Добірка наукової літератури з теми "The N-end rule"

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.
Title of thesis missing on title page; supplied from the abstract, p. [1].
Includes bibliographical references (p. 107-115).
Protein degradation is a central mechanism in the regulation of gene expression and activity. Proteolysis regulates not only homeostatic activities, but also the cell's responses to stress. A recurring question underlying this regulatory process is the specificity of substrate selection by the proteolytic machinery. I designed an unbiased selection to isolate N-terminal degradation sequences in vivo, which led to a collection of N-end rule signals. The N-end rule describes how the identity of a protein's N-terminal residue determines its metabolic stability. In E. coli, CIpAP is the principal protease that degrades proteins bearing an N-terminal phenylalanine, tyrosine, tryptophan, or leucine residue. The CIpS adaptor, which displays homology to eukaryotic ubiquitin ligases that recognize N-end signals, is a recently discovered component of the bacterial N-end rule. Using the collection of N-end signals, I was able to demonstrate that ClpS enhances N-end degradation by ClpAP but is not required in vivo or in vitro. The collection of N-end signals also provided insight into the role of sequence context in the N-end rule. Specifically, acidic residues and the length of the N-end signal affect degradation rates in vitro. These defective N-end signals also allowed us to separately define recognition specificities of ClpS and ClpAP. Whereas ClpS bound poorly to acidic N-end signals, CIpAP was unable to degrade substrates with short N-end sequences. Although two decades of biochemical and cellular data support the importance of the Nterminal residue in N-end degradation, there has been no structural information explaining how a single residue is recognized as a degradation signal.
(cont.) To this end, we solved a cocrystal structure of CIpS in complex with an N-end peptide. CIpS uses an extensive hydrogen bonding network to dock the a-amino group and a cavity lined with hydrophobic residues to recognize the N-terminal residue. Furthermore, mutation of the hydrophobic cavity altered the specificity of CIpS toward N-terminal residues. Together these findings attribute molecular functions to CIpS and ClpAP in the bacterial N-end rule and define sequence rules for the N-end signal. Furthermore, this work provides the tools and background for investigating the mechanism of substrate delivery by ClpS to ClpAP.
by Kevin H. Wang.
Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis. "June 2016." In title on title page [alpha] appears as lower case Greek letters.
Includes bibliographical references (pages 103-118).
by Benjamin J. Stein.
Ph. D.

Current protein sequencing methods include mass spectrometry and Edman degradation. We envision a novel high-throughput protein sequencing method using affinity adapters to recognize the N-terminal residue of a denatured peptide in an iterative process. This thesis takes a first step toward designing robust and selective affinity reagents. We outline our pipeline for designing selective protein adapters that recognize the N-terminal amino acid of a peptide independent of the following sequence. We based our design on a substrate recognition protein in the N-end rule pathway, ClpS. The bacterial N-recognin protein ClpS binds peptide substrates, termed N-degrons, that have a bulky hydrophobic amino acid (L/F/Y/W) at the N-terminus. Using full atom in silico models we designed hydrogen bonding and salt-bridge contacts in ClpS to novel N-degron substrates (N-end D/E/T), predicted the selectivity of these designs, and experimentally verified them. Of 11 designs, we purified nine that were soluble by SDS-PAGE, and obtained a peptide binding profile to 30 peptides with a modified ELISA assay. Most designs were non-specific or had no binding affinity. Four designs M53A, L112F, I45L, I45L_I45L_M53A had an increase in affinity to various substrates, but were not selective as they retained affinity to the native substrates (N-end L/F/Y/W). We performed molecular dynamics simulations on several proteins that were soluble or insoluble under standard expression conditions in E. coli, in order to learn parameters that were indicative of kinetic instability. Using a back-to-consensus approach, we identified a point mutant S104F that stabilizes the scaffold of ClpS as assayed by GFP fluorescence in a GFP-ClpS fusion protein. This thesis outlines the computational design pipeline we developed, which includes a RosettaScripts protocol, an in silico selectivity screen with AutoDock, and a kinetic stability confidence score from a molecular dynamics trajectory. Finally, we make suggestions toward designing selective affinity reagents for high-throughput N-end protein sequencing.

