Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress.

The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were "sulfur metabolism" and "glutathione metabolism", and the target pathways of NAP subfamily SiNACs were "ribosome" and "phenylpropanoid biosynthesis". This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

Assessment of the capability of cadmium accumulation and translocation among 31 willows: four patterns of willow biomass variation response to cadmium.

Cadmium (Cd) pollution threatens food security and the environment. Willow species (Salix, Salicaceae) exhibit a remarkable potential to restore Cd-polluted sites due to their high biomass production and high Cd accumulation capacities. This study examined the Cd accumulation and tolerance in 31 genotypes of shrub willow in hydroponic conditions at varying Cd levels (0 µM Cd, 5 µM Cd, and 20 µM Cd). The root, stem, and leaf biomass of 31 shrub willow genotypes showed significant differences to Cd exposure. Among 31 willow genotypes, four patterns of biomass variation response to Cd were identified: insensitive to Cd; growth inhibition due to excessive Cd supply (high Cd inhibition); low Cd causing inhibited growth, whereas high Cd leading to increased biomass (U-shape); and growth increment with excessive Cd exposure (high Cd induction). The genotypes belonging to the "insensitive to Cd" and/or "high Cd induction" were candidates for the utilization of phytoremediation. Based on the analysis of Cd accumulation of 31 shrub willow genotypes at high and low Cd levels, genotypes 2372, 51-3, and 1052 obtained from a cross between S. albertii and S. argyracea grew well and accumulated relatively more Cd levels than other genotypes. In addition, for Cd-treated seedlings, root Cd accumulation was positively correlated with shoot Cd accumulation and total Cd uptake, demonstrating that Cd accumulation in roots could serve as a biomarker for evaluating the Cd extraction capacity of willows, especially in hydroponics screening. The results of this study screened out willow genotypes with high Cd uptake and translocation capacities, which will provide valuable approaches for restoring Cd-contaminated soils with willows.

Molecular Epidemiology and Evolution of Coxsackievirus A9.

Nineteen CVA9 isolates were obtained between 2010 and 2019 from six provinces of mainland China, using the HFMD surveillance network established in China. Nucleotide sequencing revealed that the full-length VP1 of 19 CVA9 isolates was 906 bases encoding 302 amino acids. The combination of the thresholds of the phylogenetic tree and nucleotide divergence of different genotypes within the same serotype led to a value of 15-25%, and enabled CVA9 worldwide to be categorized into ten genotypes: A-J. The phylogenetic tree showed that the prototype strain was included in genotype A, and that the B, C, D, E, H, and J genotypes disappeared during virus evolution, whereas the F, I, and G genotypes showed co-circulation. Lineage G was the dominant genotype of CVA9 and included most of the strains from nine countries in Asia, North America, Oceania, and Europe. Most Chinese strains belonged to the G genotype, suggesting that the molecular epidemiology of China is consistent with that observed worldwide. The 165 partial VP1 strains (723 nt) showed a mean substitution rate of 3.27 × 10-3 substitution/site/year (95% HPD range 2.93-3.6 × 10-3), dating the tMRCA of CVA9 back to approximately 1922 (1911-1932). The spatiotemporal dynamics of CVA9 showed the spread of CVA9 obviously increased in recent years. Most CVA9 isolates originated in USA, but the epidemic areas of CVA9 are now concentrated in the Asia-Pacific region, European countries, and North America. Recombination analysis within the enterovirus B specie (59 serotypes) revealed eight recombination patterns in China at present, CVB4, CVB5, E30, CVB2, E11, HEV106, HEV85, and HEV75. E14, and E6 may act as recombinant donors in multiple regions. Comparison of temperature sensitivity revealed that temperature-insensitive strains have more amino acid substitutions in the RGD motif of the VP1 region, and the sites T283S, V284M, and R288K in the VP1 region may be related to the temperature tolerance of CVA9.

Spatial-temporal heterogeneity and meteorological factors of hand-foot-and-mouth disease in Xinjiang, China from 2008 to 2016.

