment were also significantly affected by cadaverine and putrescine. Furthermore, putrescine and cadaverine led to different degrees of increases of high-risk ARGs (like mecA) and opportunistic pathogens (like Delftia) in sediment, promoting the prevalence of antibiotic resistant bacteria. In conclusion, our findings revealed the influences of main metabolites of carcass decay on microbiome and resistomes, providing references for risk assessment and pollution management.

Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO

Skin microbiomes function directly in human health and are affected by various external and internal factors. However, few studies have showed the variation of human skin microbiota at multiple body sites in individuals of different national origin living in the same environment. Here, using 16S rRNA sequencing, we investigated the diversity and function of skin microbiomes in different body locations of Chinese and Pakistani individuals from a single college in China. Body location and nationality significantly affected community structures, while season and gender only impacted community member. Due to different lifestyles and likely genetic characteristics of the hosts, Proteobacteria was more abundant in Pakistanis than in Chinese individuals. There were significant differences in the Shannon diversity of skin microorganisms among different skin sites of Chinese individuals, but not in Pakistanis. PICRUSt prediction indicated that gene functions involved in carbohydrate metabolism, lipid metabolism, and xenobiotics biodegradation and metabolism were higher in bacteria collected from Pakistanis than those from Chinese individuals, but the amino acid metabolism of skin microorganisms in Chinese people was higher. The relative abundances of potential pathogenic bacteria also differed in different body locations, providing a foundation for studying skin-associated bacterial diseases. Through a meta-analysis of 233 human skin samples from eight elevational sites in western China, we found that skin microbial diversity first decreased and then increased with increasing altitude. Network analysis showed positive correlation between altitude and Lactobacillus, Chryseobacterium, or Acinetobacter. Our results uncover the variation of human skin microbiota allowing future explorations of potential significance for human health. KEY POINTS: • Body location and nationality affect skin microbiota diversity and function. • Proteobacteria was more abundant in Pakistanis than in Chinese. • Skin microbial diversity first decreased and then increased with elevated altitude.

Plateau pikas (

Animal carcasses introduce large amounts of nitrates and ammonium into the soil ecosystem. Some of this ammonium is transformed from nitrite through the nrfA-type microbial community. However, it is unclear how nrfA-type microorganisms respond to the decomposition of corpses. This study applied high-throughput sequencing to characterize the ecological succession of nrfA-type microbial communities in grassland soil. Our results showed that Cyclobacterium and Trueperella were the predominant genera for nrfA-type communities in soil with a decomposing corpse (experimental group), while Cyclobacterium and Archangium were dominant in soil without a corpse (control group). The alpha diversity indexes and the resistance and resilience indexes of the microbial communities initially increased and then decreased during decomposition. Compared with the control group, nrfA-encoding community structure in the experimental group gradually became divergent with succession and temporal turnover accelerated. Network analysis revealed that the microbial communities of the experimental group had more complex interactions than those of the control groups. Moreover, the bacterial community assembly in the experimental group was governed by stochastic processes, and the communities of the experimental group had a weaker dispersal capacity than those of the control group. Our results reveal the succession patterns of the nrfA-type microbial communities during degradation of wild animal corpses, which can offer references for demonstrating the ecological mechanism underlying the changes in the nrfA-type microbial community during carcass decay. KEY POINTS: • Corpse decay accelerates the temporal turnover of the nrfA-type community in soil. • Corpse decay changes the ecological succession of the nrfA-type community in soil. • Corpse decay leads to a complex co-occurrence pattern of the nrfA-type community in soil.

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Many contaminants were carried by dust, a common environment media that is easy to contact with human beings, and antibiotic resistance genes (ARGs) as an emergency pollutant also harbor in dust and pose serious threats to human health especially those carried by opportunistic pathogens because inactivation of antibiotics caused by ARGs may enhance pathogenicity. Considering there is a gap of investigation of dust ARGs, 16 S rRNA gene sequences and high-throughput quantitative PCR were employed to obtain information of microbial communities and accumulated ARGs in dust from different urban places, including the malls, hospitals, schools and parks, to investigate the distribution and influencing factors of ARGs and discover the potential hosts of ARGs in dust. Here, 9 types of ARGs such as sulfonamide, tetracycline, and beta-lactamase and 71 subtypes of ARGs like sul1, tetM-01, and drfA1 were detected in dust. ARGs had varying distribution in different public places and seasons in dust. The abundances of total ARGs, MLSB and tetracycline genes were higher in spring than summer. The diversity of ARGs was highest in malls, follow by hospitals, schools, and parks. Additionally, multi-drug resistance genes in dust were more abundant in hospitals than in schools and parks. The microbes were distinguished as the most important driving factors for ARGs in dust, followed by the mobile genetic elements (MGEs) and different places, while dust physicochemical parameters only exert a negligible impact. Notably, several opportunistic pathogens like the Streptococcus, Vibrio, and Pseudomonas were inferred as potential hosts of high-risk ARGs such as mecA, tetM-02, and tetO-01 in dust because of strongly positive co-occurrence. These results imply that dust is likely an important reservoir of ARGs. We should realize that ARGs may be harbored in some opportunistic pathogens occur in dust and endanger human health because of dust contacting to human easily.