Caspase-7 is a member of a family of cysteine proteases that includes apoptotic initiators (caspases-8, -9 and -10) and executors (caspases-3, -6 and -7). During apoptosis, executioner caspases are cleaved by initiator caspases either by the extrinsic (death receptors) or by the intrinsic (mitochondrial) pathway of caspase activation. Caspase-7 is an obligate dimer in the cell and cleavage of the interdomain connector (IDC), which split the catalytic domain in two subunits, at either site 1 or site 2 allows the conversion of the enzyme from the zymogen (inactive) state to the active state through a conformation switch that leads to the creation of a substrate binding pocket and the catalytic site. During caspase-7 activation, a 23-residue N-terminal peptide is also cleaved. Consequently, caspase-7 displays different N-terminal residues from those of its zymogen. This can change the stability of caspase-7 according to the N-end rule, which relates the half-life of a protein with the residue presented at its N-terminus. This degradation pathway controls the ubiquitination of the protein based on the N-terminus. To replicate the different forms of caspase-7 produced during its activation process in a controlled manner, a TEV protease cleavage site [ENLYFQ[arrow down](S/A)] was strategically inserted to mimic the different possibilities of IDC cleavage: 1) cleavage at site 1 only, 2) cleavage at site 2 only, or 3) a double cleavage. This was done in order to obtain the N-terminal residues normally presented during the cleavage of caspase-7. These constructions have been also optimized to preserve the proteolytic activity of the enzyme with as little change as possible to the length of the IDC. These constructs were cleaved by TEV protease in vitro and in cellulo and allowed the activation of apoptosis. Furthermore, the cellular half-life of caspase-7 seems to be changed by its cleavage. In conclusion, we have developed an interesting tool for the study of caspase-7.

Flooding events are becoming more common throughout the world as a result of climate change, resulting in reduced crop yields. It was recently discovered that plants sense low oxygen (O2) (associated with flooding) through regulated proteolysis of the group VII Ethylene Response Factor transcription factors (ERFVIIs), via the Cys-Arg/N-end rule pathway of ubiquitin mediated proteolysis, which also senses another gas, nitric oxide (NO). The N-terminal (Nt) Cys of physiological (e.g. ERFVIIs) and artificial substrates was shown to be key for N-end rule function, and work in mammalian systems suggested that oxidation of Nt-Cys by O2 and NO was a required prerequisite for subsequent Nt arginylation by arginyl tRNA transferases (ATEs). However the exact mechanism of Nt-Cys oxidation has not been discovered. The primary aim of this thesis was to define the mechanism of in vivo Nt-Cys oxidation essential in determining the stability of Arg/N-end rule protein substrates, including ERFVIIs. In this study a novel approach was developed to investigate the oxidation of Nt-Cys in vivo using transgenic Arabidopsis expressing Cys-2 reporter proteins (derived from the transgenes 35S::MC-polyG-HA-GUS and Ubi1::MCGGAIL-GUS). Cys-2 of the reporter proteins is made Nt constitutively by co-translational Methionine Aminopeptidase (MAP) activity. Biochemical techniques were combined with analytical chemistry to investigate the in vivo oxidation of Nt-Cys using liquid chromatography mass spectrometry (LC-MS). In addition, synthetic peptides representing the Nt-sequence of the in vivoreporter protein were used to define the oxidative and nitrosylative modifications occurring at Nt-Cys in vitro. Findings of this study include the successful development of two new in vivo O2 sensor artificial N-end rule substrates, in the plant genetic model Arabidopsis thaliana. A further outcome revealed that the ERFVII RELATED TO APETALA 2.12 (RAP2.12) is stabilised in the shoot and root apical meristem to a greater extent than in other regions of seedlings in response to hypoxia, indicating that meristematic cells could be important oxygen sensory zones. Cys-2 reporter proteins were used in in vivo studies to attempt to identify the nature of the Nt residues following N-end rule action. Although Nt-peptides derived from affinity purified Cys-2 reporter protein were not identified by LC-MS, it was possible to demonstrate that ubiquitination is required on Cys-2 reporter proteins before 26S proteasome degradation. Combined results from Nt-Cys in vitro synthetic peptides and Cys-2 reporter proteins substrates of the Arg/N-end rule pathway, provide indirect evidence that post translational modifications (PTMs)not defined before occur in vivo. Using synthetic peptides it was possible to show evidence for Nt-Cys-sulfenamide formation after oxidation of Nt-Cys. This finding suggests that Cys-sulfenamide formation, a previously recognised reversible modification preventing irreversible oxidation to Cys-sulfonic acid, could occur at Nt-Cys of in vivoprotein substrates. An important finding of this study was the observednonreactionbetween the nitrosylated Nt-Cys and H2O or conversely oxidised Nt-Cys and NO. As Plant Cysteine Oxidases (PCOs) do not require NO to oxidise Nt-Cys, this result raises further uncertainty as to how NO is involved in the oxidation of Nt-Cys, suggesting that NO may be involved in the enzymatic activation of PCOs or the arginylation of Nt-Cys by ATEs. The findings of this study did not identify the Nt-peptide of the Cys-2 reporter protein, and hence the Nt-Cys oxidation state of an in vivo substrate of the Arg/N-end rule pathway remains unidentified. Despite this the result that Nt-Cys can be oxidised to Cys-sulfenamide is novel and an important discovery to the field of reactive Cys biology and chemistry.

