Response of Picea rubens seedlings to intermittent mist varying in acidity, and in concentrations of sulfur-, and nitrogen-containing pollutants

Two-year-old red spruce seedlings ( Picea rubens Sarg .) growing in. field chambers were repeatedly exposed to acidic mist with a factorial combination of 3 fluctuating levels of acidity: median pH values of 3.0 (range of 2.5 to 3.5), 3.5 (range of 3.0 to 4.0), and 4.0 (range of 3.5 to 4.5). and 3 ion compositions: sulfate. nitrate and ammonium, and a combination of all 3 ions. The experiment was performed during the growing season over a period of 3.5 months. Mist exposures were intermittent with 5 wet-dry cycles for each 16-h overnight exposure period, Foliar necrosis occurred on seedlings treated with the most acidic mist and was most severe when the mist contained sulfate. At a median pH of 3.5, a value close to that of cloud water occurring in the eastern United States, injury developed with sulfuric acid mist, but not. when the mist contained nitric acid. The combination of high acidity and sulfate significantly decreased volume of aboveground tissues, while high acidity and nitrate increased volume. Root and needle dry weights were not affected. However, high acidity of mist was associated with increased leader shoot length. These results indicate, that there is a risk of foliar injury and changes in growth of red spruce with cloud water at a median acidity of pH 3.5 or below, especially when there are high concentrations of sulfate and low concentrations of nitrate.     

Identification of phosphorylation sites on the E3 ubiquitin ligase UBR5/EDD

UBR5 (ubiquitin protein ligase E3 component n-recognin 5)/EDD (E3 ligase identified by differential display) is an E3 ubiquitin ligase that is a potential biomarker for poor prognosis for recurrent, platinum-resistant ovarian cancer. UBR5 has a role in the DNA damage response and many such proteins are regulated by phosphorylation. UBR5 is a 309 kDa nuclear phosphoprotein that we previously identified as a substrate of the MAP kinase ERK2. With its 477 potential phosphorylation sites, little is known about UBR5 phosphorylation and how it may regulate protein function. Currently, thirty-four sites of phosphorylation on UBR5 have been reported in the literature, mostly identified by large scale proteomics studies of tissues or of cells after various treatments; however, no studies have specifically targeted the identification of UBR5 phosphorylation sites. In this study, we used Liquid Chromatography-Mass Spectrometry (LC-MS/MS) to obtain a total sequence coverage of 64.3% from combining tryptic and GluC digests on UBR5 isolated from transfected COS-1 cells. We identified 24 sites of phosphorylation, 18 of which are novel sites. This data enhances our knowledge of UBR5 phosphorylation and provides a framework for the study of how phosphorylation affects UBR5 function.     

Succination of protein thiols during adipocyte maturation: a biomarker of mitochondrial stress

Although obesity is a risk factor for development of type 2 diabetes and chemical modification of proteins by advanced glycoxidation and lipoxidation end products is implicated in the development of diabetic complications, little is known about the chemical modification of proteins in adipocytes or adipose tissue. In this study we show that S-(2-succinyl)cysteine (2SC), the product of chemical modification of proteins by the Krebs cycle intermediate, fumarate, is significantly increased during maturation of 3T3-L1 fibroblasts to adipocytes. Fumarate concentration increased > or =5-fold during adipogenesis in medium containing 30 mm glucose, producing a > or =10-fold increase in 2SC-proteins in adipocytes compared with undifferentiated fibroblasts grown in the same high glucose medium. The elevated glucose concentration in the medium during adipocyte maturation correlated with the increase in 2SC, whereas the concentration of the advanced glycoxidation and lipoxidation end products, N(epsilon)-(carboxymethyl)lysine and N(epsilon)-(carboxyethyl)lysine, was unchanged under these conditions. Adipocyte proteins were separated by one- and two-dimensional electrophoresis and approximately 60 2SC-proteins were detected using an anti-2SC polyclonal antibody. Several of the prominent and well resolved proteins were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. These include cytoskeletal proteins, enzymes, heat shock and chaperone proteins, regulatory proteins, and a fatty acid-binding protein. We propose that the increase in fumarate and 2SC is the result of mitochondrial stress in the adipocyte during adipogenesis and that 2SC may be a useful biomarker of mitochondrial stress in obesity, insulin resistance, and diabetes.     

