Convergence in simulating global soil organic carbon by structurally different models after data assimilation.

Current biogeochemical models produce carbon-climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first-order or Michaelis-Menten kinetics at the global scale. Nevertheless, a wider range of data with high-quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics-function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.

Importance of glutamine in synaptic vesicles revealed by functional studies of SLC6A17 and its mutations pathogenic for intellectual disability.

Human mutations in the gene encoding the solute carrier (SLC) 6A17 caused intellectual disability (ID). The physiological role of SLC6A17 and pathogenesis of SLC6A17-based-ID were both unclear. Here, we report learning deficits in Slc6a17 knockout and point mutant mice. Biochemistry, proteomic, and electron microscopy (EM) support SLC6A17 protein localization in synaptic vesicles (SVs). Chemical analysis of SVs by liquid chromatography coupled to mass spectrometry (LC-MS) revealed glutamine (Gln) in SVs containing SLC6A17. Virally mediated overexpression of SLC6A17 increased Gln in SVs. Either genetic or virally mediated targeting of Slc6a17 reduced Gln in SVs. One ID mutation caused SLC6A17 mislocalization while the other caused defective Gln transport. Multidisciplinary approaches with seven types of genetically modified mice have shown Gln as an endogenous substrate of SLC6A17, uncovered Gln as a new molecule in SVs, established the necessary and sufficient roles of SLC6A17 in Gln transport into SVs, and suggested SV Gln decrease as the key pathogenetic mechanism in human ID.

Sleep need, the key regulator of sleep homeostasis, is indicated and controlled by phosphorylation of threonine 221 in salt-inducible kinase 3.

Sleep need drives sleep and plays a key role in homeostatic regulation of sleep. So far sleep need can only be inferred by animal behaviors and indicated by electroencephalography (EEG). Here we report that phosphorylation of threonine (T) 221 of the salt-inducible kinase 3 (SIK3) increased the catalytic activity and stability of SIK3. T221 phosphorylation in the mouse brain indicates sleep need: more sleep resulting in less phosphorylation and less sleep more phosphorylation during daily sleep/wake cycle and after sleep deprivation (SD). Sleep need was reduced in SIK3 loss of function (LOF) mutants and by T221 mutation to alanine (T221A). Rebound after SD was also decreased in SIK3 LOF and T221A mutant mice. By contrast, SIK1 and SIK2 do not satisfy criteria to be both an indicator and a controller of sleep need. Our results reveal SIK3-T221 phosphorylation as a chemical modification which indicates and controls sleep need.

Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

Across-model spread and shrinking in predicting peatland carbon dynamics under global change.

Large across-model spread in simulating land carbon (C) dynamics has been ubiquitously demonstrated in model intercomparison projects (MIPs), and became a major impediment in advancing climate change prediction. Thus, it is imperative to identify underlying sources of the spread. Here, we used a novel matrix approach to analytically pin down the sources of across-model spread in transient peatland C dynamics in response to a factorial combination of two atmospheric CO2 levels and five temperature levels. We developed a matrix-based MIP by converting the C cycle module of eight land models (i.e., TEM, CENTURY4, DALEC2, TECO, FBDC, CASA, CLM4.5 and ORCHIDEE) into eight matrix models. While the model average of ecosystem C storage was comparable to the measurement, the simulation differed largely among models, mainly due to inter-model difference in baseline C residence time. Models generally overestimated net ecosystem production (NEP), with a large spread that was mainly attributed to inter-model difference in environmental scalar. Based on the sources of spreads identified, we sequentially standardized model parameters to shrink simulated ecosystem C storage and NEP to almost none. Models generally captured the observed negative response of NEP to warming, but differed largely in the magnitude of response, due to differences in baseline C residence time and temperature sensitivity of decomposition. While there was a lack of response of NEP to elevated CO2 (eCO2 ) concentrations in the measurements, simulated NEP responded positively to eCO2 concentrations in most models, due to the positive responses of simulated net primary production. Our study used one case study in Minnesota peatland to demonstrate that the sources of across-model spreads in simulating transient C dynamics can be precisely traced to model structures and parameters, regardless of their complexity, given the protocol that all the matrix models were driven by the same gross primary production and environmental variables.