The influences of global climatic change require an understanding of changes in soil microbial communities under precipitation. However, little is known about how soil ("gravesoil") microbial communities associated with corpse decay respond to precipitation. Here, we explored the variations of temporal turnover and assembly in gravesoil bacterial communities in the Qinghai-Tibet Plateau ecosystem via controlled rainfall simulation experiments. In our experiments, rainfall intensity was set to 2.5 and 5 mm/3 days to simulate moderate and heavy rainfall, respectively, and sampling was conducted on the 4th, 11th, 18th, 32nd, 46th and 60th day. Our results showed precipitation significantly altered bacterial abundances and community structures. Analysis of time-decay relationships revealed that precipitation resulted in a divergent succession of gravesoil bacterial community structure and abundance changes of dominant phyla, such as Chloroflexi. Moreover, in the experimental groups, our results suggested that moderate rainfall increased the deterministic processes in the initial and mid periods, whereas heavy rainfall decreased these processes of gravesoil microbial community assembly in every period compared with those in the control group. The dispersal capacity induced by stochastic processes of gravesoil microbial communities decreased over time under moderate rainfall, whereas it initially increased and then decreased under heavy rainfall. This study highlights the influence of heavy rainfall on bacterial communities during corpse decay, which can provide some inferences for predicting changes in soil microbial communities under global climatic change.

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

Animal carcasses are hotspots of ecological activity. The study of the role of microbes in carcass decomposition has been exclusively focused on microbes with higher abundance. The comparative study of abundant and rare subcommunities associated with decomposition needs in-depth exploration. The current experiment has been conducted on the decomposition of a fish carcass in a microcosm. We conducted 16S rRNA gene sequencing of the microbial communities. The correlation of the physicochemical properties of tap and Yellow river water with the microbial communities was evaluated. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were found to be the dominant phyla in both abundant and rare subcommunities. Among bacteria, the Acidobacteria, Planctomycetes, and Cyanobacteria were found only in the rare subcommunity. In both subcommunities, the abundance of Proteobacteria was found to increase over time, and that of Firmicutes to decrease. The rare subcommunity shows higher alpha diversity than the abundant one. The variation in the abundant subcommunity was influenced by time and water type, and that in the rare subcommunity was influenced by pH and water type. These results have implications for future research on the ecological role of rare and abundant subcommunities in the decomposition of carcasses in the aquatic ecosystem.

Ovarian cancer is one of the most common gynecological diseases with high mortality rates. Previous studies have shown that microRNA (miR)-638 is associated with tumorigenesis. The present study aimed to assess the role and underlying mechanisms of miR-638 in ovarian cancer. miR-638 expression was detected in ovarian cancer tissues and miR-638 was overexpressed or knocked down in ovarian cancer OVCAR-3 and Caov-3 cells. The clinical results revealed that miR-638 expression was downregulated in ovarian cancer tissues compared with in adjacent normal tissues. miR-638 expression was also found to be relatively low in OVCAR-3 cells whilst being relatively high in Caov-3 cells among the five ovarian cancer cell lines tested. miR-638 overexpression inhibited cell viability, arrested the cell cycle at the G1 phase and promoted apoptosis in OVCAR-3 cells. By contrast, miR-638 knockdown increased Caov-3 cell viability, facilitated cell cycle progression and inhibited apoptosis. miR-638 reduced the expression of high mobility group A1 (HMGA1) by directly targeting its 3' untranslated region. HMGA1 overexpression reversed the inhibition of proliferation induced by miR-638 overexpression in OVCAR-3 cells. These results suggest that miR-638 may serve to be a suppressor of ovarian cancer by regulating HMGA1, which may provide a potential therapeutic target for ovarian cancer.