L'éthylène comme la stratification au froid et le GA3, stimule la germination des graines d'Arabidopsis thaliana (Col-0) ayant une dormance primaire, à 25 °C et à l'obscurité. L'élimination de la dormance au froid n'exige pas ETR1, EIN4 et EIN2, alors que l'effet du GA3 nécessite ETR1. L'effet stimulateur de l'éthylène est associé à une réduction de l'expression des gènes impliqués dans les voies de signalisation des GAs (DELLAs) et de l'ABA (ABI5). Les graines du mutant prt6 affectées dans la voie "N-end rule" de la protéolyse, sont insensibles à l'éthylène, montrant que PRT6 intervient dans l'action de l'éthylène, et cette insensibilité résulte aussi d'une interrelation avec la balance ABA/GAs. D'autre part, les facteurs de transcription de la réponse à l'éthylène du groupe VII, (ERF VIIs), substrats de la voie "N-end rule", interviennent dans cette insensibilité. La sensibilité à l'éthylène de prt6rap2.2rap2.3rap2.12 et l'insensibilité de prt6hre1hre2, permet de montrer que les 3 RAPs et les 2 HREs interviennent respectivement en aval et en amont de PRT6. L'éthylène induit une diminution de l'expression des 3 RAPs dans Col, mais maintient ou induit celle-ci dans prt6. De plus, l'expession de HRE2 augmente dans prt6, mais diminue dans prt6rap2.2rap2.3rap2.12, suggérant que les 3 RAPs peuvent réguler l'expression de HRE2. De plus, l'éthylène modifie différentiellement le protéome de Col et de prt6 avec respectivement 587 et 30 protéines significatives. L'analyse des classes fonctionnelles a permis d'identifier la réponse à hypoxie comme processus biologique spécifique de prt6, mais leur insensibilité à l'éthylène est indépendante des ROS et de l'intensité respiratoire
Ethylene as chilling and GA3, was able to improve the germination of primary dormant seeds of Arabidopsis thaliana (Col-0) at 25 °C in darkness. Chilling did not require EIN4, ETR1 and EIN2 involved in ethylene signaling to break seed dormancy while GA required ETR1.The improving effect of ethylene in seed germination is EIN4 independent, and is associated with a decrease in ABA/GA ratio and a down-regulation of DELLAs and ABI5 genes related to GA and ABA signaling, respectively. The mutant affected in the proteolytic N-end rule pathway, prt6, was insensitive to ethylene in seed germination evidenced that PRT6 was involved in dormancy release by ethylene, and this insensitivity was related to a crosstalk with ABA/GAs. The substrates of the N-end rule pathway, ERFVIIs (HRE1, HRE2, RAP2.2, RAP2.3, and RAP2.12), might result in the insensitivity with an increased germination in prt6rap2.2rap2.3rap2.12 rather than in prt6hre1hre2, which also indicated that the 3 RAPs acted downstream of PRT6, while the 2 HREs acted upstream of PRT6. Ethylene reduced the transcript expression of the 3 RAPs in Col-0, but the 3 RAPs were maintained or induced by ethylene in prt6. Besides, HRE2 was up-regulated in prt6 seeds, but it was down-regulated in prt6rap2.2rap2.3rap2.12, suggesting that the 3 RAPs might stimulate the expression of HRE2. Ethylene differently changed the seed proteome of Col and prt6 with 587 and 30 significant proteins, respectively. The functional class scoring analysis identified one biological process, response to hypoxia, which was distinct in prt6, however the insensitivity of prt6 to ethylene was independent of ROS production or respiration intensity

Nationalism: Past as Prologue began as a single volume being compiled by Ad Akande, a scholar from South Africa, who proposed it to me as co-author about two years ago. The original idea was to examine how the damaging roots of nationalism have been corroding political systems around the world, and creating dangerous obstacles for necessary international cooperation. Since I (Bruce E. Johansen) has written profusely about climate change (global warming, a.k.a. infrared forcing), I suggested a concerted effort in that direction. This is a worldwide existential threat that affects every living thing on Earth. It often compounds upon itself, so delays in reducing emissions of fossil fuels are shortening the amount of time remaining to eliminate the use of fossil fuels to preserve a livable planet. Nationalism often impedes solutions to this problem (among many others), as nations place their singular needs above the common good. Our initial proposal got around, and abstracts on many subjects arrived. Within a few weeks, we had enough good material for a 100,000-word book. The book then fattened to two moderate volumes and then to four two very hefty tomes. We tried several different titles as good submissions swelled. We also discovered that our best contributors were experts in their fields, which ranged the world. We settled on three stand-alone books:” 1/ nationalism and racial justice. Our first volume grew as the growth of Black Lives Matter following the brutal killing of George Floyd ignited protests over police brutality and other issues during 2020, following the police assassination of Floyd in Minneapolis. It is estimated that more people took part in protests of police brutality during the summer of 2020 than any other series of marches in United States history. This includes upheavals during the 1960s over racial issues and against the war in Southeast Asia (notably