Genomic fingerprints of the world's soil ecosystems.

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.

Leveraging observed soil heterotrophic respiration fluxes as a novel constraint on global-scale models.

Microbially explicit models may improve understanding and projections of carbon dynamics in response to future climate change, but their fidelity in simulating global-scale soil heterotrophic respiration (RH ), a stringent test for soil biogeochemical models, has never been evaluated. We used statistical global RH products, as well as 7821 daily site-scale RH measurements, to evaluate the spatiotemporal performance of one first-order decay model (CASA-CNP) and two microbially explicit biogeochemical models (CORPSE and MIMICS) that were forced by two different input datasets. CORPSE and MIMICS did not provide any measurable performance improvement; instead, the models were highly sensitive to the input data used to drive them. Spatial variability in RH fluxes was generally well simulated except in the northern middle latitudes (~50°N) and arid regions; models captured the seasonal variability of RH well, but showed more divergence in tropic and arctic regions. Our results demonstrate that the next generation of biogeochemical models shows promise but also needs to be improved for realistic spatiotemporal variability of RH . Finally, we emphasize the importance of net primary production, soil moisture, and soil temperature inputs, and that jointly evaluating soil models for their spatial (global scale) and temporal (site scale) performance provides crucial benchmarks for improving biogeochemical models.

Molecular Determination of Organic Adsorption Sites on Smectite during Fe Redox Processes Using ToF-SIMS Analysis.

Turnover of soil organic carbon (SOC) is strongly affected by a balance between mineral protection and microbial degradation. However, the mechanisms controlling the heterogeneous and preferential adsorption of different types of SOC remain elusive. In this work, the heterogeneous adsorption of humic substances (HSs) and microbial carbon (MC) on a clay mineral (nontronite NAu-2) during microbial-mediated Fe redox cycling was determined using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results revealed that HSs pre-adsorbed on NAu-2 would partially inhibit structural modification of NAu-2 by microbial Fe(III) reduction, thus retarding the subsequent adsorption of MC. In contrast, NAu-2 without precoated HSs adsorbed a significant amount of MC from microbial polysaccharides as a result of Fe(III) reduction. This was attributed to the deposition of a thin Al-rich layer on the clay surface, which provided active sites for MC adsorption. This study provides direct and detailed molecular evidence for the first time to explain the preferential adsorption of MC over HSs on the surface of clay minerals in iron redox processes, which could be critical for the preservation of MC in soil. The results also indicate that ToF-SIMS is a unique tool for understanding complex organic-mineral-microbe interactions.

Nrf2 mediates the antinociceptive activity of dexmedetomidine in an acute inflammatory visceral pain rat model by activating the NF-κB sensor.

Dexmedetomidine (DEX) is a highly selective α2 adrenoceptor agonist. In this study, we evaluated the antalgic effect of DEX on acetic acid-induced acute inflammatory visceral pain (AIVP) in rats. Additionally, we evaluated the role of Nrf2 signalling in antinociception. We administered acetic acid to male Sprague Dawley rats that were treated with DEX or saline. Twenty rats were randomly classified into the following groups: normal, model, vehicle, or DEX group. Both q-RT PCR and enzyme-linked immunosorbent assay data suggested that interleukin 1ß (IL-1ß), tumour necrosis factor α, and IL-6 were upregulated in the spinal cord. Western blotting and q-RT PCR analyses were performed to detect the protein and mRNA expression levels of Nrf2, Keap1, and HO-1 in the spinal cord. The DEX group exhibited a significant downregulation in Nrf2/Keap1/HO-1 signal activation compared with the model group. Furthermore, we used the Nrf2-/- knockout AIVP rat model to determine the role of Nrf2 in the antinociceptive effect of DEX. We observed that the Nrf2 knockout blocked the Keap1/Nrf2/HO-1 signal transduction and partially abated the antinociceptive and the anti-inflammatory effects of DEX. Moreover, our data also indicated that DEX treatment decreased the activation and expression of nuclear factor (NF)-κB. However, Nrf2 silencing restored the expression of NF-κB and its phosphorylated form to physiological levels. In summary, our results suggested that Nrf2 signalling plays an important role in the antinociceptive effect of DEX in the AIVP rat model and that Nrf2 exerts its function by enhancing the activation of the NF-κB sensor. SIGNIFICANCE OF THE STUDY: Currently, using the behavioural parameters is not adequate for the diagnosis of AIVP, and there are no studies that have investigated the role and the mechanism of DEX in ameliorating visceral pain. In this study, we demonstrated that acetic acid stimulation in rats induces AIVP. Additionally, the administration of DEX inhibited the acute inflammation response and decreased the visceromotor reaction (behavioural) to algesia. Further, DEX inhibited the Keap1/Nrf2 pathway, which was activated by acetic acid treatment. We suggest that suppressing the inflammatory response could partially regulate the antinociceptive effect of DEX through Nrf2-mediated NF-κB activation associated with AIVP.

