Leveraging physics-based and explainable machine learning approaches to quantify the relative contributions of rain and air pollutants to wet deposition.

A quantitative understanding of the roles of rainfall and pollutant concentrations in wet deposition is important because they critically influence terrestrial and aquatic ecosystems. However, their relative contributions to wet deposition, which vary across regions, have not yet been identified. We propose two methods that quantitatively separate the contributions of rain and pollutant concentrations to wet deposition: one is based on simplified equations describing the wet scavenging of pollutants and the other is based on random forest models employing SHapley Additive exPlanations. Three-dimensional long-term air quality simulations from 2003 to 2019 are used as inputs for both the physics-based and machine learning models. Remarkably, the results drawn from the explainable machine learning model are consistent with those from the physics-based approach: overall, rain is a more important limiting factor than pollutant concentrations and the relative contribution of rain is larger than that of pollutants by up to a factor of 3-4 in polluted regions. In polluted regions, pollutant concentrations can remain relatively high even in the presence of precipitation owing to continuous and intense emissions; therefore, wet deposition is limited by rainfall. The contribution of rainfall is larger by 1.5-2.5 than that of pollutant concentrations in regions even with low emissions and this considerably large role of rain suggests that regional or transboundary pollutant transport plays a key role in modulating wet deposition. However, in very remote regions, once the rainfall amount exceeds a certain value, rainfall no longer contributes to increasing wet deposition because atmospheric pollutants are readily removed by rain. So, the contributions of the two factors are comparable in pristine regions. Our results can serve as a basis for explaining interannual variations in wet deposition and for future projections of wet deposition under emission control plans and climate change scenarios across regions.

Greenhouse warming and anthropogenic aerosols synergistically reduce springtime rainfall in low-latitude East Asia.

Low-latitude East Asia, particularly southern China, has experienced a markedly decreasing springtime rainfall in recent years whereas rainfall trends are weak in mid-latitude East Asia. Details of human influences on this contrasting feature remain uncertain. This study provides a quantification of the relative roles of greenhouse warming and aerosols in the observed spring rainfall trends over East Asia using a state-of-the-art numerical model. Greenhouse warming drives more rapid temperature increases over high-latitude East Asia potentially associated with reduced spring snow than the western North Pacific, which induces an anomalous anticyclone over the East China Sea. This circulation change results in a northwestward extension of the western North Pacific subtropical high, reducing rainfall at low latitudes while moderately increasing rainfall at mid-latitudes. In contrast, anthropogenic aerosols reduce rainfall in both low- and mid-latitude East Asia. Hence, the two anthropogenic factors synergistically reduce rainfall at low latitudes, with a stronger contribution of greenhouse warming (~34%) than aerosols (~17%). In mid-latitude East Asia, their contributions are offset, resulting in weak rainfall trends. Further, the anthropogenic influences are found to be relatively larger under drier conditions, suggesting that a more severe drought can occur in low-latitude East Asia under future drought-conducive conditions.

Technical note: AQMEII4 Activity 1: evaluation of wet and dry deposition schemes as an integral part of regional-scale air quality models.

We present in this technical note the research protocol for phase 4 of the Air Quality Model Evaluation International Initiative (AQMEII4). This research initiative is divided into two activities, collectively having three goals: (i) to define the current state of the science with respect to representations of wet and especially dry deposition in regional models, (ii) to quantify the extent to which different dry deposition parameterizations influence retrospective air pollutant concentration and flux predictions, and (iii) to identify, through the use of a common set of detailed diagnostics, sensitivity simulations, model evaluation, and reduction of input uncertainty, the specific causes for the current range of these predictions. Activity 1 is dedicated to the diagnostic evaluation of wet and dry deposition processes in regional air quality models (described in this paper), and Activity 2 to the evaluation of dry deposition point models against ozone flux measurements at multiple towers with multiyear observations (to be described in future submissions as part of the special issue on AQMEII4). The scope of this paper is to present the scientific protocols for Activity 1, as well as to summarize the technical information associated with the different dry deposition approaches used by the participating research groups of AQMEII4. In addition to describing all common aspects and data used for this multi-model evaluation activity, most importantly, we present the strategy devised to allow a common process-level comparison of dry deposition obtained from models using sometimes very different dry deposition schemes. The strategy is based on adding detailed diagnostics to the algorithms used in the dry deposition modules of existing regional air quality models, in particular archiving diagnostics specific to land use-land cover (LULC) and creating standardized LULC categories to facilitate cross-comparison of LULC-specific dry deposition parameters and processes, as well as archiving effective conductance and effective flux as means for comparing the relative influence of different pathways towards the net or total dry deposition. This new approach, along with an analysis of precipitation and wet deposition fields, will provide an unprecedented process-oriented comparison of deposition in regional air quality models. Examples of how specific dry deposition schemes used in participating models have been reduced to the common set of comparable diagnostics defined for AQMEII4 are also presented.

