Natalie M. Mahowald, Longlei Li, Samuel Albani
et al.
Abstract. Estimating past aerosol radiative effects and their uncertainties is an important topic in climate science. Aerosol radiative effects propagate into large uncertainties in estimates of how present and future climate evolves with changing greenhouse gas emissions. A deeper understanding of how aerosols affected the atmospheric energy budget under past climates is hindered in part by a lack of relevant paleo-observations and in part because less attention has been paid to the problem. Because of the lack of information we do not seek here to determine the change in the radiative forcing due to aerosol changes but rather to estimate the uncertainties in those changes. Here we argue that current uncertainties from emission uncertainties (90 % confidence interval range spanning 2.8 W m−2) are just as large as model spread uncertainties (2.8 W m−2) in calculating preindustrial to present-day aerosol radiative effects. There are no estimates of radiative forcing for important aerosols such as wildfire and dust aerosols in most paleoclimate time periods. However, qualitative analysis of paleoclimate proxies suggests that changes in aerosols between different past climates are similar in magnitude to changes in aerosols between the preindustrial and present day; plus, there is the added uncertainty from the variability in aerosols and fires in the preindustrial. From the limited literature we crudely estimate a paleoclimate aerosol uncertainty for the Last Glacial Maximum relative to preindustrial of 4.8 W m−2, and we estimate the uncertainty in the aerosol feedback in the natural Earth system over the paleoclimate (Last Glacial Maximum to preindustrial) to be about 3.2 W m−2 K−1. In order to more accurately assess the uncertainty in historical aerosol radiative effects, we propose a new model intercomparison project, which would include multiple plausible emission scenarios tested across a range of state-of-the-art climate models over the historical period. These emission scenarios would then be compared to the available independent aerosol observations to constrain which are most probable. In addition, future efforts should work to characterize and constrain paleo-aerosol forcings and uncertainties. Careful propagation of aerosol uncertainties in the literature is required to ensure an accurate quantification of uncertainties in projections of future climate changes.
A. J. Barclay, A. R. W. McKellar, N. Moazzen-Ahmadi
The O-D stretch fundamental region of the deuterated water dimer, (D2O)2, is further studied using a pulsed supersonic slit jet and a tunable optical parametric oscillator infrared source. The previously unobserved acceptor symmetric O-D stretch fundamental vibration is detected, with Ka = 0 <-- 0 and 1 <-- 0 sub-bands at about 2669 and 2674 cm-1, respectively. Analysis indicates that the various water dimer tunneling splittings generally decrease in the excited vibrational state, similar to the three other previously observed O-D stretch fundamentals. Two new (D2O)2 combination bands are observed, giving information on intermolecular vibrations in the excited O-D stretch states. The likely vibrational assignments for these and a previously observed combination band are discussed.
INTRODUCTION Among numerous invasive procedures for the research of biomarkers, blood-based indicators are regarded as marginally non-invasive procedures in the diagnosis and prognosis of demyelinating disorders, including multiple sclerosis (MS). In this study, we looked into the blood-derived gene expression profiles of patients with multiple sclerosis to investigate their clinical traits and linked them with dysregulated gene expressions to establish diagnostic and prognostic indicators. METHODS We included 51 patients with relapsing-remitting MS (RRMS, n = 31), clinically isolated syndrome (CIS, n = 12), primary progressive MS (PPMS, n = 8) and a control group (n = 51). Using correlational analysis, the transcriptional patterns of chosen gene panels were examined and subsequently related with disease duration and the expanded disease disability score (EDSS). In addition, principal component analysis, univariate regression, and logistic regression analysis were employed to highlight distinct profiles of genes and prognosticate the excellent biomarkers of this illness. RESULTS Our findings demonstrated that neurofilament light (NEFL), tumor necrosis factor α (TNF-α), Tau, and clusterin (CLU) were revealed to be increased in recruited patients, whereas the presenilin-1 (PSEN1) and cell-surface glycoprotein-44 (CD44) were downregulated. Principal Component Analysis revealed distinct patterns between the MS and control groups. Correlation analysis indicated co-dependent dysregulated genes and their differential expression with clinical findings. Furthermore, logistic regression demonstrated that Clusterin (AUC=0.940), NEFL (AUC=0.775), TNF-α (AUC=0.817), Tau (AUC=0.749), PSEN1 (AUC=0.6913), and CD44 (AUC=0.832) had diagnostic relevance. Following the univariate linear regression, a significant regression equation was found between EDSS and IGF-1 (R2 adj = 0.10844; p= 0.0060), APP (R2 adj = 0.1107; p= 0.0098), and PSEN1 (R2 adj = 0.1266; p=0.0102). CONCLUSION This study exhibits dynamic gene expression patterns that represent the significance of specified genes that are prospective diagnostic and prognostic biomarkers for multiple sclerosis.