Vietnam). We choose a volume on racism because it is one of nationalism’s main motive forces. This volume provides a worldwide array of work on nationalism’s growth in various countries, usually by authors residing in them, or in the United States with ethnic ties to the nation being examined, often recent immigrants to the United States from them. Our roster of contributors comprises a small United Nations of insightful, well-written research and commentary from Indonesia, New Zealand, Australia, China, India, South Africa, France, Portugal, Estonia, Hungary, Russia, Poland, Kazakhstan, Georgia, and the United States. Volume 2 (this one) describes and analyzes nationalism, by country, around the world, except for the United States; and 3/material directly related to President Donald Trump, and the United States. The first volume is under consideration at the Texas A & M University Press. The other two are under contract to Nova Science Publishers (which includes social sciences). These three volumes may be used individually or as a set. Environmental material is taken up in appropriate places in each of the three books. * * * * * What became the United States of America has been strongly nationalist since the English of present-day Massachusetts and Jamestown first hit North America’s eastern shores. The country propelled itself across North America with the self-serving ideology of “manifest destiny” for four centuries before Donald Trump came along. Anyone who believes that a Trumpian affection for deportation of “illegals” is a new thing ought to take a look at immigration and deportation statistics in Adam Goodman’s The Deportation Machine: America’s Long History of Deporting Immigrants (Princeton University Press, 2020). Between 1920 and 2018, the United States deported 56.3 million people, compared with 51.7 million who were granted legal immigration status during the same dates. Nearly nine of ten deportees were Mexican (Nolan, 2020, 83). This kind of nationalism, has become an assassin of democracy as well as an impediment to solving global problems. Paul Krugman wrote in the New York Times (2019:A-25): that “In their 2018 book, How Democracies Die, the political scientists Steven Levitsky and Daniel Ziblatt documented how this process has played out in many countries, from Vladimir Putin’s Russia, to Recep Erdogan’s Turkey, to Viktor Orban’s Hungary. Add to these India’s Narendra Modi, China’s Xi Jinping, and the United States’ Donald Trump, among others. Bit by bit, the guardrails of democracy have been torn down, as institutions meant to serve the public became tools of ruling parties and self-serving ideologies, weaponized to punish and intimidate opposition parties’ opponents. On paper, these countries are still democracies; in practice, they have become one-party regimes….And it’s happening here [the United States] as we speak. If you are not worried about the future of American democracy, you aren’t paying attention” (Krugmam, 2019, A-25). We are reminded continuously that the late Carl Sagan, one of our most insightful scientific public intellectuals, had an interesting theory about highly developed civilizations. Given the number of stars and planets that must exist in the vast reaches of the universe, he said, there must be other highly developed and organized forms of life. Distance may keep us from making physical contact, but Sagan said that another reason we may never be on speaking terms with another intelligent race is (judging from our own example) could be their penchant for destroying themselves in relatively short order after reaching technological complexity. This book’s chapters, introduction, and conclusion examine the worldwide rise of partisan nationalism and the damage it has wrought on the worldwide pursuit of solutions for issues requiring worldwide scope, such scientific co-operation public health and others, mixing analysis of both. We use both historical description and analysis. This analysis concludes with a description of why we must avoid the isolating nature of nationalism that isolates people and encourages separation if we are to deal with issues of world-wide concern, and to maintain a sustainable, survivable Earth, placing the dominant political movement of our time against the Earth’s existential crises. Our contributors, all experts in their fields, each have assumed responsibility for a country, or two if they are related. This work entwines themes of worldwide concern with the political growth of nationalism because leaders with such a worldview are disinclined to co-operate internationally at a time when nations must find ways to solve common problems, such as the climate crisis. Inability to cooperate at this stage may doom everyone, eventually, to an overheated, stormy future plagued by droughts and deluges portending shortages of food and other essential commodities, meanwhile destroying large coastal urban areas because of rising sea levels. Future historians may look back at our time and wonder why as well as how our world succumbed to isolating nationalism at a time when time was so short for cooperative intervention which is crucial for survival of a sustainable earth. Pride in language and culture is salubrious to individuals’ sense