The mRNA deadenylation process, catalyzed by the CCR4 deadenylase, is known to be the major factor controlling mRNA decay rates in Saccharomyces cerevisiae. We have identified the proline-rich region and RRM1 domains of poly(A) binding protein (PAB1) as necessary for CCR4 deadenylation. Deletion of either of these regions but not other regions of PAB1 significantly reduced PAB1-PAB1 protein interactions, suggesting that PAB1 oligomerization is a required step for deadenylation. Moreover, defects in these two regions inhibited the formation of a novel, circular monomeric PAB1 species that forms in the absence of poly(A). Removal of the PAB1 RRM3 domain, which promoted PAB1 oligomerization and circularization, correspondingly accelerated CCR4 deadenylation. Circular PAB1 was unable to bind poly(A), and PAB1 multimers were severely deficient or unable to bind poly(A), implicating the PAB1 RNA binding surface as critical in making contacts that allow PAB1 self-association. These results support the model that the control of CCR4 deadenylation in vivo occurs in part through the removal of PAB1 from the poly(A) tail following its self-association into multimers and/or a circular species. Known alterations in the P domains of different PAB proteins and factors and conditions that affect PAB1 self-association would, therefore, be expected to be critical to controlling mRNA turnover in the cell.mRNA degradation is a process involving the interaction and exchange of multiple multisubunit complexes and RNA binding proteins (8). Central to mRNA degradation is the removal of the poly(A) tail (deadenylation) that is controlled by a number of proteins associating with the mRNA in a structure termed the mRNP. Principal among these factors present in the mRNP are the poly(A) binding protein (PAB1), translation initiation and termination factors, the cytoplasmic deadenylases, and the factors that bind to the mRNA and elicit alterations in the mRNA degradative rate. The processes of mRNA degradation and deadenylation and the protein complexes that are involved are highly evolutionarily conserved from Saccharomyces cerevisiae to humans.The principal pathway for mRNA degradation in yeast proceeds through several steps. First, there is an initial trimming of about 15 to 20 nucleotides (nt) of the poly(A) tail to a length of about 60 to 80 nt that is specific for each mRNA and that appears to be carried out by PAN2/PAN3, presumably a cytoplasmic process (2,19,48). This trimming requires PAB1 and the translation termination factors eRF1 and eRF3 (5, 24), and all these factors are known to associate with each other (10, 23, 24, 29). Second, the major part of deadenylation utilizes the CCR4-NOT deadenylase complex (16,48). CCR4 is the catalytic component of this complex (7, 47) and shortens the poly(A) tail of mRNA to an end point size of about 8 to 12 nt (14). Poly(A) tail shortening down to an oligo(A) form (8 to 12 A's) may lead, in turn, to the reduced ability of PAB1 to bind the poly(A) tail that may alter the translation initiation...

Nitrous acid (HONO) is a major precursor of tropospheric hydroxyl radical (OH) that accelerates the formation of secondary pollutants. The HONO sources, however, are not well understood, especially in polluted areas. Based on a comprehensive winter field campaign conducted at a rural site of the North China Plain, a box model (MCM v3.3.1) was used to simulate the daytime HONO budget and nitrate formation. We found that HONO photolysis acted as the dominant source for primary OH with a contribution of more than 92%. The observed daytime HONO could be well explained by the known sources in the model. The heterogeneous conversion of NO2 on ground surfaces and the homogeneous reaction of NO with OH were the dominant HONO sources with contributions of more than 36% and 34% to daytime HONO, respectively. The contribution from the photolysis of particle nitrate and the reactions of NO2 on aerosol surfaces were found to be negligible in clean periods (2%) and slightly higher during polluted periods (8%). The relatively high OH levels due to fast HONO photolysis at the rural site remarkably accelerated gas-phase reactions, resulting in the fast formation of nitrate as well as other secondary pollutants in the daytime.