Evangeline M. Foster, Marco Fernandes, Adrià Dangla-Valls
et al.
Clusterin (CLU) is one of the most significant genetic risk factors for late onset Alzheimer’s disease (AD). However, the mechanisms by which CLU contributes to AD development and pathogenesis remain unclear. Studies have demonstrated that the trafficking and localisation of glycosylated CLU proteins is altered by CLU-AD mutations and amyloid-β (Aβ), which may contribute to AD pathogenesis. However, the roles of non-glycosylated and glycosylated CLU proteins in mediating Aβ toxicity have not been studied in human neurons. iPSCs with altered CLU trafficking were generated following the removal of CLU exon 2 by CRISPR/Cas9 gene editing. Neurons were generated from control (CTR) and exon 2 −/− edited iPSCs and were incubated with aggregated Aβ peptides. Aβ induced changes in cell death and neurite length were quantified to determine if altered CLU protein trafficking influenced neuronal sensitivity to Aβ. Finally, RNA-Seq analysis was performed to identify key transcriptomic differences between CLU exon 2 −/− and CTR neurons. The removal of CLU exon 2, and the endoplasmic reticulum (ER)-signal peptide located within, abolished the presence of glycosylated CLU and increased the abundance of intracellular, non-glycosylated CLU. While non-glycosylated CLU levels were unaltered by Aβ25–35 treatment, the trafficking of glycosylated CLU was altered in control but not exon 2 −/− neurons. The latter also displayed partial protection against Aβ-induced cell death and neurite retraction. Transcriptome analysis identified downregulation of multiple extracellular matrix (ECM) related genes in exon 2 −/− neurons, potentially contributing to their reduced sensitivity to Aβ toxicity. This study identifies a crucial role of glycosylated CLU in facilitating Aβ toxicity in human neurons. The loss of these proteins reduced both, cell death and neurite damage, two key consequences of Aβ toxicity identified in the AD brain. Strikingly, transcriptomic differences between exon 2 −/− and control neurons were small, but a significant and consistent downregulation of ECM genes and pathways was identified in exon 2 −/− neurons. This may contribute to the reduced sensitivity of these neurons to Aβ, providing new mechanistic insights into Aβ pathologies and therapeutic targets for AD.
Background: There is an urgent need for the detection of aggressive prostate cancer. Glycoproteins play essential roles in cancer development, while urine is a noninvasive and easily obtainable biological fluid that contains secretory glycoproteins from the urogenital system. Therefore, here we aimed to identify urinary glycoproteins that are capable of differentiating aggressive from non-aggressive prostate cancer. Methods: Quantitative mass spectrometry data of glycopeptides from a discovery cohort comprised of 74 aggressive (Gleason score ≥8) and 68 non-aggressive (Gleason score = 6) prostate cancer urine specimens were acquired via a data independent acquisition approach. The glycopeptides showing distinct expression profiles in aggressive relative to non-aggressive prostate cancer were further evaluated for their performance in distinguishing the two groups either individually or in combination with others using repeated 5-fold cross validation with logistic regression to build predictive models. Predictive models showing good performance from the discovery cohort were further evaluated using a validation cohort. Results: Among the 20 candidate glycoproteins, urinary ACPP outperformed the other candidates. Urinary ACPP can also serve as an adjunct to serum PSA to further improve the discrimination power for aggressive prostate cancer (AUC= 0.82, 95% confidence interval 0.75 to 0.89). A three-signature panel including urinary ACPP, urinary CLU, and serum PSA displayed the ability to distinguish aggressive prostate cancer from non-aggressive prostate cancer with an AUC of 0.86 (95% confidence interval 0.8 to 0.92). Another three-signature panel containing urinary ACPP, urinary LOX, and serum PSA also demonstrated its ability in recognizing aggressive prostate cancer (AUC=0.82, 95% confidence interval 0.75 to 0.9). Moreover, consistent performance was observed from each panel when evaluated using a validation cohort. Conclusion: We have identified glycopeptides of urinary glycoproteins associated with aggressive prostate cancer using a quantitative mass spectrometry-based glycoproteomic approach and demonstrated their potential to serve as noninvasive urinary glycoprotein biomarkers worthy of further validation by a multi-center study.