Effectiveness of photodynamic therapy with 5-aminolevulinic acid for Bowenoid papulosis: A retrospective study with long-term follow-up.

BACKGROUND: Bowenoid papulosis (BP) is a rare infectious skin disease that occurs in sexually active young people. BP is associated with human papillomavirus (HPV)16 and 18 infections, spreads through sexual contact, and tends to become cancerous. Currently, there are different BP treatment methods, and few reports on the efficacy of photodynamic therapy (PDT) with 5-aminolevulinic acid (ALA) (ALA-PDT). We compared the differences in the clearance and recurrence rates of BP between the ALA-PDT group and other groups, and explored methods to improve clinical effects and reduce lesion recurrence by combining clinical retrospective data. METHODS: We enrolled patients who were diagnosed with bowel papulosis" between January 1, 2009, and December 31, 2020. Patient information, such as ID number, hospitalization number, admission time, name, age, gender, telephone number, admission record, discharge record, outpatient medical history, HPV type analysis, histopathological examination, and treatment plan were recorded. Outcomes were obtained and recorded through outpatient visits, telephone, and online follow-ups from patients who had reached the treatment endpoint. We compared and evaluated the differences in lesion clearance rate, lesion recurrence rate, and patient satisfaction between the ALA-PDT group and other groups using statistical analysis. RESULTS: The lesion clearance rate of the ALA-PDT group was significantly higher than that of the control group, the lesion recurrence rate was lower than that of the control group, and patient satisfaction was higher than that of the control group. The lesion clearance rate of the ALA-PDT group was higher than that of the microwave and radiofrequency groups, the lesion recurrence rate of the ALA-PDT group was significantly lower than that of the microwave and radiofrequency groups, and patient satisfaction was significantly higher than that of the microwave and radiofrequency groups. In the lesions of patients with BP, in addition to HPV16 and HPV18 types, other types were also detected, and most of them were mixed types of HPV infection. Age, sex, and duration of disease were not risk factors that affected BP recurrence. CONCLUSIONS: ALA-PDT for BP has the advantages of high lesion clearance rate, low lesion recurrence rate, and high patient satisfaction. ALA-PDT is worthy of recommendation as a preferred treatment plan for the treatment of BP.

LKB1 is physiologically required for sleep from Drosophila melanogaster to the Mus musculus.

Liver Kinase B1 (LKB1) is known as a master kinase for 14 kinases related to the adenosine monophosphate-activated protein kinase. Two of them salt inducible kinase 3 and adenosine monophosphate-activated protein kinase α have previously been implicated in sleep regulation. We generated loss-of-function mutants for Lkb1 in both Drosophila and mice. Sleep, but not circadian rhythms, was reduced in Lkb1-mutant flies and in flies with neuronal deletion of Lkb1. Genetic interactions between Lkb1 and threonine to alanine mutation at residue 184 of adenosine monophosphate-activated protein kinase in Drosophila sleep or those between Lkb1 and Threonine to Glutamic Acid mutation at residue 196 of salt inducible kinase 3 in Drosophila viability have been observed. Sleep was reduced in mice after virally mediated reduction of Lkb1 in the brain. Electroencephalography analysis showed that nonrapid eye movement sleep and sleep need were both reduced in Lkb1-mutant mice. These results indicate that liver kinase B1 plays a physiological role in sleep regulation conserved from flies to mice.

STE20 phosphorylation of AMPK-related kinases revealed by biochemical purifications combined with genetics.

We have recently purified mammalian sterile 20 (STE20)-like kinase 3 (MST3) as a kinase for the multifunctional kinases, AMP-activated protein kinase-related kinases (ARKs). However, unresolved questions from this study, such as remaining phosphorylation activities following deletion of the Mst3 gene from human embryonic kidney cells and mice, led us to conclude that there were additional kinases for ARKs. Further purification recovered Ca2+/calmodulin-dependent protein kinase kinases 1 and 2 (CaMKK1 and 2), and a third round of purification revealed mitogen-activated protein kinase kinase kinase kinase 5 (MAP4K5) as potential kinases of ARKs. We then demonstrated that MST3 and MAP4K5, both belonging to the STE20-like kinase family, could phosphorylate all 14 ARKs both in vivo and in vitro. Further examination of all 28 STE20 kinases detected variable phosphorylation activity on AMP-activated protein kinase (AMPK) and the salt-inducible kinase 3 (SIK3). Taken together, our results have revealed novel relationships between STE20 kinases and ARKs, with potential physiological and pathological implications.