of history and identity. Excess nationalism that prevents international co-operation on harmful worldwide maladies is quite another. As Pope Francis has pointed out: For all of our connectivity due to expansion of social media, ability to communicate can breed contempt as well as mutual trust. “For all our hyper-connectivity,” said Francis, “We witnessed a fragmentation that made it more difficult to resolve problems that affect us all” (Horowitz, 2020, A-12). The pope’s encyclical, titled “Brothers All,” also said: “The forces of myopic, extremist, resentful, and aggressive nationalism are on the rise.” The pope’s document also advocates support for migrants, as well as resistance to nationalist and tribal populism. Francis broadened his critique to the role of market capitalism, as well as nationalism has failed the peoples of the world when they need co-operation and solidarity in the face of the world-wide corona virus pandemic. Humankind needs to unite into “a new sense of the human family [Fratelli Tutti, “Brothers All”], that rejects war at all costs” (Pope, 2020, 6-A). Our journey takes us first to Russia, with the able eye and honed expertise of Richard D. Anderson, Jr. who teaches as UCLA and publishes on the subject of his chapter: “Putin, Russian identity, and Russia’s conduct at home and abroad.” Readers should find Dr. Anderson’s analysis fascinating because Vladimir Putin, the singular leader of Russian foreign and domestic policy these days (and perhaps for the rest of his life, given how malleable Russia’s Constitution has become) may be a short man physically, but has high ambitions. One of these involves restoring the old Russian (and Soviet) empire, which would involve re-subjugating a number of nations that broke off as the old order dissolved about 30 years ago. President (shall we say czar?) Putin also has international ambitions, notably by destabilizing the United States, where election meddling has become a specialty. The sight of Putin and U.S. president Donald Trump, two very rich men (Putin $70-$200 billion; Trump $2.5 billion), nuzzling in friendship would probably set Thomas Jefferson and Vladimir Lenin spinning in their graves. The road of history can take some unanticipated twists and turns. Consider Poland, from which we have an expert native analysis in chapter 2, Bartosz Hlebowicz, who is a Polish anthropologist and journalist. His piece is titled “Lawless and Unjust: How to Quickly Make Your Own Country a Puppet State Run by a Group of Hoodlums – the Hopeless Case of Poland (2015–2020).” When I visited Poland to teach and lecture twice between 2006 and 2008, most people seemed to be walking on air induced by freedom to conduct their own affairs to an unusual degree for a state usually squeezed between nationalists in Germany and Russia. What did the Poles then do in a couple of decades? Read Hlebowicz’ chapter and decide. It certainly isn’t soft-bellied liberalism. In Chapter 3, with Bruce E. Johansen, we visit China’s western provinces, the lands of Tibet as well as the Uighurs and other Muslims in the Xinjiang region, who would most assuredly resent being characterized as being possessed by the Chinese of the Han to the east. As a student of Native American history, I had never before thought of the Tibetans and Uighurs as Native peoples struggling against the Independence-minded peoples of a land that is called an adjunct of China on most of our maps. The random act of sitting next to a young woman on an Air India flight out of Hyderabad, bound for New Delhi taught me that the Tibetans had something to share with the Lakota, the Iroquois, and hundreds of other Native American states and nations in North America. Active resistance to Chinese rule lasted into the mid-nineteenth century, and continues today in a subversive manner, even in song, as I learned in 2018 when I acted as a foreign adjudicator on a Ph.D. dissertation by a Tibetan student at the University of Madras (in what is now in a city called Chennai), in southwestern India on resistance in song during Tibet’s recent history. Tibet is one of very few places on Earth where a young dissident can get shot to death for singing a song that troubles China’s Quest for Lebensraum. The situation in Xinjiang region, where close to a million Muslims have been interned in “reeducation” camps surrounded with brick walls and barbed wire. They sing, too. Come with us and hear the music. Back to Europe now, in Chapter 4, to Portugal and Spain, we find a break in the general pattern of nationalism. Portugal has been more progressive governmentally than most. Spain varies from a liberal majority to military coups, a pattern which has been exported to Latin America. A situation such as this can make use of the term “populism” problematic, because general usage in our time usually ties the word into a right-wing connotative straightjacket. “Populism” can be used to describe progressive (left-wing) insurgencies as well. José Pinto, who is native to Portugal and also researches and writes in Spanish as well as English, in “Populism in Portugal and Spain: a Real Neighbourhood?” provides insight into these historical paradoxes. Hungary shares some historical inclinations with Poland (above). Both emerged from Soviet