Background The gasdermins (GSDMs) family is proposed to be pore-forming effector proteins that cause cell membrane permeabilization and pyroptosis. Despite our increasing knowledge of GSDMD, GSDME and GSDMB, the biological functions and the regulation of GSDM expression and activation remain elusive for most GSDMs. In this study, we analyzed the molecular characteristics and oncogenic role of GSDM family genes systematically. Methods TCGA, CCLE, cBioPortal, GEPIA, CellMiner and BioGRID databases were utilized in this study. Immunohistochemical analysis and a series of in vitro experiments were conducted. Results We found that, in cancer, GSDM genes and their expressions extensively changed, which were associated with patient survival. The expression of GSDMs was widely associated with cancer-related pathways, drug resistance, immune subtypes, tumor microenvironment and cancer cell stemness. However, an intra- and inter-cancer heterogeneity was discovered regarding the corresponding GSDM gene. We found that GSDMA and GSDMB regulated drug resistance to the opposite direction of GSDME. In colorectal cancer, GSDME might be a positive regulator in cell invasion and metastasis through cell migration and angiogenesis, while GSDMA, GSDMB and GSDMD might be a negatively regulator of cell migration. Conclusions GSDM family genes might play important roles in cancer other than pyroptosis. We suggest more efforts be made to investigate the GSDM family and each GSDM gene be studied as an entity in each type of cancer.

BACKGROUND Peritoneal fibrosis (PF) can reduce the efficiency of peritoneal dialysis and eventually lead to ultrafiltration failure. Epithelial-mesenchymal transition (EMT) of peritoneal mesothelial cells (PMCs) is the start of PF. Macrophages are involved in the process. This study was to investigate the effect of macrophage polarization on EMT of PMCs. METHODS Monocyte-macrophage cells (THP-1) were treated to induce macrophage subsets (M1, M2a, M2c). The inducing was assessed by detecting protein and mRNA expression of cytokines using ELISA and RT-PCR. Subsequently, PMCs were co-cultured with M1, M2a and M2c, respectively, in Transwell chambers for 48 h and then expressions of E-cadherin and α-SMA were determined in PMCs. The PMCs that were not co-cultured with macrophages served as control PMCs. One-way ANOVA and SNK-q test were used to conduct statistics and P

Serious concerns have been raised regarding resistomes causing by corpse decomposition in the aquatic environment, which pose threats to the water environment and human health. However, antibiotic resistance genes (ARGs) in large-volume tap water and their temporal stability during corpse decay are poorly explored. Here, high-throughput quantitative polymerase chain reaction (HT-qPCR) and amplicon sequencing were applied to profile ARGs and bacterial communities in experimental and control groups containing 50 L of tap water at 7th, 15th and 100th day during corpse decomposition. We found that most of the ARGs in experimental groups had higher abundance compared with the control groups independent of time. And the absolute abundance of some ARGs in the carcass groups was even enriched by 259 to 413,640-folds. The tetracycline and beta-lactamase resistance genes of the experimental groups were obviously enriched compared with control groups, and the ARG profiles were convergent during different decay stages, which indicated the long-term persistence of ARGs. Treatment, dissolved oxygen (DO) and pH were three important factors determining ARG profiles during corpse decomposition. Twelve opportunistic pathogens, especially Burkholderia, Legionella and Halomonas, remarkably increased as decomposition proceeded. Network analysis showed that opportunistic pathogens were significantly associated with ARGs. Our results emphasize that corpse decay increases the abundance and diversity of ARGs in large-volume drinking water independent of time while exhibits temporal persistence of ARGs, thereby uncovering the harmful effects of animal cadavers. It also provides valuable suggestions for the risk assessment and management of source water caused by corpse decay.

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is well explored and studied, but there is a scarcity of knowledge and research related to their role in decomposing animal carcasses. Microbes play an important role in carcass decomposition. The origins of microbial communities associated with a carcass, including the internal and external microbiome, are discussed in this review. The succession and methods used for the detection and exploration of decomposition-associated microbial communities have been briefly described. Also, the applications of carcass-associated microbial taxa have been outlined. This review is intended to understand the dynamics of microbial communities associated with the carcass and pave the way to estimate postmortem interval and its role in recycling nutrients.

Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.