The study aims to depict the temporal and spatial distributions of hand-foot-and-mouth disease (HFMD) in Xinjiang, China and reveal the relationships between the incidence of HFMD and meteorological factors in Xinjiang. With the national surveillance data of HFMD in Xinjiang and meteorological parameters in the study area from 2008 to 2016, in GeoDetector Model, we examined the effects of meteorological factors on the incidence of HFMD in Xinjiang, China, tested the spatial-temporal heterogeneity of HFMD risk, and explored the temporal-spatial patterns of HFMD through the spatial autocorrelation analysis. From 2008 to 2016, the HFMD distribution showed a distinct seasonal pattern and HFMD cases typically occurred from May to July and peaked in June in Xinjiang. Relative humidity, precipitation, barometric pressure and temperature had the more significant influences on the incidence of HFMD than other meteorological factors with the explanatory power of 0.30, 0.29, 0.29 and 0.21 (P<0.000). The interaction between any two meteorological factors had a nonlinear enhancement effect on the risk of HFMD. The relative risk in Northern Xinjiang was higher than that in Southern Xinjiang. Global spatial autocorrelation analysis results indicated a fluctuating trend over these years: the positive spatial dependency on the incidence of HFMD in 2008, 2010, 2012, 2014 and 2015, the negative spatial autocorrelation in 2009 and a random distribution pattern in 2011, 2013 and 2016. Our findings revealed the correlation between meteorological factors and the incidence of HFMD in Xinjiang. The correlation showed obvious spatiotemporal heterogeneity. The study provides the basis for the government to control HFMD based on meteorological information. The risk of HFMD can be predicted with appropriate meteorological factors for HFMD prevention and control.

Spatiotemporal characters and influence factors of hand, foot and mouth epidemic in Xinjiang, China.

Hand, foot and mouth (HFM) disease is a common childhood illness. The paper aims to capture the spatiotemporal characters, and investigate the influence factors of the HFM epidemic in 15 regions of Xinjiang province from 2008 to 2017, China. Descriptive statistical analysis shows that the children aged 0-5 years have a higher HFM incidence, mostly boys. The male-female ratio is 1.5:1. Through the scanning method, we obtain the first cluster high-risk areas. The cluster time is usually from May to August every year. A spatiotemporal model is proposed to analyze the impact of meteorological factors on HFM disease. Comparing with the spatial model, the model is more effective in terms of R2, AIC, deviation, and mean-square error. Among meteorological factors, the number of HFM cases generally increases with the intensity of rainfall. As the temperature increases, there are more HFM patients. Some regions are mostly influenced by wind speed. Further, another spatiotemporal model is introduced to investigate the relationship between HFM disease and socioeconomic factors. The results show that socioeconomic factors have significant influence on the disease. In most areas, the risk of HFM disease tends to rise with the increase of the gross domestic product, the ratios of urban population and tertiary industry. The incidence is closely related to the number of beds and population density in some regions. The higher the ratio of primary school, the lower the number of HFM cases. Based on the above analysis, it is the key measure to prevent and control the spread of the HFM epidemic in high-risk areas, and influence factors should not be ignored.

Spatial-temporal mapping and risk factors for hand foot and mouth disease in northwestern inland China.