Variations and controlling factors of soil denitrification rate.

The denitrification process profoundly affects soil nitrogen (N) availability and generates its byproduct, nitrous oxide, as a potent greenhouse gas. There are large uncertainties in predicting global denitrification because its controlling factors remain elusive. In this study, we compiled 4301 observations of denitrification rates across a variety of terrestrial ecosystems from 214 papers published in the literature. The averaged denitrification rate was 3516.3 ± 91.1 µg N kg-1  soil day-1 . The highest denitrification rate was 4242.3 ± 152.3 µg N kg-1  soil day-1 under humid subtropical climates, and the lowest was 965.8 ± 150.4 µg N kg-1 under dry climates. The denitrification rate increased with temperature, precipitation, soil carbon and N contents, as well as microbial biomass carbon and N, but decreased with soil clay contents. The variables related to soil N contents (e.g., nitrate, ammonium, and total N) explained the variation of denitrification more than climatic and edaphic variables (e.g., mean annual temperature (MAT), soil moisture, soil pH, and clay content) according to structural equation models. Soil microbial biomass carbon, which was influenced by soil nitrate, ammonium, and total N, also strongly influenced denitrification at a global scale. Collectively, soil N contents, microbial biomass, pH, texture, moisture, and MAT accounted for 60% of the variation in global denitrification rates. The findings suggest that soil N contents and microbial biomass are strong predictors of denitrification at the global scale.

Country-level land carbon sink and its causing components by the middle of the twenty-first century.

BACKGROUND: Countries have long been making efforts by reducing greenhouse-gas emissions to mitigate climate change. In the agreements of the United Nations Framework Convention on Climate Change, involved countries have committed to reduction targets. However, carbon (C) sink and its involving processes by natural ecosystems remain difficult to quantify. METHODS: Using a transient traceability framework, we estimated country-level land C sink and its causing components by 2050 simulated by 12 Earth System Models involved in the Coupled Model Intercomparison Project Phase 5 (CMIP5) under RCP8.5. RESULTS: The top 20 countries with highest C sink have the potential to sequester 62 Pg C in total, among which, Russia, Canada, USA, China, and Brazil sequester the most. This C sink consists of four components: production-driven change, turnover-driven change, change in instantaneous C storage potential, and interaction between production-driven change and turnover-driven change. The four components account for 49.5%, 28.1%, 14.5%, and 7.9% of the land C sink, respectively. CONCLUSION: The model-based estimates highlight that land C sink potentially offsets a substantial proportion of greenhouse-gas emissions, especially for countries where net primary production (NPP) likely increases substantially and inherent residence time elongates.

Warming reduces the production of a major annual forage crop on the Tibetan Plateau.

Climate warming has been proposed to increase primary production of natural grasslands in cold regions. However, how climate warming affects the production of artificial pastures in cold regions remains unknown. To address this question, we used open-top chambers to simulate warming in a major artificial pasture (forage oat) on the cold Tibetan Plateau for three consecutive years. Surprisingly, climate warming decreased aboveground and belowground biomass production by 23.1%-44.8% and 35.0%-46.5%, respectively, without a significant impact on their ratio. The adverse effects on biomass production could be attributed to the adverse effects of high-temperatures on leaf photosynthesis through increases in water vapor pressure deficit (by 0.05-0.10 kPa), damages to the leaf oxidant system, as indicated by a 46.6% increase in leaf malondialdehyde content, as well as reductions in growth duration (by 4.7-6.7 days). The adverse effects were also related to exacerbated phosphorus limitation, as indicated by decreases in soil available phosphorus and plant phosphorus concentrations by 31.9%-40.7% and 14.3%-49.4%, respectively, and increases in the plant nitrogen: phosphorus ratio by 19.2%-108.3%. The decrease in soil available phosphorus concentration could be attributed to reductions in soil phosphatase activities (by 9.6%-18.5%). The findings of this study suggest an urgent need to advance agronomic techniques and cultivate more resilient forage genotypes to meet the increasing demand of forage for feeding livestock and to reduce grazing damage to natural grasslands on the warming-sensitive Tibetan Plateau.