The Qinghai-Tibet Plateau is a harsh environment characterized by low temperature, high altitude and hypoxia, although some native mammals may adapt well to the extreme climate. However, how animal gut microbial community structure and function adapt to extreme cold climates is not well understood. Plateau pika (Ochotona curzoniae) is an ideal animal model with which to study the effects of climate change on host adaptation by studing intestinal microorganisms. Here, we used 16S rRNA sequencing technology combined with physiological methods to investigate plateau pika gut microbiota in summer and winter. Due to limited diet resources, the pikas in winter have a lower ability of degradation and fermentation for plant-based food (reduced cellulase activity and total short-chain fatty acids) by decreasing gut microbial diversity and some functional microbes, such as fiber-degrading bacteria Oscillospira and Treponema. Metagenomic prediction showed that most of those gene functions associated with metabolism (e.g. energy metabolism and lipid metabolism) were less abundant in winter, implying that the plateau pika slows diet fermentation and weakens energy requirements in the cold season. Our results have significance for explaining the mechanism of wild plateau mammals adapting to a high-altitude cold environment from the perspective of gut microbiome.

Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH3-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH3-N, NO3-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.

A mutant library of the key amino acid residue site E387 in γ-glutamyltranspeptidase was constructed to screen the mutant enzymes with significantly improved thermal stability (E387Q). The reaction temperature of the mutant enzyme (E387Q) was 10℃ higher than that of the parent enzyme. Ultrasound-assisted synthesis of L-theanine by γ-glutamyltranspeptidase was investigated. The effects of ultrasonic power, reaction pH and substrate concentration on the enzymatic synthesis of L-theanine were studied by the response surface method. The results showed that the optimal process conditions are ultrasonic power of 100 W, reaction pH of 9, substrate L-glutamine concentration of 120 mmol/L, reaction temperature of 45℃, and L-theanine yield of 89.1%. The yield of L-theanine is 2.61 times higher than that obtained without ultrasound. Ultrasound can significantly promote the synthesis of L-theanine by γ-glutamyltranspeptidase.

The prevalence and transmission of antibiotic resistance genes (ARGs) and opportunistic pathogens in water environments can pose great threat to public health. However, the dissemination of ARGs and opportunistic pathogens from water environments to humans has been poorly explored. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to explore the seasonal distribution of ARGs and opportunistic pathogens in the Yellow River water (source water) and tap water, as well as their relationships with healthy humans at Lanzhou, China. Physiochemical analysis was applied to detect water quality parameters and heavy metal contents. The absolute abundance and diversity of ARGs in the Yellow River and tap water demonstrated distinct seasonal patterns. In winter, the Yellow river water had the highest ARG abundance and diversity, while tap water owned the lowest. Mobile genetic elements (MGEs) were the predominant driver of ARG profiles in both the Yellow river and tap water. Null model analysis showed that ARG assembly in the Yellow River was more influenced by stochastic processes than tap water and this was independent of seasons. Total organic carbon and arsenic contents exhibited positive correlations with many ARGs. Opportunistic pathogens Aeromonas and Pseudomonas may be potential hosts for ARGs. Approximately 80% of detected ARGs were shared between water samples and the human gut. These persistent ARGs could not be entirely eliminated through drinking water treatment processes. Thus, it is crucial to protect sources of tap water from anthropogenic pollution and improve water treatment technologies to reduce the dissemination of ARGs and ensure drinking-water biosafety for human health.

The threat of food safety and the limited analytical methods with high performance promote the growing interest in the development of pathogenic bacteria biosensors. This study presents a pathogenic bacteria biosensing system, where a novel three-dimensional (3D) chip acts as an analytical carrier and DNA-programmed hybridization chain reaction (HCR) causes signal amplification. The 3D chip is designed featuring a compact multichannel structure. It has a large surface area for sensitive sensing and exhibits multiple functions of target capture, separation, rinsing, and signal detection to simplify the analysis processes. HCR, which enables the fluorophore's polymerization, is designed as two signal amplification modes, each with unique advantages. Mode I achieves highly sensitive detection in a "sandwich" assay format, in which a long HCR-amplified probe is used to boost the fluorescence signal. In mode II, the assembly of HCR is performed on the inner surface of the 3D chip. Especially, a group of rapid-assembly HCR sequences is proposed, of which the assembly time as short as 15 min stands out among the related works previously reported. Under the optimal conditions, the proposed biosensing system has the limits of detection (LOD) of 4 and 8 cfu/mL in mode I for Staphylococcus aureus detection and in mode II for Salmonella enterica Typhimurium detection, respectively. The specificity and the real sample applications are evaluated. This multichannel-structured 3D chip based on HCR signal amplification has potential applications in food safety monitoring and biosensor development.