Uncloaking a Lost Cause: Decolonizing ancestry estimation in the United States

Since the professionalization of US-based forensic anthropology in the 1970s, ancestry estimation has been included as a standard part of the biological profile, because practitioners have assumed it necessary to achieve identifications in medicolegal contexts. Simultaneously, forensic anthropologists have not fully considered the racist context of the criminal justice system in the United States related to the treatment of Black, Indigenous, and People of Color; nor have we considered that ancestry estimation might actually hinder identification efforts because of entrenched racial biases. Despite ongoing criticisms from mainstream biological anthropology that ancestry estimation perpetuates race science, forensic anthropologists have continued the practice. Recent years have seen the prolific development of retooled typological approaches with 21st century statistical prowess to include methods for estimating ancestry from cranial morphoscopic traits, despite no evidence that these traits reflect microevolutionary processes or are suitable genetic proxies for population structure; and such approaches have failed to critically evaluate the societal consequences for perpetuating the biological race concept. Around the country, these methods are enculturated in every aspect of the discipline ranging from university classrooms, to the board-certification examination marking the culmination of training, to standard operating procedures adopted by forensic anthropology laboratories. Here, we use critical race theory to interrogate the approaches utilized to estimate ancestry to include a critique of the continued use of morphoscopic traits, and we assert that the practice of ancestry estimation contributes to white supremacy. Based on the lack of scientific support that these traits reflect evolutionary history, and the inability to disentangle skeletal-based ancestry estimates from supporting the biological validity of race, we urge all forensic anthropologists to abolish the practice of ancestry estimation.     