A unified complex index to characterize two types of ENSO simultaneously.

It is widely considered the El Nino-South Oscillation (ENSO) has several different types which can be simply classified as eastern Pacific (EP) type and central Pacific (CP) type. However, indices proposed so far can only characterize one single type of ENSO. In this paper, we develop a unified index which can characterize two types of ENSO simultaneously. The new index named as unified complex ENSO index (UCEI) is defined in the complex plane whose real part is NINO3 + NINO4 and imagine part is NINO3-NINO4. The modulus (r) and quadrants (θ) represent the ENSO strength and the ENSO types, respectively. Apart from the EP and CP types, the UCEI could further distinguish the MIX type of ENSO. Besides, the UCEI can capture the type-transforming processes within one ENSO event. Applying UCEI on historical events from 1950 to 2017 demonstrates the new index could be a very useful tool for the research of different types of ENSO.

The triggering receptor expressed by myeloid cells-1 activates TLR4-MyD88-NF-κB-dependent signaling to aggravate ventilation-induced lung inflammation and injury in mice.

The triggering receptor expressed by myeloid cells-1 (TREM-1) plays an important role in infectious and autoimmune diseases but how it contributes to ventilation-induced lung injury (VILI) and inflammation is unclear. Here, we examine the possibility that TREM-1 activates signaling dependent on Toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (Myd88) and nuclear factor (NF)-κB, which leads in turn to VILI. In a mouse model of VILI, which we validated based on lung edema and histopathology as well as cytokine levels, we examine mRNA and protein levels of TREM-1, TLR4, MyD88, NF-κB and its inhibitory protein I-κB in animals subjected to ventilation at normal or high tidal volume. The extent of lung edema, injury and inflammation were higher in the high tidal volume animals, as were the expression levels of all proteins examined. Treatment with TREM-1 agonist aggravated these effects, whereas treatment with TREM-1 antagonist attenuated them. Our results suggest that aggravation of VILI by TREM-1 in mice may be associated with TLR4-MyD88-NF-κB-dependent signaling.

Characterization of iron oxide nanoparticle films at the air-water interface in Arctic tundra waters.

Massive amounts of organic carbon have accumulated in Arctic permafrost and soils due to anoxic and low temperature conditions that limit aerobic microbial respiration. Alternative electron acceptors are thus required for microbes to degrade organic carbon in these soils. Iron or iron oxides have been recognized to play an important role in carbon cycle processes in Arctic soils, although the exact form and role as an electron acceptor or donor remain poorly understood. Here, Arctic biofilms collected during the summers of 2016 and 2017 from tundra surface waters on the Seward Peninsula of western Alaska were characterized with a suite of microscopic and spectroscopic methods. We hypothesized that these films contain redox-active minerals bound to biological polymers. The major components of the films were found to be iron oxide nanoparticle aggregates associated with extracellular polymeric substances. The observed mineral phases varied between films collected in different years with magnetite (Fe2+Fe23+O4) nanoparticles (<5nm) predominantly identified in the 2016 films, while for films collected in 2017 ferrihydrite-like amorphous iron oxyhydroxides were found. While the exact formation mechanism of these Artic iron oxide films remains to be explored, the presence of magnetite and other iron oxide/oxyhydroxide nanoparticles at the air-water interface may represent a previously unknown source of electron acceptors for continual anaerobic microbial respiration of organic carbon within poorly drained Arctic tundra.