Background/Aims: Insulin-like growth factor-1 (IGF-1) plays important roles in cellular proliferation, differentiation, and growth. Previous studies showed that single-nucleotide polymorphisms (SNPs) of IGF-1 are associated with various diseases. This case-control study aimed to examine the relationship between IGF-1 polymorphisms and IgA nephropathy (IgAN) risk in a Chinese Han population. Methods: We recruited 351 IgAN patients and 310 healthy controls from Northwestern China. Sequenom MassARRAY was utilized to examine the genotypes of two common IGF-1 SNPs (rs1520220 and rs2195239). Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by the Chi square test to evaluate the associations between IGF-1 and IgAN. Results: Our study demonstrated that IGF-1 gene rs1520220 and rs2195239 polymorphisms did not confer susceptibility to IgAN. We found no correlation between gender, blood pressure, proteinuria, eGFR, and IgAN in both SNPs. However, the rs1520220 and rs2195239 variants were correlated with M1 and E1 in patients with IgAN (M0/M1: CC vs. CG+GG: OR = 1.62, P = 0.04; E0/E1: CC vs. CG+GG: OR = 1.95, P = 0.004; GG vs. GC+CC: OR = 1.90, P = 0.004, respectively). Conclusion: These results indicate that IGF-1 gene polymorphisms play crucial roles in the histopathological progression of IgAN in the Chinese Han population.

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH4+ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH4+ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

Corpse degradation may release amounts of hazardous materials (e.g., cadaverine, putrescine and ammonia) into surrounding areas, which deteriorate environments and result in nitrogen contamination. Nitrate or nitrite can be reduced to nitrogen gas by denitrifying bacteria, thus alleviating nitrogen contamination and purifying aquatic environments. However, the reaction of nirS-encoding denitrifiers to carcass degradation is less studied. Therefore, water physiochemical analysis and high-throughput sequencing were applied to explore the successional pattern of nirS denitrifying communities in the Yellow River water and tap water during three stages of animal cadaver decay (submerged fresh, advanced floating decay as well as sunken remains) and relevant control group. Nitrate nitrogen (NO3-N) and ammonia nitrogen (NH4+-N) concentration in corpse groups were highly elevated compared with control groups. The dominant phylum for nirS denitrifying communities was Proteobacteria. Abundant denitrifying genera Paracoccus, Alicycliphilus and Diaphorobacter were detected, and these genera have been reported to participate in the degradation of organic pollutants. Particularly, nirS-type community structures were remarkably influenced by corpse decay and became similar with succession. Water total dissolved solids (TDS), salinity, conductivity (CON) and phosphate were primary impacting factors driving the community structures, but the effect of water type was almost negligible. Notably, denitrifying community assembly was dominated by deterministic processes rather than stochastic processes, and the relative importance of deterministic processes among most corpse groups was higher than that in control groups, indicating that environmental filtering regulates the denitrifying communities. Our results provide new insight into environmental purification for hazardous materials produced by corpse degradation, thereby providing valuable advice to environmental administration.

Background/Aims: IFN-γ was reported to be involved in the development and progression of Immunoglobulin A nephropathy (IgAN), however, few studies have investigated the association between IFN-γ polymorphisms and IgAN. Therefore, we performed a case-control study to assess the association between IFN-γ polymorphisms and the risk of IgAN. Methods: Sequenom MassARRAY was used to genotype two SNPs (rs1861494 and rs2430561) in 351 patients with IgAN and 310 healthy controls. Associations were evaluated as odd ratios (OR) with 95% confidence intervals (CI). Results: No association was found between IFN-γ rs1861494 and IgAN risk or clinical parameters. For rs2430561, the AA genotype was more common in patients with IgAN, compared with controls (AT vs. AA: OR = 0.57, P = 0.035). IFN-γ-rs2430561 T allele may be a protective factor for IgAN susceptibility (T vs. A: OR = 0.59, P = 0.04). Subgroup analysis based on clinical features revealed no significant association between rs2430561 polymorphism and clinical data such as gender, 24-h urine protein, blood pressure, Oxford classifcation and estimated glomerular fltration rate. IgAN patients had a higher IFN-γ serum level than healthy controls and patients with rs1861494 AA genotype had a higher IFN-γ serum level compared with those with AG/GG genotypes. Conclusions: IFN-γ polymorphisms may be involved in the development and progression of IgAN.