Although mucopolysaccharidoses (MPS), inherited metabolic diseases from the group of lysosomal storage diseases (LSD), are monogenic disorders, recent studies indicated that their molecular mechanisms are complicated. Storage of glycosaminoglycans (GAGs), arising from a deficiency in one of the enzymes involved in the degradation of these compounds, is the primary cause of each MPS type. However, dysfunctions of various cellular organelles and disturbance of cellular processes have been reported which contribute considerably to pathomechanisms of the disease. Here, we present a complex transcriptomic analysis in which all types and subtypes of MPS were investigated, with special emphasis on genes related to cell activation processes. Complex changes in expression of these genes were found in fibroblasts of all MPS types, with number of transcripts revealing higher or lower levels (relative to control fibroblasts) between 19 and over 50, depending on MPS type. Genes in which expression was significantly affected in most MPS types code for proteins involved in following processes, classified according to Gene Ontology knowledge database: cell activation, cell growth, cell recognition, and cell division. Levels of some transcripts (including CD9, CLU, MME and others) were especially significantly changed (over five times relative to controls). Our results are discussed in the light of molecular pathomechanisms of MPS, indicating that secondary and/or tertiary changes, relative to GAG storage, might significantly modulate cellular dysfunctions and contribute to molecular mechanisms of the disease. This may influence the efficacy of various therapies and suggests why various treatments are not fully effective in improving the complex symptoms of MPS.
Hexavalent chromium [Cr(VI)] is ubiquitous in the environment and is commonly used in various industrial processes. Clusterin (CLU) is an extracellular chaperone protein which exerts the anti-apoptotic function. In this study, we aimed to explore the effect of CLU on Cr(VI)-induced mitochondrial fission and apoptosis. We revealed that the apoptosis rate of L02 hepatocytes treated with Cr (VI) was increased. CLU over-expression could protect the hepatocytes from Cr(VI)-induced mitochondrial apoptosis. Furthermore, Cr(VI) triggered the intracellular calcium overload, resulting in the activation of xanthine oxidase (XO). Cr(VI) induced reactive oxygen species (ROS) overproduction, led to dynamin-related protein 1 (Drp1) translocation to mitochondria and the subsequent mitochondrial fission, contributing to the caspase-3-dependent mitochondrial apoptosis as evidenced by higher mitochondrial permeability transition pore (mPTP) opening rate, lower mitochondrial membrane potential (MMP), and more alanine transaminase (ALT)/aspartate transaminase (AST) leakage into the culture medium. However, CLU over-expression could trigger the AMP-activated protein kinase (AMPK) pathway, which was followed by the increase of sarcoplasmic reticulum Ca2+-ATPase (SERCA2a) expression. CLU-induced AMPK/SERCA2a activation attenuated calcium overload, caspase-3 activation, and ultimate mitochondrial apoptosis. All in all, the present study demonstrated that Cr(VI) induced hepatocytes apoptosis via Ca2+-ROS-Drp1-mitochondrial fission axis and CLU alleviated the mitochondrial apoptosis through activation of the AMPK/SERCA2a pathway.