BACKGROUND: Hand foot and mouth disease (HFMD) is becoming one of the common human infectious diseases in China. Previous studies have described HFMD in tropical or coastal areas of Asia-Pacific countries. However, limited studies have thoroughly studied the epidemiology and potential risk factors for HFMD in inland areas with complex environmental conditions. METHODOLOGY/PRINCIPAL FINDINGS: Using the data from 2009 to 2018 on reported cases of Xinjiang Uighur Autonomous Region, we characterized the epidemic features of HFMD. Panel negative binomial model was used to identify climate, geographical and demographic determinants for HFMD incidence. A total of 70856 HFMD cases (average annual incidence: 305 per million persons) were reported in Xinjiang during the 10-year study period, of which 10393 (14.7%) were laboratory-confirmed and 98 (0.1%) were severe. HFMD peaked in summer every year during the study period, and incidence in 2012, 2015, 2016 and 2018 had minor peaks in autumn. After adjusting the school or holiday month, multiple factors were found to affect HFMD epidemiology: urban area being major land cover type (incidence risk ratio, IRR 2.08; 95% CI 1.50, 2.89), higher gross domestic product per capita (IRR 1.14; 95% CI 1.11, 1.16), rise in monthly average temperature (IRR 1.65; 95% CI 1.61, 1.69) and monthly accumulative precipitation (IRR 1.20; 95% CI 1.16, 1.24) predicted increase in the incidence of HFMD; farmland being major land cover type (IRR 0.72; 95% CI 0.64, 0.81), an increase of percentage of the minority (IRR 0.91; 95% CI 0.89, 0.93) and population density (IRR 0.98; 95% CI 0.98, 0.99) were related to a decrease in the incidence of HFMD. CONCLUSIONS/SIGNIFICANCE: In conclusion, the epidemic status of HFMD in Xinjiang is characterized by low morbidity and fatality. Multiple factors have significant influences on the occurrence and transmission of HFMD in Xinjiang.

Survey of Traveler's Diarrhea: Epidemiology and Testing Reveal the Source.

OBJECTIVE: To understand the causes and transmission routes of, as well as risk factors, for a Salmonella outbreak in a tour group. METHOD: A retrospective cohort design was used to conduct an epidemiological field investigation. Real-time fluorescent quantitative PCR, bacterial culture, and serological identification methods were used for pathogen detection and identification. RESULT: There were 7 cases of illness, and the attack rate was 46.67%. The onset date was concentrated on May 9 and 10. All cases were found in the tour group, and no cases occurred in the nontour group. The results of this retrospective cohort study showed that the consumption of boiled eggs for breakfast on May 9 was a common factor (R 2 = 6.67, P=0.023). Salmonella enteritidis was identified from the patients' stool and vomit. CONCLUSION: The food poisoning epidemic was caused by Salmonella enteritidis. In the summer and autumn, attention should be paid to preservation, processing, and cooking of food to avoid bacterial contamination. To prevent sickness, travelers should know the disease prevalence at their destinations in advance.

Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis.

The complete Holothuria leucospilata mitochondrial genome was determined and analyzed in this work. It had a circular mapping molecular with a total length of 15,904 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analysis showed that H. leucospilata clustered together with Holothuria scabra and Holothuria forskali. The complete mitochondrial genome provided in this work would be used for elucidation of Holothuroidea conservation genetics and evolutionary relationships.

The H2/CH4 ratio during serpentinization cannot reliably identify biological signatures.

Serpentinization potentially contributes to the origin and evolution of life during early history of the Earth. Serpentinization produces molecular hydrogen (H2) that can be utilized by microorganisms to gain metabolic energy. Methane can be formed through reactions between molecular hydrogen and oxidized carbon (e.g., carbon dioxide) or through biotic processes. A simple criterion, the H2/CH4 ratio, has been proposed to differentiate abiotic from biotic methane, with values approximately larger than 40 for abiotic methane and values of <40 for biotic methane. The definition of the criterion was based on two serpentinization experiments at 200 °C and 0.3 kbar. However, it is not clear whether the criterion is applicable at a wider range of temperatures. In this study, we performed sixteen experiments at 311-500 °C and 3.0 kbar using natural ground peridotite. Our results demonstrate that the H2/CH4 ratios strongly depend on temperature. At 311 °C and 3.0 kbar, the H2/CH4 ratios ranged from 58 to 2,120, much greater than the critical value of 40. By contrast, at 400-500 °C, the H2/CH4 ratios were much lower, ranging from 0.1 to 8.2. The results of this study suggest that the H2/CH4 ratios cannot reliably discriminate abiotic from biotic methane.

The complete mitochondrial genome sequence of Acentrogobius sp. (Gobiiformes: Gobiidae) and phylogenetic studies of Gobiidae.