Background/Aims: IgA nephropathy (IgAN) is a common form of primary glomerulonephritis worldwide. Previous studies indicated that IL-10 single nucleotide polymorphisms (SNP) play an important role in IgAN pathogenesis, but the results were controversy. This study aimed to investigate the association between IL-10 SNPs (rs1800872, rs1800871, and rs1800896) with IgAN in a Chinese Han population. Methods: We conducted a case–control study that included 351 patients with IgAN and 310 age-, gender- and ethnicity-matched healthy controls. Three promoter SNPs (rs1800872, rs1800871, and rs1800896) of IL-10 were genotyped by Sequenom MassARRAY. Odds ratios (ORs) with 95% confidence intervals (CI) were used to assess the relationship with IgAN. Results: We found that the rs1800896 did not correlate with IgAN risk, whereas rs1800872 and rs1800871 were significantly associated with increased IgAN risk in all genetic models. The haplotype analysis indicated that the CCA haplotype was associated with increased IgAN risk (OR = 1.36; 95% CI = 1.05–1.75). Moreover, there were no associations between these SNPs and blood pressure or gender, whereas the rs1800896 variant was correlated with higher 24-hour urine protein in patients with IgAN. Conclusion: Taken together, these results suggest that IL-10 is a susceptibility gene in patients with IgAN.

// Jie Gao 1, * , Xinghan Liu 2, * , Linting Wei 1, * , Dan Niu 3 , Jiali Wei 4 , Li Wang 1 , Heng Ge 1 , Meng Wang 2 , Qiaoling Yu 5 , Tianbo Jin 6 , Tian Tian 2 , Zhijun Dai 2 , Rongguo Fu 1 1 Department of Nephrology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China 2 Department of Oncology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China 3 Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China 4 Department of Nephrology, Hainan general hospital, Haikou 570311, China 5 Department of Pathology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China 6 National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an 710069, China * These authors have contributed equally to this work Correspondence to: Jie Gao, email: gxej_cn@sina.com Rongguo Fu, email: pipifu@126.com Keywords: monocyte chemoattractant protein-1, IgA nephropathy, polymorphism, risk, case-control study Received: September 16, 2016 Accepted: October 12, 2016 Published: October 24, 2016 ABSTRACT Monocyte chemoattractant protein-1 (MCP-1) and its receptor CCR2 stimulate inflammation response by activating and recruiting monocytes/macrophages. MCP-1 and CCR2 polymorphisms were reported to be associated with various diseases. To explore the relationship between MCP-1 and CCR2 polymorphisms and IgA nephropathy (IgAN), we conducted this case-control study by enrolling 351 IgAN patients and 310 health controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate potential associations of MCP-1 and CCR2 polymorphisms with susceptibility and clinical parameters of IgAN. No statistical differences between IgAN group and the control group in the MCP-1 -2518 and CCR2 +190 genotypic groups were observed ( P > 0.05). Individuals with MCP-1 -2518 GG genotypes had a higher blood pressure (GG vs. AA+AG: OR = 1.79, 95% CI = 1.07-2.99, P = 0.026) and Lee’s grade (GG vs. AA+AG: OR = 2.05, 95% CI = 1.19-3.54, P = 0.009; GG vs. AA: OR = 2.24, 95% CI = 1.19-4.20, P = 0.01), compared with patients with AA/AG genotypes. A significant association between CCR2 +190 polymorphism and Lee’s grades was observed (GA+AA vs. GG: OR = 2.66, 95% CI = 1.63-4.35, P < 0.001; GA vs. AA+GG: OR = 2.27, 95% CI = 1.39-3.70, P = 0.001). Our results indicated that MCP-1 and CCR2 polymorphisms may influence the progression of IgAN, but not increase/decrease its susceptibility.

Optical emission of laser ablation plasma on a shale target surface provides sensitive laser-induced breakdown spectrometry (LIBS) detection of major, minor or trace elements. An exploratory study for the characterization of the plasma induced on shale materials was carried out with the aim to trigger a crucial step towards the quantitative LIBS measurement. In this work, the experimental strategies that optimize the plasma generation on a pressed shale pellet surface are presented. The temporal evolution properties of the plasma induced by ns Nd:YAG laser pulse at the fundamental wavelength in air were investigated using time-resolved space-integrated optical emission spectroscopy. The electron density as well as the temperatures of the plasma were diagnosed as functions of the decay time for the bulk plasma analysis. In particular, the values of time-resolved atomic and ionic temperatures of shale elements, such as Fe, Mg, Ca, and Ti, were extracted from the well-known Boltzmann or Saha–Boltzmann plot method. Further comparison of these temperatures validated the local thermodynamic equilibrium (LTE) within specific interval of the delay time. In addition, the temporal behaviors of the signal-to-noise ratio of shale elements, including Si, Al, Fe, Ca, Mg, Ba, Li, Ti, K, Na, Sr, V, Cr, and Ni, revealed the coincidence of their maximum values with LIBS LTE condition in the time frame, providing practical implications for an optimized LIBS detection of shale elements. Analytical performance of LIBS was further evaluated with the linear calibration procedure for the most concerned trace elements of Sr, V, Cr, and Ni present in different shales. Their limits of detection obtained are elementally dependent and can be lower than tens of parts per million with the present LIBS experimental configurations. However, the occurrence of saturation effect for the calibration curve is still observable with the increasing trace element content, indicating that, due to the complex composition of shale materials, the omnipresent “matrix effect” is still a great challenging for the performance of quantitative LIBS measurement even in the framework of the LTE approach.