dominance in an air of developing freedom and multicultural diversity after the Berlin Wall fell and the Soviet Union collapsed. Then, gradually at first, right wing-forces began to tighten up, stripping structures supporting popular freedom, from the courts, mass media, and other institutions. In Chapter 5, Bernard Tamas, in “From Youth Movement to Right-Liberal Wing Authoritarianism: The Rise of Fidesz and the Decline of Hungarian Democracy” puts the renewed growth of political and social repression into a context of worldwide nationalism. Tamas, an associate professor of political science at Valdosta State University, has been a postdoctoral fellow at Harvard University and a Fulbright scholar at the Central European University in Budapest, Hungary. His books include From Dissident to Party Politics: The Struggle for Democracy in Post-Communist Hungary (2007). Bear in mind that not everyone shares Orbán’s vision of what will make this nation great, again. On graffiti-covered walls in Budapest, Runes (traditional Hungarian script) has been found that read “Orbán is a motherfucker” (Mikanowski, 2019, 58). Also in Europe, in Chapter 6, Professor Ronan Le Coadic, of the University of Rennes, Rennes, France, in “Is There a Revival of French Nationalism?” Stating this title in the form of a question is quite appropriate because France’s nationalistic shift has built and ebbed several times during the last few decades. For a time after 2000, it came close to assuming the role of a substantial minority, only to ebb after that. In 2017, the candidate of the National Front reached the second round of the French presidential election. This was the second time this nationalist party reached the second round of the presidential election in the history of the Fifth Republic. In 2002, however, Jean-Marie Le Pen had only obtained 17.79% of the votes, while fifteen years later his daughter, Marine Le Pen, almost doubled her father's record, reaching 33.90% of the votes cast. Moreover, in the 2019 European elections, re-named Rassemblement National obtained the largest number of votes of all French political formations and can therefore boast of being "the leading party in France.” The brutality of oppressive nationalism may be expressed in personal relationships, such as child abuse. While Indonesia and Aotearoa [the Maoris’ name for New Zealand] hold very different ranks in the United Nations Human Development Programme assessments, where Indonesia is classified as a medium development country and Aotearoa New Zealand as a very high development country. In Chapter 7, “Domestic Violence Against Women in Indonesia and Aotearoa New Zealand: Making Sense of Differences and Similarities” co-authors, in Chapter 8, Mandy Morgan and Dr. Elli N. Hayati, from New Zealand and Indonesia respectively, found that despite their socio-economic differences, one in three women in each country experience physical or sexual intimate partner violence over their lifetime. In this chapter ther authors aim to deepen understandings of domestic violence through discussion of the socio-economic and demographic characteristics of theit countries to address domestic violence alongside studies of women’s attitudes to gender norms and experiences of intimate partner violence. One of the most surprising and upsetting scholarly journeys that a North American student may take involves Adolf Hitler’s comments on oppression of American Indians and Blacks as he imagined the construction of the Nazi state, a genesis of nationalism that is all but unknown in the United States of America, traced in this volume (Chapter 8) by co-editor Johansen. Beginning in Mein Kampf, during the 1920s, Hitler explicitly used the westward expansion of the United States across North America as a model and justification for Nazi conquest and anticipated colonization by Germans of what the Nazis called the “wild East” – the Slavic nations of Poland, the Baltic states, Ukraine, and Russia, most of which were under control of the Soviet Union. The Volga River (in Russia) was styled by Hitler as the Germans’ Mississippi, and covered wagons were readied for the German “manifest destiny” of imprisoning, eradicating, and replacing peoples the Nazis deemed inferior, all with direct references to events in North America during the previous century. At the same time, with no sense of contradiction, the Nazis partook of a long-standing German romanticism of Native Americans. One of Goebbels’ less propitious schemes was to confer honorary Aryan status on Native American tribes, in the hope that they would rise up against their oppressors. U.S. racial attitudes were “evidence [to the Nazis] that America was evolving in the right direction, despite its specious rhetoric about equality.” Ming Xie, originally from Beijing, in the People’s Republic of China, in Chapter 9, “News Coverage and Public Perceptions of the Social Credit System in China,” writes that The State Council of China in 2014 announced “that a nationwide social credit system would be established” in China. “Under this system, individuals, private companies, social organizations, and governmental agencies are assigned a score which will be calculated based on their trustworthiness and daily actions such as transaction