Leading modes of tropical Pacific subsurface ocean temperature and associations with two types of El Niño.

Using empirical orthogonal function (EOF) analysis of the monthly tropical Pacific subsurface ocean temperature anomalies (SOTA) from 1979 to 2014, we detected three leading modes in the tropical Pacific subsurface temperature. The first mode has a dipole pattern, with warming in the eastern Pacific and cooling in the western Pacific, and is closely related to traditional El Niño. The second mode has a monopole pattern, with only warming in the central Pacific subsurface. The third mode has a zonal tripole pattern, with warming in the off-equatorial central Pacific and cooling in the far eastern Pacific and western Pacific. The second and third modes are both related to El Niño Modoki. Mode 1 is linked with a Kelvin wave that propagates from the central to the eastern Pacific and is induced by the anomalous westerlies that propagate from the western to the central Pacific. Mode 2 is also linked with a Kelvin wave that propagates from the western to the central Pacific induced by the enhancement of westerlies over the western Pacific. Mode 3 is linked with a Rossby wave that propagates from the central to the western Pacific driven by the anomalous easterlies over the eastern Pacific.

Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics.

An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

[Expression of mutation type GJA8 gene and wild type GJA8 gene of a congenital inherited nuclear cataract family in eukaryotic cells].

OBJECTIVE: To clone the sequence of mutation type GJA8 gene (mGJA8) and wild type GJA8 gene (wGJA8) of a congenital inherited nuclear cataract family and study their expression in eukaryotic cell lines in vitro. METHODS: The mGJA8 and wGJA8 were amplified from this family's DNA and healthy people's DNA by PCR respectively. The mGJA8 and wGJA8 were recombined with plasmid pEGFP-N1 respectively. The accuracy of pEGFP-N1-GJA8 was confirmed by restriction enzyme digestion and DNA sequencing. Finally pEGFP-N1- mGJA8 and pEGFP-N1- wGJA8 and GFP protein were transfected into COS7 cells by lipofectin. The expression of pEGFP-N1-GJA8 and GFP fusion protein were to observe under fluorescence microscope, and to detect by Western-blotting and immunohistochemical staining. RESULTS: The mGJA8 and wGJA8 were cloned successfully. With restricting enzyme digestion analysis and DNA sequencing, recombinant plasmid pEGFP-N1-mGJA8 and pEGFP-N1-wGJA8 were constructed correctly and their GFP fusions were expressed in transfected COS7 cells. The expression of pEGFP-N1-mGJA8 and pEGFP-N1-wGJA8 fusion protein were observed under fluorescence microscope, and detected by Western-blotting and immunohistochemical staining successfully. CONCLUSIONS: The mGJA8 gene and wGJA8 gene are cloned successfully, and pEGFP-N1-mGJA8 and pEGFP-N1-mGJA8 fusion protein can be expressed in COS7 cells, which establish the foundation for further studying the mechanism of this congenital inherited nuclear cataract family.

Protective effect of puerarin on diabetic retinopathy in rats.

Puerarin is a major active ingredient extracted from the traditional Chinese medicine Ge-gen. The purpose of this study is to investigate the protective effect of puerarin on diabetic retinopathy (DR) and its mechanisms in rats. Seventy-two male Wistar rats were selected and divided at random into three main groups: control group, streptozotocin (STZ) group and puerarin + STZ group. Retinal histopathological observation and electron microscopic examination were performed; retinal vascular endothelial growth factor (VEGF) and hypoxia inducible factor 1 (HIF-1alpha) gene expressions were examined by Reverse transcription-polymerase chain reaction (RT-PCR) analysis. Results showed that the DR induced by STZ was significantly reduced by the treatment of puerarin as judged by the reduction of morphological changes of inner nuclear layer and outer nuclear layer at any time-point. Puerarin regulates expressions of VEGF and HIF-1alpha stimulated by STZ. It was concluded that puerarin exerts significant protective effects against DR in rats, likely regulating angiogenesis factors expressions, and thus may be an effective and promising medicine for treatment of DR.