The mechanism of immunoglobulin A nephropathy (IgAN) remains unclear. Genetic factors may be associated with the risk of IgAN. This study aims to identify the possible association of M268T (rs699) in the Angiotensinogen (AGT) gene and A1166C (rs5186) in the Angiotensin II receptor type 1 (ATR1) gene with IgAN risk.Study subjects included 351 patients with IgAN and 310 controls from the Chinese population. The tag SNPs (tSNPs) were genotyped by Sequenom MassARRAY RS1000. Statistical analysis of the association between tSNPs and IgAN was performed using the χ(2) test and SNPStats software.The AGT (M268T) genotypes were distributed in IgAN as CC 61.9%, CT 34.8%, and TT 3.2%, while in controls CC 64.1%, CT 31.3%, and TT 4.6%. Distribution of ATR1 (A1166C) was AA 87.7%, CA 12.3%, and CC 0%, while in controls AA 87.2%, CA 12%, and CC 0.8%. We further analyzed tSNPs under different inheritance models and found that there were no significant differences in the genotypes and allele frequencies of rs699 and rs5186 between two groups (p 0.05). We also analyzed tSNPs based on the rate of pressure, proteinuria and Lee's classification, and no significant differences were found in the models (p 0.05).rs699 in the AGT gene and rs5186 in the ATR1 gene were not associated with the risk and clinical outcomes of IgAN.

According to the medium and long term development planning of railway networks, China will built “eight vertical and horizontal” high speed railway network during 13th five-year. With the rapid development of mobile smart terminals, the rail dedicated communication system using GSM-R system cannot satisfy the passengers' communication requirement. As high frequency communication has been considered in 3GPP new radio to achieve higher capacity, this paper studies the high-speed communication using 60GHz millimeter wave. In this paper, we propose a beam switching mechanism based on train position information in high speed railway scenario. The proposed mechanism can realize fast intra-TRP/inter-TRP beam switching and the simulation result demonstrates Gigabit data rate can be provided for passengers.

Background/Aims: Endothelial nitric oxide synthase (eNOS) is one of the most important enzymes for producting nitric oxide (NO), which regulate the function of many organs and cells. The single nucleotide polymorphisms (SNPs) of eNOS were found to be associated with many kidney diseases. However, it is lack of relevant studies to evaluate the associations between eNOS polymorphisms and immunoglobulin A nephropathy (IgAN). This case-control study aimed to evaluate the relationship between eNOS polymorphisms and IgAN. Methods: We recruited 351 IgAN patients and 310 age- and sex-matched healthy controls from Northwest China. Sequenom MassARRAY was used to detect the genotypes of two common eNOS SNPs (rs1799983 and rs2070744). Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by the Chi square test to evaluate the associations between eNOS and IgAN. Phase 2.1 was used to conduct haplotype analysis. Results: In the overall analysis, we found that the rs1799983 polymorphism was associated with a decreased risk of IgAN (G/T vs. G/G: OR=0.57, 95%CI=0.34–0.96; G/T+T/T vs. G/G: OR=0.52, 95%CI=0.31–0.86; G/T vs. G/G-T/T: OR=0.60, 95%CI=0.36–0.99; Log-additive model: OR=0.48, 95%CI=0.30–0.78). Haplotype analysis indicated that Trs1799983Crs2070744 is a protective factor against IgAN (OR=0.62, 95%CI=0.42––0.92). However, no significant differences were found between the two SNPs (rs1799983 and rs2070744) and clinical features (age, sex, blood pressure, and Lee’s grade) of IgAN. Conclusion: The eNOS gene rs1799983 polymorphism and Trs1799983Crs2070744 haplotype may reduce the risk of IgAN in Chinese populations.

