Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils

Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea

Enhanced production of highly methylated brGDGTs linked to anaerobic bacteria from sediments of the Mariana Trench

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are widely used in terrestrial paleoclimatic reconstructions. Recent studies have reported that brGDGTs can also be produced by marine bacteria. However, the environmental factors influencing marine-derived brGDGTs and their source organisms remain largely unknown. Here, we investigated the distribution and composition of brGDGTs and a suite of their putative derivatives called overly branched GDGTs (obGDGTs) in the Mariana Trench core sediments (water depth 8300 m, core length 320 cm), as well as the composition of bacterial communities. The ratio of the branched over isoprenoid tetraethers (BIT) was 0.03-0.21 (average 0.07; SD = 0.04; n = 21) and the ratio ΣIIIa/ΣIIa of brGDGTs was 0.93-7.47 (average 3.39; SD = 1.73; n = 21), which support the in situ production of brGDGTs. Co-occurrence network analysis revealed that a total of 33 types of bacteria at the order level (e.g., Armatimonadota DG-56, Proteobacteria Rhodospirillales, Chloroflexi SAR202_clade) were closely related to the distribution of brGDGTs and obGDGTs, which could be potential sources for these compounds. The abrupt increase in brGDGT and obGDGT concentrations in deeper oxygen-depleted sediments and their good correlations with anaerobic bacterial abundances suggest that these brGDGTs and obGDGTs may be produced by anaerobic bacteria residing in the anoxic sediments. Considerable variation in the degrees of methylation and cyclization of brGDGTs (obGDGTs) under different redox conditions indicate that sediment oxygen levels may have a profound impact on the presence and abundance of brGDGTs and obGDGTs, which should be considered when applying them for paleo-temperature or pH reconstructions. This study shows that brGDGTs and obGDGTs obtained from the Mariana Trench were probably produced by a variety of bacterial phyla indigenous in the hadal ocean, which are different from Acidobacteria commonly considered to be major terrestrial sources of brGDGTs

Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils

Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea

Hand, Foot, and Mouth Disease in China: critical community size and spatial vaccination strategies

Hand Foot and Mouth Disease (HFMD) constitutes a considerable burden for health care systems across China. Yet this burden displays important geographic heterogeneity that directly affects the local persistence and the dynamics of the disease, and thus the ability to control it through vaccination campaigns. Here, we use detailed geographic surveillance data and epidemic models to estimate the critical community size (CCS) of HFMD associated enterovirus serotypes CV-A16 and EV-A71 and we explore what spatial vaccination strategies may best reduce the burden of HFMD. We found CCS ranging from 336,979 (±225,866) to 722,372 (±150,562) with the lowest estimates associated with EV-A71 in the southern region of China where multiple transmission seasons have previously been identified. Our results suggest the existence of a regional immigration-recolonization dynamic driven by urban centers. If EV-A71 vaccines doses are limited, these would be optimally deployed in highly populated urban centers and in high-prevalence areas. If HFMD vaccines are included in China's National Immunization Program in order to achieve high coverage rates (>85%), routine vaccination of newborns largely outperforms strategies in which the equivalent number of doses is equally divided between routine vaccination of newborns and pulse vaccination of the community at large

Accuracy of epidemiological inferences based on publicly available information: retrospective comparative analysis of line lists of human cases infected with influenza A(H7N9) in China