[Comparative study of eukaryotic cell expression of wild-type and Pro370Leu mutation type myocilin gene].

OBJECTIVE: To compare the eukaryotic cell expression of wild-type myocilin (MYOC) (wMYOC) gene and Pro370Leu mutation type MYOC (mMYOC) gene so as to understand the mechanism of primary open angle glaucoma (POAG). METHODS: HeLa cells were cultured and then transfected with the vector pEGFP-N3-wMYOC, recombinant plasmid with wild type MYOC gene and enhanced green fluorescein gene, or the vector pDsRed2-N1-mMYOC, recombinant plasmid with mutation MYOC gene and red fluorescein gene, respectively, or co-transfected with these 2 plasmids. Corresponding blank vectors pEGFP-N3 and pDsRed2-N1 were used as markers. Fluorescence microscopy was used to observe the localization of red fluorescence and green fluorescence. Laser co-focusing microscopy was used to observe the effect of co-transfection. The green and red fluorescein antibodies were examined by Western blotting. RESULTS: Green fluorescence was observed in the cytoplasm of the HeLa cells transfected with the blank vector pEGFP-N3, in an even distribution; and red fluorescence was observed in the cytoplasm of the HeLa cells transfected with the blank vector pDsRed2-N1, in an even distribution too. The cells transfected with pEGFP-N3-wMYOC showed evenly-distributed green fluorescence in the cytoplasm, and the cells transfected with pDsRed2-N1-mMYOC showed red fluorescence in the cytoplasm in a state of aggregation. Both red and green fluorescence could be seen in the cells co-transfected with pEGFP-N3-wMYOC and pDsRed2-N1-mMYOC, both in a state of aggregation and co-localization. Laser co-focusing microscopy showed the same results. Protein with the relative molecular weight of 83,000, identical to that of the recombinant protein of wMYOC protein and green fluorescein, could be found in the culture fluid and cell lysate of the pEGFP-N3-wMYOC-transfected cells; however, could be found in the lysate only but not in the culture fluid of the co-transfected cells. Protein with the relative molecular weight of 81,000, identical to that of the recombinant protein of mMYOC protein and red fluorescein, could be found in the cell lysates of the pDsRed2-N1-mMYOC-transfected cells and the pEGFP-N3-wMYOC and pDsRed2-N1-mMYOC co-transfected cells, but not in the culture fluid of both cells. CONCLUSION: Both the WMYOC and mMYOC genes can be expressed and localized in the cytoplasm. mMYOC protein shoes a tendency of aggregation and disorder in secretion, and affects the expression and secretion of wMYOC, thus influencing the factions of the trabecular meshwork and causing POAG.

[A heterozygous transversion of connexin 50 in a family with congenital nuclear cataract in the northeast of China].

OBJECTIVE: To identify the genetic defect causing autosomal dominant congenital cataract (ADCC) in a five-generation family in the northeast of China. METHODS: Linkage analysis was carried out with polymorphic microsatellites on the Human MapPairs marker set, special known loci. Mutation analysis of the candidate gene in the critical region was performed to detect the potential mutation. RESULTS: The maximum Lod score (2.44 at recombination fraction theta=0) was obtained for markers D1S498,D1S305, and D1S2844. The cataract locus in this family constellation was mapped to 1q21.1 and 21.44 cM interval between D1S2344 and D1S2844, which were known to flank the gene coding Connexin 50 (Cx50) or gap junction protein alpha-8 (GJA8). Sequencing of the coding region of GJA8 gene showed a heterozygous transversion T>G in exon 2, which resulted in the substitution of glycine for valine at amino acid 64, and this position was in the first connexin signature region that characterized this protein. CONCLUSION: This is the first report on a mutation in the first connexin signature region of the GJA8 and a different mutation within Cx50 revealed in this family, which might account for the phenotypic differences observed. Furthermore, this study confirmed that GJA8 plays a vital role in the maintenance of human lens transparency.