Divergent responses of primary production to increasing precipitation variability in global drylands.

Interannual variability in precipitation has increased globally as climate warming intensifies. The increased variability impacts both terrestrial plant production and carbon (C) sequestration. However, mechanisms driving these changes are largely unknown. Here, we examined mechanisms underlying the response of aboveground net primary production (ANPP) to interannual precipitation variability in global drylands with mean annual precipitation (MAP) <500 mm year-1 , using a combined approach of data synthesis and process-based modeling. We found a hump-shaped response of ANPP to precipitation variability along the MAP gradient. The response was positive when MAP < ~300 mm year-1 and negative when MAP was higher than this threshold, with a positive peak at 140 mm year-1 . Transpiration and subsoil water content mirrored the response of ANPP to precipitation variability; evaporation responded negatively and water loss through runoff and drainage responded positively to precipitation variability. Mean annual temperature, soil type, and plant physiological traits all altered the magnitude but not the pattern of the response of ANPP to precipitation variability along the MAP gradient. By extrapolating to global drylands (<500 mm year-1  MAP), we estimated that ANPP would increase by 15.2 ± 6.0 Tg C year-1 in arid and hyper-arid lands and decrease by 2.1 ± 0.5 Tg C year-1 in dry sub-humid lands under future changes in interannual precipitation variability. Thus, increases in precipitation variability will enhance primary production in many drylands in the future.

Latitudinal patterns of terrestrial phosphorus limitation over the globe.

Phosphorus limitation on terrestrial plant growth is being incorporated into Earth system models. The global pattern of terrestrial phosphorus limitation, however, remains unstudied. Here, we examined the global-scale latitudinal pattern of terrestrial phosphorus limitation by analysing a total of 1068 observations of aboveground plant production response to phosphorus additions at 351 forest, grassland or tundra sites that are distributed globally. The observed phosphorus-addition effect varied greatly (either positive or negative), depending significantly upon fertilisation regime and production measure, but did not change significantly with latitude. In contrast, phosphorus-addition effect standardised by fertilisation regime and production measure was consistently positive and decreased significantly with latitude. Latitudinal gradient in the standardised phosphorus-addition effect was explained by several mechanisms involving substrate age, climate, vegetation type, edaphic properties and biochemical machinery. This study suggests that latitudinal pattern of terrestrial phosphorus limitation is jointly shaped by macro-scale driving forces and the fundamental structure of life.

Long-term measurements in a mixed-grass prairie reveal a change in soil organic carbon recalcitrance and its environmental sensitivity under warming.

Soil respiration, the major pathway for ecosystem carbon (C) loss, has the potential to enter a positive feedback loop with the atmospheric CO2 due to climate warming. For reliable projections of climate-carbon feedbacks, accurate quantification of soil respiration and identification of mechanisms that control its variability are essential. Process-based models simulate soil respiration as functions of belowground C input, organic matter quality, and sensitivity to environmental conditions. However, evaluation and calibration of process-based models against the long-term in situ measurements are rare. Here, we evaluate the performance of the Terrestrial ECOsystem (TECO) model in simulating total and heterotrophic soil respiration measured during a 16-year warming experiment in a mixed-grass prairie; calibrate model parameters against these and other measurements collected during the experiment; and explore whether the mechanisms of C dynamics have changed over the years. Calibrating model parameters against observations of individual years substantially improved model performance in comparison to pre-calibration simulations, explaining 79-86% of variability in observed soil respiration. Interannual variation of the calibrated model parameters indicated increasing recalcitrance of soil C and changing environmental sensitivity of microbes. Overall, we found that (1) soil organic C became more recalcitrant in intact soil compared to root-free soil; (2) warming offset the effects of increasing C recalcitrance in intact soil and changed microbial sensitivity to moisture conditions. These findings indicate that soil respiration may decrease in the future due to C quality, but this decrease may be offset by warming-induced changes in C cycling mechanisms and their responses to moisture conditions.