To study the metabolites of glycyrrhetic acid (GA) in rat bile, an analytical method was developed to identify GA and its metabolites by liquid chromatography mass spectrometry (LC-MS). Rat bile was collected after i.v. injection of GA. Three major GA-related peaks were detectable in rat bile by high-performance liquid chromatography (HPLC) analysis at 254 nm. LC-MS spectra showed their protonated molecular ions at m/z 727, 647, and 551. Furthermore, the three metabolites were also confirmed to exist in rat bile on LC-MS total ion chromatogram (TIC). Taken together with the susceptible nature to beta-glucuronidase digestion and alkaline conditions, they were identified to be a novel sulfate-glucuronide diconjugate and the known monoglucuronide and sulfate conjugate, respectively.

A modern trend in the development of laser-based analytical instruments is to integrate more functions in a single device, which could supply complementary information and improve the capability to identify different components. This review presents historical development of the combined analysis by laser-induced breakdown spectroscopy (LIBS) and Raman Spectroscopy, which briefly describes basic instrumental principles and technological aspects of the hyphenated technique, as well as the requirements in the design of interactive instruments, including laser systems, optical systems for laser beam delivery, emission collection devices, and spectrum measurement systems. Various configurations of the combined instrumentation have been designed and used depending on the different applications, such as pigment analysis in the cultural heritage field, detection of explosives, analysis of geological samples, and applications in future planetary missions. In addition, the feasibility, applicability, and...

In this letter, we propose a distance-based ordered detection (DBD) algorithm for spatial modulation (SM) to reduce the receiver complexity and achieve a near maximum likelihood (ML) performance. The proposed algorithm firstly compensates the channel attenuation and obtains the estimated symbols with transmit antenna indices, then orders the indices based on the distances between these symbols and their demodulation constellations. A searching method is developed to obtain the final decision through a trade-off between performance and complexity. The equivalence between DBD and ML algorithms is also proved by theoretical analysis. Furthermore, a new low-complexity soft output DBD (SODBD) algorithm is developed for coded SM systems. The simulation results show that DBD algorithm has a close performance to ML algorithm while effectively reducing the complexity compared to conventional near-ML algorithms.

Background/Aims: IFN-γ was reported to be involved in the development and progression of Immunoglobulin A nephropathy (IgAN), however, few studies have investigated the association between IFN-γ polymorphisms and IgAN. Therefore, we performed a case-control study to assess the association between IFN-γ polymorphisms and the risk of IgAN. Methods: Sequenom MassARRAY was used to genotype two SNPs (rs1861494 and rs2430561) in 351 patients with IgAN and 310 healthy controls. Associations were evaluated as odd ratios (OR) with 95% confidence intervals (CI). Results: No association was found between IFN-γ rs1861494 and IgAN risk or clinical parameters. For rs2430561, the AA genotype was more common in patients with IgAN, compared with controls (AT vs. AA: OR = 0.57, P = 0.035). IFN-γ-rs2430561 T allele may be a protective factor for IgAN susceptibility (T vs. A: OR = 0.59, P = 0.04). Subgroup analysis based on clinical features revealed no significant association between rs2430561 polymorphism and clinical data such as gender, 24-h urine protein, blood pressure, Oxford classifcation and estimated glomerular fltration rate. IgAN patients had a higher IFN-γ serum level than healthy controls and patients with rs1861494 AA genotype had a higher IFN-γ serum level compared with those with AG/GG genotypes. Conclusions: IFN-γ polymorphisms may be involved in the development and progression of IgAN.

Megsin is a mesangial cell-predominant gene that encodes a serpin family protein which is expressed in the renal mesangium. Overexpression of megsin has been observed in the glomeruli of patients with IgA nephropathy (IgAN). The aim of this study was to evaluate the association of megsin polymorphisms (rs1055901 and rs1055902) with IgAN in a Chinese population. We examined 351 patients with histologically proven IgAN and compared them with 310 age, sex, and ethnicity-matched healthy subjects. Two single nucleotide polymorphisms (SNPs) in megsin were genotyped by Sequenom MassARRAY. SPSS 18.0 was used for statistical analyses, and SNP Stats to test for associations between these polymorphisms and IgAN risk. Odds ratios with 95% confidence intervals were used to assess the relationships. We found that rs1055901 and rs1055902 SNPs were not correlated with susceptibility to IgAN in Northwest Chinese population. Analyses of the relationship between genotypes and clinical variables indicated that in patients with IgAN, rs1055901 was associated with 24-hour proteinuria, an increase in blood pressure, and Lee's grade (P = 0.04, 0.02, and 0.04, respectively), and rs1055902 was associated with 24-hour proteinuria and Lee's grade (P = 0.03 and 0.01, respectively). However, the results showed no association between these gene variants and sex of the patients. These results indicate that megsin gene variants may play a role in the severity, development, and/or progression of IgAN in Northwest Chinese population.