At present, few morphological descriptions are available for Acentrogobius species and there exist some confused issues on the species classification and phylogeny. In this study, we first determined and described the complete mitochondrial genome of Acentrogobius sp. The complete mitogenome sequence is 17 083 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.9% A, 26.2% T, 28.5% C, and 16.4% G, with a slight AT bias (55.1%). To furthermore validate the new determined sequences, phylogenetic trees involving all the Gobiidae species available in GenBank database were constructed. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Gobiiformes.

Clinical and genetic mapping of X chromosome in the X-linked dominant inherited Alport's syndrome.

To study the hereditary mode and clinical characteristics and detect mutations of gene COL4A5 encoding type IV collagen a5 chain among family members of an X-linked dominant inherited Alport's syndrome (AS) family of China, we studied all of 38 family members of whom 2 volunteers underwent renal biopsy. Genomic DNA from all members of the AS family was characterized. All of 51 exons of COL4A5 gene were amplified by polymerase chain reaction (PCR) with the primers synthesized according to the published flanking intervening sequences. PCR products were further analyzed by agarose gel electrophoresis and single strand conformation polymorphism (SSCP) analysis. The study subjects revealing polymorphism by SSCP analysis were directly sequenced. Suspected exons were analyzed with reverse sequencing. Six males and 9 females of the family were diagnosed to have AS by clinical manifestations, family history and/or renal biopsy. Four patients died of end-stage renal disease (ESRD), and 1 patient received kidney transplantation. In the rest of the family members renal function remained normal, however, 22 (58%) revealed hematuria, 11/22 (59%) of them also had proteinuria. The hearing loss was detected in 6 (16%) and ocular lesion in 20 (53%) of family members. By PCR-SSCP analysis, 17 PCR products were identified with different mobility of single strand DNA in volunteers and 9 suspected mutations were revealed with DNA sequencing analysis, but all of which could not be proven by bidirectional sequencing analysis. We conclude that the incidence of hematuria and ophthalmopathy is higher in the X-linked dominant inherited AS in this Chinese family, while some patients have isolated hematuria. Bidirectional sequence analysis should be taken to identify mutations of certain genes. No mutations were found on the region of exons of gene COL4A5.

[Study on the surface markers on peripheral blood dendritic cells and their secretion of IL-12 and IFN-alpha in SLE patients].

AIM: To analyze the surface markers on peripheral blood dendritic cells (DCs) in SLE patients and explore the relationship between the DCs and pathogenesis of SLE. METHODS: The peripheral blood monouclear cells (PBMCs) were separated by density gradient centrifugation. After culture of 3 hours in tissue culture flask, the suspended cells were removed and GM-CSF, IL-4 and TNF-alpha were used to stimulate the proliferation and maturation of the peripheral blood DCs from normal persons and SLE patients. The surface markers on the DCs were analyzed by flow cytometry and the levels of IL-12 and IFN-alpha in supernatants were measured by ELISA after culture of 9 days. RESULTS: The positive percentages of CD1a, CD11c, CD40, CD83 and CD123 expressed on DCs of SLE patients were (58.88+/-7.64)%, (54.4+/-10.88)%, (37.29+/-8.08)%, (57.76+/-11.54)% and (13.14+/-4.44)%, respectively, whereas those of normal subjects were (47.71+/-4.01)%, (43.12+/-8.82)%, (28.59+/-7.07)%, (48.31+/-8.79)% and (9.85+/-3.97)%, respectively, (P<0.05). But the positive proportion of CD80 expression was (55.16+/-10.12)% in SLE group and (47.95+/-12.21)% in the control group, without significant difference (P>0.05). The level of IL-12 in SLE group was (9.78+/-0.76) ng/L, higher than that in normal group. The level of IFN-alpha in SLE group (2.95+/-0.61) ng/L was not significant difference from that in control group (2.70+/-0.29) ng/L (P>0.05). And there was no significant difference in IL-12 and IFN-alpha levels between non-active and active stages of SLE patients. CONCLUSION: The DCs may be involved in the pathogenetic process of SLE possibly by means of enhancement of antigen presenting function of DCs and secretion of IL-12.