Background: Appropriate public health responses to infectious disease threats should be based on best-available evidence, which requires timely reliable data for appropriate analysis. During the early stages of epidemics, analysis of ‘line lists’ with detailed information on laboratory-confirmed cases can provide important insights into the epidemiology of a specific disease. The objective of the present study was to investigate the extent to which reliable epidemiologic inferences could be made from publicly-available epidemiologic data of human infection with influenza A(H7N9) virus. Methods: We collated and compared six different line lists of laboratory-confirmed human cases of influenza A(H7N9) virus infection in the 2013 outbreak in China, including the official line list constructed by the Chinese Center for Disease Control and Prevention plus five other line lists by HealthMap, Virginia Tech, Bloomberg News, the University of Hong Kong and FluTrackers, based on publicly-available information. We characterized clinical severity and transmissibility of the outbreak, using line lists available at specific dates to estimate epidemiologic parameters, to replicate real-time inferences on the hospitalization fatality risk, and the impact of live poultry market closure. Results: Demographic information was mostly complete (less than 10% missing for all variables) in different line lists, but there were more missing data on dates of hospitalization, discharge and health status (more than 10% missing for each variable). The estimated onset to hospitalization distributions were similar (median ranged from 4.6 to 5.6 days) for all line lists. Hospital fatality risk was consistently around 20% in the early phase of the epidemic for all line lists and approached the final estimate of 35% afterwards for the official line list only. Most of the line lists estimated >90% reduction in incidence rates after live poultry market closures in Shanghai, Nanjing and Hangzhou. Conclusions: We demonstrated that analysis of publicly-available data on H7N9 permitted reliable assessment of transmissibility and geographical dispersion, while assessment of clinical severity was less straightforward. Our results highlight the potential value in constructing a minimum dataset with standardized format and definition, and regular updates of patient status. Such an approach could be particularly useful for diseases that spread across multiple countries

Spin-orbit-coupled triangular-lattice spin liquid in rare-earth chalcogenides

Spin-orbit coupling is an important ingredient in many spin liquid candidate materials, especially among the rare-earth magnets and Kitaev materials. We explore the rare-earth chalcogenides NaYbS$_2$ where the Yb$^{3+}$ ions form a perfect triangular lattice. Unlike its isostructural counterpart YbMgGaO$_4$ and the kagom\'{e} lattice herbertsmithite, this material does not have any site disorders both in magnetic and non-magnetic sites. We carried out the thermodynamic and inelastic neutron scattering measurements. The magnetic dynamics could be observed with a broad gapless excitation band up to 1.0 meV at 50 mK and 0 T, no static long-range magnetic ordering is detected down to 50 mK. We discuss the possibility of Dirac spin liquid for NaYbS$_2$. We identify the experimental signatures of field-induced transitions from the disordered spin liquid to an ordered antiferromagnet with an excitation gap at finite magnetic fields and discuss this result with our Monte Carlo calculation of the proposed spin model. Our findings could inspire further interests in the spin-orbit-coupled spin liquids and the magnetic ordering transition from them

Association of β2-Agonist Receptor Gene Polymorphisms with Acute Exacerbations of COPD: A Prospective Observational Study

Objective. To investigate the relationship between β2-agonist receptor gene polymorphisms and acute exacerbations of chronic obstructive pulmonary disease (COPD). Methods. Retrospective analysis of 99 patients in the respiratory and critical care unit of Fujian Provincial Hospital from 2018 to 2020. The clinical characteristics of different genotypes were compared, and the treatments of different genotypes and the analysis of factors associated with acute exacerbations of COPD were compared. Results. During the 12-month follow-up period, 53 patients developed acute exacerbations, with the 16Arg/Arg homozygous requiring significantly more antibiotics and hormones than the other two genotypes; when agonist receptor 16 gene polymorphism was associated with the risk of acute exacerbation, 16Arg/Gly patients had a 5.286-fold increased risk of acute exacerbation (OR = 6.286, 95% CI. 1.476–26.759, P=0.013). 16Arg/Arg patients had a 5.060-fold increased risk of acute exacerbation (OR = 6.060, 95% confidence interval: 1.407–26.161, P=0.016). Conclusion. Acute exacerbation of 16Arg/Arg COPD is very serious; 16Arg/Gly increases the risk of acute exacerbation in COPD patients; and provides help for future treatment and management options of the disease

Study on the mechanism of water inrush in the arid western mining area

The analysis found that the coal mining process in the western mining area has the mining loss and disaster effect of the water-rich aquifer of the coal seam roof, which is mainly manifested by the overburden water in the roof. On this basis, the formation and development of the separation water of the roof is proposed, and the mechanism of the water inrush from the layer is revealed. It is found that there is hydrostatic pressure and hydrodynamic pressure in the separated water, under the combined action of bed separation water pressure, the mining-induced fracture and water-isolation layer tension fracture are connected, which causes water inrushing in the coal working face of the mine, and provides a theoretical guarantee for the large-scale development of coal resources in western mining areas