Multiple cis-acting signals, some weak by necessity, collectively direct robust transport of oskar mRNA to the oocyte.

Localization of mRNAs can involve multiple steps, each with its own cis-acting localization signals and transport factors. How is the transition between different steps orchestrated? We show that the initial step in localization of Drosophila oskar mRNA - transport from nurse cells to the oocyte - relies on multiple cis-acting signals. Some of these are binding sites for the translational control factor Bruno, suggesting that Bruno plays an additional role in mRNA transport. Although transport of oskar mRNA is essential and robust, the localization activity of individual transport signals is weak. Notably, increasing the strength of individual transport signals, or adding a strong transport signal, disrupts the later stages of oskar mRNA localization. We propose that the oskar transport signals are weak by necessity; their weakness facilitates transfer of the oskar mRNA from the oocyte transport machinery to the machinery for posterior localization.

RNA sequences required for the noncoding function of oskar RNA also mediate regulation of Oskar protein expression by Bicoid Stability Factor.

The Drosophila oskar (osk) mRNA is unusual in having both coding and noncoding functions. As an mRNA, osk encodes a protein which is deployed specifically at the posterior of the oocyte. This spatially-restricted deployment relies on a program of mRNA localization and both repression and activation of translation, all dependent on regulatory elements located primarily in the 3' untranslated region (UTR) of the mRNA. The 3' UTR also mediates the noncoding function of osk, which is essential for progression through oogenesis. Mutations which most strongly disrupt the noncoding function are positioned in a short region (the C region) near the 3' end of the mRNA, in close proximity to elements required for activation of translation. We show that Bicoid Stability Factor (BSF) binds specifically to the C region of the mRNA. Both knockdown of bsf and mutation of BSF binding sites in osk mRNA have the same consequences: Osk expression is largely eliminated late in oogenesis, with both mRNA localization and translation disrupted. Although the C region of the osk 3' UTR is required for the noncoding function, BSF binding does not appear to be essential for that function.

oskar RNA plays multiple noncoding roles to support oogenesis and maintain integrity of the germline/soma distinction.

The Drosophila oskar (osk) mRNA is unusual in that it has both coding and noncoding functions. As an mRNA, osk encodes a protein required for embryonic patterning and germ cell formation. Independent of that function, the absence of osk mRNA disrupts formation of the karyosome and blocks progression through oogenesis. Here we show that loss of osk mRNA also affects the distribution of regulatory proteins, relaxing their association with large RNPs within the germline, and allowing them to accumulate in the somatic follicle cells. This and other noncoding functions of the osk mRNA are mediated by multiple sequence elements with distinct roles. One role, provided by numerous binding sites in two distinct regions of the osk 3' UTR, is to sequester the translational regulator Bruno (Bru), which itself controls translation of osk mRNA. This defines a novel regulatory circuit, with Bru restricting the activity of osk, and osk in turn restricting the activity of Bru. Other functional elements, which do not bind Bru and are positioned close to the 3' end of the RNA, act in the oocyte and are essential. Despite the different roles played by the different types of elements contributing to RNA function, mutation of any leads to accumulation of the germline regulatory factors in the follicle cells.

Lipoteichoic acid from Lactobacillus plantarum induces nitric oxide production in the presence of interferon-γ in murine macrophages.

Lipoteichoic acid (LTA) is a major immuno-stimulating component of Gram-positive bacteria. LTA from the beneficial bacterium Lactobacillus plantarum induces weak nitric oxide (NO) production in murine macrophages. Currently, it is not clear if LTA from L. plantarum is able to stimulate the innate immune response, even in the presence of inflammation. In the present study, we prepared highly pure and structurally intact LTA from L. plantarum and investigated its ability to induce NO in the presence of interferon (IFN)-γ in the RAW 264.7 murine macrophage cell line and bone marrow-derived macrophages (BMMs) from mice. L. plantarum LTA alone was unable to induce NO production, even at 30µg/ml. However, LTA in the presence of IFN-γ significantly induced NO production in RAW 264.7 cells. The observed NO production was inhibited by a NO synthase (NOS) inhibitor l-NAME and an inducible NOS (iNOS) inhibitor l-NIL, suggesting that iNOS is specifically required for this action. Western blot analysis and reverse transcription and polymerase chain reaction further confirmed that L. plantarum LTA increased protein and mRNA levels of iNOS, respectively. However, such induction was substantially inhibited in BMMs from Toll-like receptor 2 (TLR2)-deficient mice and the macrophages treated with an inhibitor blocking platelet-activating factor receptor. In addition, L. plantarum LTA plus IFN-γ induced IFN-ß expression and STAT1 phosphorylation, which are key pathways for inducing iNOS expression. Electrophoretic mobility shift assay demonstrated that L. plantarum LTA in the presence of IFN-γ remarkably increased the DNA-binding activity of NF-κB transcription factor, which is known to be involved in the iNOS gene expression. Collectively, these results suggest that LTA from L. plantarum alone has no inflammatory potential but does induce NO production under conditions of inflammation, such as the presence of IFN-γ.

dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition.

The molecular mechanisms driving the conserved metazoan developmental shift referred to as the mid-blastula transition (MBT) remain mysterious. Typically, cleavage divisions give way to longer asynchronous cell cycles with the acquisition of a gap phase. In Drosophila, rapid synchronous nuclear divisions must pause at the MBT to allow the formation of a cellular blastoderm through a special form of cytokinesis termed cellularization. Drosophila Fragile X mental retardation protein (dFMRP; FMR1), a transcript-specific translational regulator, is required for cellularization. The role of FMRP has been most extensively studied in the nervous system because the loss of FMRP activity in neurons causes the misexpression of specific mRNAs required for synaptic plasticity, resulting in mental retardation and autism in humans. Here, we show that in the early embryo dFMRP associates specifically with Caprin, another transcript-specific translational regulator implicated in synaptic plasticity, and with eIF4G, a key regulator of translational initiation. dFMRP and Caprin collaborate to control the cell cycle at the MBT by directly mediating the normal repression of maternal Cyclin B mRNA and the activation of zygotic frühstart mRNA. These findings identify two new targets of dFMRP regulation and implicate conserved translational regulatory mechanisms in processes as diverse as learning, memory and early embryonic development.

Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer.

Toll-like receptor 2 (TLR2) initiates potent immune responses by recognizing diacylated and triacylated lipopeptides. Its ligand specificity is controlled by whether it heterodimerizes with TLR1 or TLR6. We have determined the crystal structures of TLR2-TLR6-diacylated lipopeptide, TLR2-lipoteichoic acid, and TLR2-PE-DTPA complexes. PE-DTPA, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid, is a synthetic phospholipid derivative. Two major factors contribute to the ligand specificity of TLR2-TLR1 or TLR2-TLR6 heterodimers. First, the lipid channel of TLR6 is blocked by two phenylalanines. Simultaneous mutation of these phenylalanines made TLR2-TLR6 fully responsive not only to diacylated but also to triacylated lipopeptides. Second, the hydrophobic dimerization interface of TLR2-TLR6 is increased by 80%, which compensates for the lack of amide lipid interaction between the lipopeptide and TLR2-TLR6. The structures of the TLR2-lipoteichoic acid and the TLR2-PE-DTPA complexes demonstrate that a precise interaction pattern of the head group is essential for a robust immune response by TLR2 heterodimers.

Bacillus anthracis lethal toxin attenuates lipoteichoic acid-induced maturation and activation of dendritic cells through a unique mechanism.

Lethal toxin (LT), produced by the gram-positive bacterium Bacillus anthracis, was identified as a major etiologic agent causing anthrax due to its strong immunotoxicity. Gram-positive bacteria express lipoteichoic acid (LTA), which is considered as a counterpart to lipopolysaccharide (LPS) of gram-negative bacteria, but differs from LPS in the structure and function. Since dendritic cells (DCs) are essential for the appropriate initiation of immune response, we investigated the effect of LT on LTA-induced DC maturation using immature DCs prepared by differentiation of C57BL/6 mouse bone marrow cells. When immature DCs were matured with LTA in the presence of LT, the expression of representative markers for DC maturation such as CD80, CD83, and CD86 together with MHC class I and II molecules was inhibited. LT ameliorated the attenuation of endocytic capacity during DC maturation by LTA while such effect was not observed in LPS-matured DCs. Furthermore, exposure to LT resulted in a decrease in the expression of pro-inflammatory cytokines including IL-6, TNF-alpha, and IL-12p40 in LTA-stimulated DCs as in LPS-stimulated DCs. Interestingly, LT showed a minimal change in LTA-induced IL-1beta expression while LT highly enhanced the LPS-induced IL-1beta expression. Those inhibitory effects might be associated with LT interference of LTA-signaling pathways mediated through mitogen-activated protein kinases (MAPKs) since LT suppressed phosphorylation of MAPK, which was induced by LTA. Meanwhile, no change was observed in the expression of putative anthrax toxin receptors, TEM8 and CMG2, or Toll-like receptor 2. These results suggest that LT suppresses the maturation and activation of DCs stimulated with LTA, similar to the suppression in the LPS-stimulated DCs, but via a distinct mechanism.