history, professional conduct, obedience to law, corruption, tax evasion, and academic plagiarism.” The “nationalism” in this case is that of the state over the individual. China has 1.4 billion people; this system takes their measure for the purpose of state control. Once fully operational, control will be more subtle. People who are subject to it, through modern technology (most often smart phones) will prompt many people to self-censor. Orwell, modernized, might write: “Your smart phone is watching you.” Ming Xie holds two Ph.Ds, one in Public Administration from University of Nebraska at Omaha and another in Cultural Anthropology from the Chinese Academy of Social Sciences, Beijing, where she also worked for more than 10 years at a national think tank in the same institution. While there she summarized news from non-Chinese sources for senior members of the Chinese Communist Party. Ming is presently an assistant professor at the Department of Political Science and Criminal Justice, West Texas A&M University. In Chapter 10, analyzing native peoples and nationhood, Barbara Alice Mann, Professor of Honours at the University of Toledo, in “Divide, et Impera: The Self-Genocide Game” details ways in which European-American invaders deprive the conquered of their sense of nationhood as part of a subjugation system that amounts to genocide, rubbing out their languages and cultures -- and ultimately forcing the native peoples to assimilate on their own, for survival in a culture that is foreign to them. Mann is one of Native American Studies’ most acute critics of conquests’ contradictions, and an author who retrieves Native history with a powerful sense of voice and purpose, having authored roughly a dozen books and numerous book chapters, among many other works, who has traveled around the world lecturing and publishing on many subjects. Nalanda Roy and S. Mae Pedron in Chapter 11, “Understanding the Face of Humanity: The Rohingya Genocide.” describe one of the largest forced migrations in the history of the human race, the removal of 700,000 to 800,000 Muslims from Buddhist Myanmar to Bangladesh, which itself is already one of the most crowded and impoverished nations on Earth. With about 150 million people packed into an area the size of Nebraska and Iowa (population less than a tenth that of Bangladesh, a country that is losing land steadily to rising sea levels and erosion of the Ganges river delta. The Rohingyas’ refugee camp has been squeezed onto a gigantic, eroding, muddy slope that contains nearly no vegetation. However, Bangladesh is majority Muslim, so while the Rohingya may starve, they won’t be shot to death by marauding armies. Both authors of this exquisite (and excruciating) account teach at Georgia Southern University in Savannah, Georgia, Roy as an associate professor of International Studies and Asian politics, and Pedron as a graduate student; Roy originally hails from very eastern India, close to both Myanmar and Bangladesh, so he has special insight into the context of one of the most brutal genocides of our time, or any other. This is our case describing the problems that nationalism has and will pose for the sustainability of the Earth as our little blue-and-green orb becomes more crowded over time. The old ways, in which national arguments often end in devastating wars, are obsolete, given that the Earth and all the people, plants, and other animals that it sustains are faced with the existential threat of a climate crisis that within two centuries, more or less, will flood large parts of coastal cities, and endanger many species of plants and animals. To survive, we must listen to the Earth, and observe her travails, because they are increasingly our own.

Abstract Johanson–Blizzard syndrome (JBS; OMIM 243800) is an autosomal recessive condition comprising multiple congenital anomalies and frequent mental retardation. Its most constant features are nasal wing hypoplasia and congenital exocrine pancreatic insufficiency, which is most likely due to intrauterine-onset destruction of acinar cells. Additional features include short stature, oligodontia, deafness, scalp defects, hypothyroidism, imperforate anus, and genitourinary malformations. JBS results from homozygous or compound heterozygous mutations at UBR1, leading to a loss of function of the homonymous ubiquitin (Ub) ligase of the N-end rule pathway. JBS is the first and only human disorder of this system that is known so far. The N-end rule pathway represents a highly conserved and ubiquitously expressed component of the Ub-proteasome system, which controls the levels of many intracellular proteins. The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal amino acid residue in that specific residues act as destabilizing signals (N-degrons). A large number of proteins are potential substrates of this pathway. The restricted organ involvement in JBS possibly re8ect “leaks” in the overlapping substrate spectra of the pathway’s Ub ligases UBR1 and UBR2, but the individual proteins whose increased levels or prolonged half-life are primarily involved in the pathogenesis of the manifestations of JBS are not yet known. There is emerging evidence that clinical variability of JBS is at least in part related to the genotype.