Clusterin (CLU) is a multifunctional protein localized extracellularly and intracellularly. Although CLU‐knockout (KO) mice are more susceptible to renal ischemia‐reperfusion injury (IRI), the mechanisms underlying the actions of CLU in IRI are not fully understood. Macrophages are key regulators of IRI severity and tissue repair. Therefore, we investigated the role of CLU in macrophage polarization and phagocytosis. Renal IRI was induced in wild‐type (WT) or CLU‐KO C57BL/6 mice by clamping the renal pedicles for 30 min at 32°C. Peritoneal macrophages were activated via an intraperitoneal injection of lipopolysaccharide (LPS). Renal tissue damage was examined using histology, whereas leukocyte phenotypes were assessed using flow cytometry and immunohistochemistry. We found that monocytes/macrophages expressed the CLU protein that was upregulated by hypoxia. The percentages of macrophages (F4/80+, CD11b+ or MAC3+) infiltrating the kidneys of WT mice were significantly less than those in CLU‐KO mice after IRI. The M1/M2 phenotype ratio of the macrophages in WT kidneys decreased at day 7 post‐IRI when the injury was repaired, whereas that in KO kidneys increased consistently as tissue injury persisted. In response to LPS stimulation, WT mice produced fewer M1 macrophages, but not M2, than the control did. Phagocytosis was stimulated by CLU expression in macrophages compared with the CLU null controls and by the exogenous CLU protein. In conclusion, CLU suppresses macrophage infiltration and proinflammatory M1 polarization during the recovery period following IRI, and enhances phagocytic activity, which may be partly responsible for tissue repair in the kidneys of WT mice after injury.
Sporadic cerebral amyloid angiopathy (CAA) is characterized by cerebrovascular amyloid-β (Aβ) deposition, which leads to lobar hemorrhage and dementia. Biological molecules affecting the development of CAA have not been fully characterized. In this study, we performed proteome analysis of biopsied leptomeningeal and cortical vessels obtained from 6 CAA patients and 5 non-CAA patients who underwent surgery for large lobar hemorrhages. We found that 6 proteins, including Aβ, apolipoprotein E (apoE), clusterin (CLU), albumin, complement C4 and vitronectin were significantly upregulated in the vessels of CAA patients as compared to non-CAA patients. ApoE and CLU were found in all CAA patients. We next examined the effects of apoE and CLU on the early phase of Aβ aggregation, using a simple yet powerful in vitro model of CAA, which recapitulates the intramural periarterial drainage pathway model. We found that physiological concentrations of apoE and CLU delayed the initiation time of amyloid growth kinetics in a concentration-dependent manner. These data indicate that apoE and CLU may act as extracellular chaperones to inhibit Aβ amyloid deposition in CAA.
Spatial separation of water dimer from water monomer and larger water-clusters through the electric deflector is presented. A beam of water dimer with $93~\%$ purity and a rotational temperature of $1.5~$K was obtained. Following strong-field ionization using a $35~$fs laser pulse with a wavelength centered around $800~$nm and a peak intensity of $10^{14}~\text{W}/\text{cm}^2$ we observed proton transfer and $46~\%$ of the ionized water dimer broke apart into a hydronium ion $\text{H}_3\text{O}^+$ and neutral OH.
S. García-Obregón, M. Azkargorta, I. Seijas
et al.