JNK1/2 regulate Bid by direct phosphorylation at Thr59 in response to ALDH1L1

BH3 interacting-domain death agonist (Bid) is a BH3-only pro-apoptotic member of the Bcl-2 family of proteins. Its function in apoptosis is associated with the proteolytic cleavage to the truncated form tBid, mainly by caspase-8. tBid translocates to mitochondria and assists Bax and Bak in induction of apoptosis. c-Jun N-terminal kinase (JNK)-dependent alternative processing of Bid to jBid was also reported. We have previously shown that the folate stress enzyme 10-formyltetrahydrofolate dehydrogenase (ALDH1L1) activates JNK1 and JNK2 in cancer cells as a pro-apoptotic response. Here we report that in PC-3 prostate cancer cells, JNK1/2 phosphorylate Bid at Thr59 within the caspase cleavage site in response to ALDH1L1. In vitro, all three JNK isoforms, JNK 1–3, phosphorylated Thr59 of Bid with JNK1 being the least active. Thr59 phosphorylation protected Bid from cleavage by caspase-8, resulting in strong accumulation of the full-length protein and its translocation to mitochondria. Interestingly, although we did not observe jBid in response to ALDH1L1 in PC-3 cells, transient expression of Bid mutants lacking the caspase-8 cleavage site resulted in strong accumulation of jBid. Of note, a T59D mutant mimicking constitutive phosphorylation revealed more profound cleavage of Bid to jBid. JNK-driven Bid accumulation had a pro-apoptotic effect in our study: small interfering RNA silencing of either JNK1/2 or Bid prevented Bid phosphorylation and accumulation, and rescued ALDH1L1-expressing cells. As full-length Bid is a weaker apoptogen than tBid, we propose that the phosphorylation of Bid by JNKs, followed by the accumulation of the full-length protein, delays attainment of apoptosis, and allows the cell to evaluate the stress and make a decision regarding the response strategy. This mechanism perhaps can be modified by the alternative cleavage of phospho-T59 Bid to jBid at some conditions.BH3 interacting-domain death agonist (Bid), a member of BH3-only group of proteins in the Bcl-2 family, functions as a sensor of cellular damage and activator of pro-apoptotic Bax and Bak.^{1, 2} Bid is a 23 kDa protein localized primarily in the cytosol, but upon apoptotic stimuli it is cleaved to yield a truncated 15 kDa C-terminal fragment tBid. tBid translocates to the mitochondrial membrane, where it interacts with Bax and Bak, enhancing their oligomerization and leading to outer membrane permeabilization, loss of membrane potential and release of mitochondrial apoptogens.^{3, 4} The canonical example of the activation of Bid cleavage is the FAS-mediated apoptosis, and Bid is viewed as the key molecule in the integration of death receptor and mitochondrial apoptotic pathways.^{5, 6} The interaction of tBid with Bax or Bak proceeds through the BH3 domain of Bid and occurs only after the protein is localized to mitochondria.⁷ In the full-length Bid, the BH3 domain can be masked by the N-terminal portion of the protein through the interaction with an α-helical BH-3-like region, the BH3-B domain.^{5, 8} The caspase-8 cleavage in the middle of the large flexible loop connecting the BH3 and BH3-B domains leads to structural rearrangements of the C-terminal portion of Bid enabling its insertion into mitochondrial membrane.⁹ The dissociation of the N-terminal fragment in the presence of the mitochondrial membrane and conformational changes of tBid molecule make the BH3 domain accessible for Bax or Bak.¹⁰ Other proteolytic enzymes can cleave Bid within the loop but caspase-8 appears to be a major factor generating tBid.⁸ Full-length Bid can also translocate to mitochondria and induce apoptosis^{11, 12, 13, 14} but its pro-apoptotic activity is weaker than the activity of tBid.¹⁵ It has been hypothesized that in contrast to tBid, the conformational changes enabling the translocation of full-length Bid to mitochondria are reversible.⁹Several studies have also indicated the cleavage-independent pro-survival function of Bid in S-phase checkpoint and highlighted the regulation of Bid by phosphorylation at several residues.^{16, 17} Thus, ATM/ATR protein kinases can phosphorylate Bid at Ser61, Ser64 and Ser78, which protects from caspase-8 cleavage.¹⁷ In response to DNA damage, Bid is phosphorylated by ATM protein kinase and translocates to the nucleus to contribute to the decision of cell fate.^{16, 17} Interestingly, the ablation of phosphorylation at Ser61 and Ser78 ATM sites caused accumulation of full-length Bid in the mitochondria of hematopoetic stem cells and increased cellular proliferation.¹⁸ Furthermore, the phosphorylation of murine Bid at Thr58, Ser61 and Ser64 near the caspase-8 cleavage site by casein kinase I and II protected the protein from cleavage, thus making it less active towards the induction of apoptosis.¹⁹ Moreover, the pro-survival function of Bid was suggested by the finding that its loss inhibited tumorigenesis of T cells.²⁰ Overall, phosphorylation of Bid can serve as a switch between the pro-apoptotic and pro-survival functions of the protein.Although phosphorylation of Bid by c-Jun N-terminal kinase (JNK) has not been demonstrated so far, it has been reported that the alternative processing of Bid, which generates jBid, is JNK-dependent.²¹ Interestingly, the accumulation of full-length Bid and its translocation to mitochondria was observed in HeLa cells in response to staurosporine,²² a known JNK activator.²³ Tight relationships between JNK and Bid have been also demonstrated in mouse models of TNFα-induced liver injury.²⁴ This study indicated that Bid is downstream of JNK in TNFα-induced apoptosis and the pro-apoptotic activity of JNK2 is mainly mediated by Bid. Here we report that in PC-3 cells, JNK1/2 phosphorylate Bid at Thr59 in response to folate stress enzyme 10-formyltetrahydrofolate dehydrogenase (ALDH1L1), thus protecting Bid from caspase-8 cleavage. This leads to apoptosis owing to a strong accumulation and mitochondrial translocation of full-length Bid.