Impaired osteoclastogenesis by staphylococcal lipoteichoic acid through Toll-like receptor 2 with partial involvement of MyD88.

Degenerative bone disease, marked by excessive loss of calcified matrix, is often associated with bacterial infections. Osteoclasts, which mediate the bone-resorptive process, are derived mainly from myeloid precursor cells of the monocyte/macrophage lineage, from which cells with phagocytic and inflammatory capacities may alternatively arise. Here, we investigated the effect of LTA, a major cell-wall virulence factor of Gram-positive bacteria, on osteoclast differentiation. Osteoclast precursors were prepared from C57BL/6 mouse BM using M-CSF and RANKL. When osteoclastogenesis was induced in the presence of staphylococcal LTA, LTA dose-dependently inhibited the differentiation of osteoclast precursors to mature osteoclasts. A corresponding inhibition of bone-resorptive function was observed in the reduced resorption area on calcium phosphate-coated culture plates. In contrast, the phagocytic and inflammatory potential of the osteoclast precursors increased in the presence of LTA. TLR2, known to recognize LTA, might be essential for the LTA inhibition of osteoclastogenesis, as the inhibition did not occur in the precursors from TLR2-deficient mice. Importantly, MyD88-dependent and MyD88-independent pathways would participate in the inhibition, as determined using MyD88-deficient cells. Moreover, LTA inhibited phosphorylation of ERK and JNK in osteoclast precursors stimulated with M-CSF and RANKL, concomitantly with a decreased DNA-binding activity of AP-1. These results suggest that staphylococcal LTA inhibits osteoclast differentiation primarily through TLR2 but also in part through MyD88 signaling, which in turn, inhibits activation of ERK, JNK, and AP-1.

Differential immunostimulatory effects of Gram-positive bacteria due to their lipoteichoic acids.

Lipoteichoic acid (LTA) is a major immunostimulating component in the cell wall of Gram-positive bacteria as lipopolysaccharide of Gram-negative bacteria. However, LTA is expressed on not only pathogenic but also nonpathogenic Gram-positive bacteria. In order to examine whether the immunostimulating potentials of Gram-positive bacteria are correlated with their LTAs, we prepared highly pure LTAs from Staphylococcus aureus (pathogenic), Bacillus subtilis (non-pathogenic), or Lactobacillus plantarum (beneficial). When a murine macrophage cell-line, RAW 264.7, was stimulated with heat-killed bacteria, both S. aureus and B. subtilis induced nitric oxide (NO) production in a dose-dependent manner while L. plantarum showed a minimal induction. Interestingly, purified LTAs from S. aureus and B. subtilis, but not from L. plantarum, were able to induce the production of NO. The differential inflammatory potentials of LTAs coincided with their abilities to activate Toll-like receptor 2 (TLR2), which is known to recognize Gram-positive bacteria and LTA, and transcription factors NF-kappaB and AP-1. Similar results were obtained with the expression of cytokines related to inflammation by RAW 264.7 and human peripheral blood mononuclear cells as well. The ability of LTA to induce TNF-alpha and NO production was abolished when the LTAs were treated with 0.2 N NaOH. Collectively, we suggest that the immunostimulating potentials of Gram-positive bacteria differ due to their LTAs with differential potencies in the stimulation of TLR2.

A food-born heterocyclic amine, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), suppresses tumor necrosis factor-alpha expression in lipoteichoic acid-stimulated RAW 264.7 cells.

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a heterocyclic amine with strong carcinogenic and mutagenic potential, is created abundantly in the overcooking of meat and fish. Carcinogenic toxicants are often implicated in immunosuppression, where cancer cells are not easily eliminated by the host immune system. Here, we investigated the effect of PhIP on tumor necrosis factor-alpha (TNF-alpha) expression by murine macrophage-like cells (RAW 264.7) stimulated with lipoteichoic acid (LTA), a major virulence factor of Gram-positive bacteria. Upon exposure to LTA purified from Staphylococcus aureus, TNF-alpha expression was substantially induced, whereas pretreatment with PhIP significantly inhibited LTA-induced TNF-alpha expression. LTA is known to activate Toll-like receptor 2 (TLR2) and NF-kappaB, resulting in TNF-alpha expression. Interestingly, PhIP did not interfere with LTA-binding to TLR2, its stimulation of TLR2, or the DNA-binding activity of NF-kappaB. However, treatment with actinomycin D facilitated the PhIP-induced attenuation of TNF-alpha mRNA expression, implying that PhIP might decrease TNF-alpha mRNA stability rather than its biosynthesis. Furthermore, Western blot analysis demonstrated that PhIP reduced the phosphorylation of ERK1/2 and JNK but not p38 kinase in LTA-stimulated cells. The addition of a protein kinase C (PKC) activator, phorbol 12-myristate 13-acetate, rescued PhIP-inhibited TNF-alpha expression in LTA-stimulated cells. These results suggest that PhIP downregulates TNF-alpha expression in LTA-stimulated macrophages by decreasing TNF-alpha mRNA stability and signaling pathways related to PKC, ERK1/2, and JNK activation.