Vital roles of soil microbes in driving terrestrial nitrogen immobilization.

Nitrogen immobilization usually leads to nitrogen retention in soil and, thus, influences soil nitrogen supply for plant growth. Understanding soil nitrogen immobilization is important for predicting soil nitrogen cycling under anthropogenic activities and climate changes. However, the global patterns and drivers of soil nitrogen immobilization remain unclear. We synthesized 1350 observations of gross soil nitrogen immobilization rate (NIR) from 97 articles to identify patterns and drivers of NIR. The global mean NIR was 8.77 ± 1.01 mg N kg-1  soil day-1 . It was 5.55 ± 0.41 mg N kg-1  soil day-1 in croplands, 15.74 ± 3.02 mg N kg-1  soil day-1 in wetlands, and 15.26 ± 2.98 mg N kg-1  soil day-1 in forests. The NIR increased with mean annual temperature, precipitation, soil moisture, soil organic carbon, total nitrogen, dissolved organic nitrogen, ammonium, nitrate, phosphorus, and microbial biomass carbon. But it decreased with soil pH. The results of structural equation models showed that soil microbial biomass carbon was a pivotal driver of NIR, because temperature, total soil nitrogen, and soil pH mostly indirectly influenced NIR via changing soil microbial biomass. Moreover, microbial biomass carbon accounted for most of the variations in NIR among all direct relationships. Furthermore, the efficiency of transforming the immobilized nitrogen to microbial biomass nitrogen was lower in croplands than in natural ecosystems (i.e., forests, grasslands, and wetlands). These findings suggested that soil nitrogen retention may decrease under the land use change from forests or wetlands to croplands, but NIR was expected to increase due to increased microbial biomass under global warming. The identified patterns and drivers of soil nitrogen immobilization in this study are crucial to project the changes in soil nitrogen retention.

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

Drought mildly reduces plant dominance in a temperate prairie ecosystem across years.

Shifts in dominance and species reordering can occur in response to global change. However, it is not clear how altered precipitation and disturbance regimes interact to affect species composition and dominance.We explored community-level diversity and compositional similarity responses, both across and within years, to a manipulated precipitation gradient and annual clipping in a mixed-grass prairie in Oklahoma, USA. We imposed seven precipitation treatments (five water exclusion levels [-20%, -40%, -60%, -80%, and -100%], water addition [+50%], and control [0% change in precipitation]) year-round from 2016 to 2018 using fixed interception shelters. These treatments were crossed with annual clipping to mimic hay harvest.We found that community-level responses were influenced by precipitation across time. For instance, plant evenness was enhanced by extreme drought treatments, while plant richness was marginally promoted under increased precipitation.Clipping promoted species gain resulting in greater richness within each experimental year. Across years, clipping effects further reduced the precipitation effects on community-level responses (richness and evenness) at both extreme drought and added precipitation treatments. Synthesis: Our results highlight the importance of studying interactive drivers of change both within versus across time. For instance, clipping attenuated community-level responses to a gradient in precipitation, suggesting that management could buffer community-level responses to drought. However, precipitation effects were mild and likely to accentuate over time to produce further community change.

Photodynamic therapy combined with surgical management of extensive anogenital condylomatosis in a patient with systemic lupus erythematosus.

Infections with human papillomavirus in the anogenital area result in warty, papillary, and condylomatous lesions. The giant anogenital wart is relatively uncommon. Treatment of giant wart is challenging, especially in the immunosuppressive population. Here, a patient with systemic lupus erythematosis had extensive, fast-growing, recurrent anogenital condylomatosis shaped as giant cauliflowers. We reported this case and the successful treatment of photodynamic therapy combined with surgical management. It provided the feasibility for surgical ablation combined with ALA-PDT performed for these kinds of challenging cases.