BACKGROUND Sepsis is a life-threatening illness with a challenging diagnosis. Current serum biomarkers are not sensitive enough for diagnosis. With the aim of finding proteins associated with sepsis, serum protein profile was compared between patients and healthy donors and serum classical inflammatory proteins were analyzed in both groups. METHODS Serum protein profiles were characterized by two-dimensional electrophoresis (2DE). Identification of the proteins was carried out by mass spectrophotometry and their validation was performed by Enzyme-Linked-ImmunoSorbent Assay (ELISA) in a cohort of 85 patients and 67 healthy donors. Seven classical inflammatory proteins were analyzed in the same cohort by ELISA: interleukin-2 receptor α-chain (sCD25), scavenger receptor cysteine-rich-type-1 (sCD163), tumor-necrosis factor receptor superfamily-member-6 (sFas), hemeoxigenase-1 decycling (HO-1), interleukin-6 (IL-6), interleukin-18 (IL-18) and intercellular adhesion-molecule-1 (sICAM-1). RESULTS After 2DE, 20 significantly differently expressed spots were identified by mass spectrometry analysis, revealing deregulation of six different proteins upon sepsis and 50% were validated by ELISA: Antithrombin-III (AT-III), Clusterin (CLUS) and Serum amyloid A-1 (SAA-1). Serum concentration of AT-III and CLUS was significantly lower in patients' serum, whereas SAA-1 showed higher values in septic patients. Serum concentration of the seven inflammatory proteins was significantly increased in septic patients. Functional analysis of the ten deregulated proteins revealed an enrichment of proteins related mainly to the activation of the immune response. CONCLUSION We have identified a panel of ten potential sepsis marker proteins biologically connected and validated in a large number of patients, whose analysis could be considered as a complementary tool for the diagnosis of sepsis.
A. J. Barclay, K. Esteki, A. R. W. McKellar
et al.
Spectra of ethylene dimers and trimers are studied in the nu11 and (for the dimer) nu9 fundamental band regions of C2H4 (~2990 and 3100 cm-1) using a tunable optical parametric oscillator source to probe a pulsed supersonic slit jet expansion. The deuterated trimer has been observed previously, but this represents the first rotationally resolved spectrum of (C2H4)3. The results support the previously determined cross-shaped (D2d) dimer and barrel-shaped (C3h or C3) trimer structures. However, the dimer spectrum in the nu9 fundamental region of C2H4 is apparently very perturbed and a previous rotational analysis is not well verified.
Understanding of the atomic structures and ways in which the atoms interacting is critical to the understanding of chemistry. In this paper applied the concepts of game theory in explaining reactions between elements of the periodic table. The findings in this study suggest that the coordination and anti coordination, also cooperation and non-cooperation between atoms and molecules lead to bonding formation according to the game theory. Therefore, the chemical behavior and physical treats of any chemical reaction can be predicted. Multiple examples of each batch of the chemical reactions is expressed to support the useability of our claims.
ABSTRACT Mitochondrial function is tied to the nucleus, in that hundreds of proteins encoded by nuclear genes must be imported into mitochondria. While post-translational import is fairly well understood, emerging evidence supports that mitochondrial site-specific import, or co-translational import, also occurs. However, the mechanism and the extent to which it is used are not fully understood. We have previously shown Clueless (Clu), a conserved multi-domain protein, associates with mitochondrial outer membrane proteins, including Translocase of outer membrane 20, and genetically and physically interacts with the PINK1–Parkin pathway. The human ortholog of Clu, Cluh, was shown to bind nuclear-encoded mitochondrially destined mRNAs. Here we identify the conserved tetratricopeptide domain of Clu as predominantly responsible for binding mRNA. In addition, we show Clu interacts with the ribosome at the mitochondrial outer membrane. Taken together, these data support a model whereby Clu binds to and mitochondrially targets mRNAs to facilitate mRNA localization to the outer mitochondrial membrane, potentially for site-specific or co-translational import. This role may link the presence of efficient mitochondrial protein import to mitochondrial quality control through the PINK1–Parkin pathway. Summary: Clueless is a ribonucleoprotein that is crucial for mitochondrial function. Here we show Clueless can bind the ribosome at the mitochondrial outer membrane, suggesting it may play a role in mitochondrial co-translational import.
Lifetimes of complexes formed during ultracold collisions are of current experimental interest as a possible cause of trap loss in ultracold gases of alkali-dimers. Microsecond lifetimes for complexes formed during ultracold elastic collisions of K2 with Rb are reported, from numerically-exact quantum-scattering calculations. The reported lifetimes are compared with those calculated using a simple density-of-states approach, which are shown to be reasonable. Long-lived complexes correspond to narrow scattering resonances which we examine for the statistical signatures of quantum chaos, finding that the positions and widths of the resonances follow the Wigner-Dyson and Porter-Thomas distributions respectively.