Lipoteichoic acid partially contributes to the inflammatory responses to Enterococcus faecalis.

Enterococcus faecalis, a pathogenic gram-positive bacterium, is closely related to refractory apical periodontitis. Because lipoteichoic acid (LTA) is considered a major virulence factor of gram-positive bacteria, in the present study, highly pure LTA from E. faecalis was prepared, and its ability to stimulate murine macrophages was investigated in comparison with those of the killed whole cells. Upon exposure to E. faecalis LTA, RAW 264.7 (a murine macrophage cell line) produced a significantly (p < 0.05) high level of tumor necrosis factor-alpha (TNF-alpha) and nitric oxide (NO) in a concentration-dependent manner. It is to note that the LTA was able to stimulate Toll-like receptor 2 (TLR2) but not TLR4. Concomitantly, LTA enhanced the DNA-binding activity of a transcription factor, nuclear factor-kappa B (NF-kappaB), which plays an important role in the transcriptional activation of genes encoding inflammatory mediators. In contrast, heat-killed E. faecalis stimulated both TLR2 and TLR4, whereas the killed E. faecalis whole cells induced significant (p < 0.05) levels of TNF-alpha and NO in RAW 264.7 cells as their LTA did. These results suggest that LTA partially contributes to E. faecalis-induced inflammatory responses.

Endotoxin contamination in commercially available pokeweed mitogen contributes to the activation of murine macrophages and human dendritic cell maturation.

Commercially available pokeweed mitogen (PWM) has been reported to activate macrophages, leading to production of proinflammatory cytokines and nitric oxide (NO). However, we found that polymyxin B (PMB), a specific inhibitor of endotoxin activity, inhibited the PWM-induced expression of proinflammatory cytokines and NO and the activation of Toll-like receptor 4 (TLR4). A kinetic-turbidimetric Limulus amebocyte lysate assay demonstrated that commercial PWM contained substantial endotoxin, over 10(4) endotoxin units/mg of the PWM. A PWM repurified by PMB-coupled beads no longer induced the expression of proinflammatory cytokines, TLR4 activation, or dendritic cell maturation. However, the repurified PWM remained able to induce proliferation of human lymphocytes, which is a representative characteristic of PWM. These results suggest that commercial PWM might be contaminated with a large amount of endotoxin, resulting in the attribution of misleading immunological properties to PWM.

Comparison of proteome between hepatitis B virus- and hepatitis C virus-associated hepatocellular carcinoma.

PURPOSE: Hepatocellular carcinoma (HCC) is one of the most common malignant cancers closely associated with chronic infection by the hepatitis B virus (HBV) or the hepatitis C virus (HCV) throughout the world. Differential expression of the proteome in HBV- and HCV-associated HCC was investigated to identify any useful biomarkers indicating virus-specific hepatocarcinogenesis. EXPERIMENTAL DESIGN: Twenty-one pairs of specimens (tumorous and surrounding nontumorous liver tissues) were obtained from 21 HCC patients. They were divided into three HCC types by viral markers: 7 hepatitis B surface antigen-positive (B-type HCC), 7 anti-HCV-positive (C-type HCC), and 7 hepatitis B surface antigen-negative and anti-HCV-negative. Total proteins were analyzed by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and alterations in the proteome were examined. RESULTS: Sixty proteins were identified that show significant changes in the expression level between nontumorous and tumorous tissues. Among these, 14 proteins were commonly changed in all three of the HCC types, but 46 proteins showed a tendency of viral marker specificity. CONCLUSIONS: The identified proteins were classified according to the viral factor as being involved in B-type and C-type HCC. These results suggest strongly that the expression pattern of proteome in HCC tissues is closely associated with etiologic factors. The different protein profiles between B-type and C-type HCC indicate that the pathogenetic mechanisms of hepatocarcinogenesis may be different according to the viral factor, HBV and HCV.