A fundamental problem in proteomics is the identification of protein complexes and their components. We have used analytical ultracentrifugation with a fluorescence detection system (AU-FDS) to precisely and rapidly identify translation complexes in the yeast Saccharomyces cerevisiae. Following a one-step affinity purification of either poly(A)-binding protein (PAB1) or the large ribosomal subunit protein RPL25A in conjunction with GFP-tagged yeast proteins/RNAs, we have detected a 77S translation complex that contains the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G, and PAB1. This 77S structure, not readily observed previously, is consistent with the monosomal translation complex. The 77S complex abundance decreased with translational defects and following the stress of glucose deprivation that causes translational stoppage. By quantitating the abundance of the 77S complex in response to different stress conditions that block translation initiation, we observed that the stress of glucose deprivation affected translation initiation primarily by operating through a pathway involving the mRNA cap binding protein eIF4E whereas amino acid deprivation, as previously known, acted through the 43S complex. High salt conditions (1M KCl) and robust heat shock acted at other steps. The presumed sites of translational blockage caused by these stresses coincided with the types of stress granules, if any, which are subsequently formed.

The Nucleocapsid Protein (N Protein) of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV2) is located in the viral core. Immunoglobulin G (IgG) targeting N protein is detectable in the serum of infected patients. The effect of high titers of IgG against N-protein on clinical outcomes of SARS-CoV2 disease has not been described. We studied 400 RT-PCR confirmed SARS-CoV2 patients to determine independent factors associated with poor outcomes, including Medical Intensive Care Unit (MICU) admission, prolonged MICU stay and hospital admissions, and in-hospital mortality. We also measured serum IgG against the N protein and correlated its concentrations with clinical outcomes. We found that several factors, including Charlson comorbidity Index (CCI), high levels of IL6, and presentation with dyspnea were associated with poor clinical outcomes. It was shown that higher CCI and higher IL6 levels were independently associated with in-hospital mortality. Anti-N protein IgG was detected in the serum of 55 (55%) patients at the time of admission. A high concentration of antibodies, defined as signal to cut off ratio (S/Co) > 1.5 (75 percentile of all measurements), was found in 25 (25%) patients. The multivariable logistic regression models showed that between being an African American, higher CCI, lymphocyte counts, and S/Co ratio > 1.5, only S/Co ratio were independently associated with MICU admission and longer length of stay in hospital. This study recommends that titers of IgG targeting N-protein of SARS-CoV2 at admission is a prognostic factor for the clinical course of disease and should be measured in all patients with SARS-CoV2 infection.

Oxidative modifications of LDL are a major risk factor in the development of vascular disease and are known to induce endothelial dysfunction, one of the earliest manifestations of atherosclerosis (1, 2). Our studies focus on the oxidized LDL (oxLDL)-induced impact on endothelial biomechanics and its role in vascular dysfunction.Our recent studies showed that the stiffness of aortic endothelial cells (ECs) is significantly increased by exposing the cells to oxLDL in vitro or by dyslipidemia in the dietinduced porcine atherosclerosis model in vivo (3, 4). An increase in endothelial stiffness was accompanied by an increase in endothelial contractile forces generated on the cell-substrate interface and an enhanced ability of ECs to form branching networks in 3D cultures (3, 4), which is considered a prerequisite of angiogenesis (5). Moreover, earlier studies demonstrated a correlation between increased endothelial force and network formation across several endothelial subtypes (6). We proposed, therefore, that oxLDL-induced endothelial stiffening may lead to increased angiogenic activity of ECs during the development of atherosclerotic plaques. This process is expected to be of major clinical importance because neovascularization of the plaques is increasingly recognized as a critical process and a major risk factor for plaque vulnerability (7). The goal of this study is to elucidate the mechanism of oxLDL-induced endothelial stiffening and evaluate a link between this effect and the ability of ECs to form functional capillaries. Abstract Endothelial biomechanics is