In the majority of the recent grammars of Middle Egyptian/Earlier Egyptian there is no negative construction n sDm=f containing a present/imperfective sDm=f form. This article discusses the question whether such a negative construction might be attestable — a question which can only be understood by revisiting the complicated research history. After an overview of the relevant steps of research history a list of several instances is offered where the negative construction n sDm=f with a present/imperfective sDm=f form and present/imperfective function could be assumed, and also the problems emerging in connection with them are named. Furthermore, it will be shown that the verb form in question might be identified with the circumstantial sDm=f/jr+=f, not with the Second Tense jrr=f. At the end the semantics of the negative construction are discussed and how it differs from the n sDm.n=f construction. The conclusion is that n sDm=f expresses negative continuous action, in direct opposition to n sDm.n=f expressing negative habitual action.

The paper on the first place summarizes the fatigue yield approach as a cause-effect interaction between fatigue damage progression and fatigue endurance. Secondly it investigates the fatigue strength worsening on experimental S-N data and the load variability effects in shipbuilding. Next it applies the Classification Society’s rule-based procedure for fatigue analysis of ship’s structure that uses a simplified fatigue strength assessment method. The example elaborates fatigue yield effect on the seagoing operation of a double hull 47400 tdw tanker. At the end the paper recommends the procedure for assessment of ship lifetime shortening due to the fatigue yielding under constant and variable amplitude block loadings.

Fatigue is a phenomenon, which needs to be considered in the present day’s vessel design. The welded joints are particularly affected by the fatigue damage due to high stress concentrations caused by the metallurgical discontinuities present in the weld. For oil tankers and bulk carriers adequate guidelines for the fatigue strength assessment have been established by the classification societies. But for navy vessel, like offshore patrol vessel, the design guidelines for the fatigue strength analysis are not widely available. In the present paper, an attempt has been made to calculate the fatigue life of offshore patrol vessel (OPV). In general five stages of work is involved in calculating fatigue life of any ship structure. These are, load calculation, nominal and hot spot stress computation, long-term stress distribution, selection of S-N curve and the fatigue damage calculation. In the present study, the wave loads are obtained by the rule based estimation. The finite element analysis with the submodeling approach has been used to get the hot spot stress at critical locations. The two-parameter Weibull curve has been used to get the long-term distribution of stress. And at the end, the fatigue damage and the fatigue life have been computed using the Palmgren-Miner linear cumulative damage theory at the critical locations of the vessel.

When a fleet of trains is nearing the end of its service life, the city transit authorities have to decide whether to replace the aging train inventory or apply life extension remediation to the existing fleet. Replacement of the entire inventory comes at a significant cost. Therefore, evaluation of the remaining service life and possible life extension methods for the current fleet is worth investigating. The objective of this study is the evaluation of remaining service life of existing municipal trains and assessment of risk associated with life extension in order to help authorities in the decision making process of applying life extension measures or purchasing new equipment. The main factors limiting service life is exceedance of material fatigue resistance and fracture. To this end, finite element models (FEM) of the train cars in question were created in ABAQUS® modeling software to find locations of stress concentration under prescribed service loads. Locations of concern from the FEM were then used as the basis for instrumentation planning for on-site testing. A single train unit was instrumented with strain gages and accelerometers and then loaded and tested under regular operating conditions. Collected data from the on-site test was then used for calibration and validation of the FEM. Load-time history was constructed based on the calibrated FEM and the data from testing. Calculation of fatigue damage accumulation was done in accordance to the Rain-flow counting algorithm and Palmgren-Miner rule. The remaining fatigue life was evaluated based on available S-N curves from test data. Loads, as well as material resistance are random variables; therefore a reliability approach has to be applied in the calculation of risk associated with service life extension in order to make a sound recommendation as to the risk of continued service beyond the prescribed service life. Statistical parameters of load and resistance where gathered and used in calculations for this recommendation. This paper presents the approach for service life evaluation/extension, reliability and stochastic methods for risk assessment in a real world example.

Abstract Code Case N-513 provides evaluation rules and criteria for temporary acceptance of flaws, including through-wall flaws, in moderate energy piping. The application of the Code Case is restricted to Class 2 and 3 systems, so that safety issues regarding short-term system operation are minimized. The first version of the Code Case was published in 1997. Since then, there have been five revisions to the Code Case that have been published by ASME. The Code Case has been used numerous times by utilities to avoid unscheduled shutdowns without impacting plant safety. Recent revisions of Code Case N-513 continue to expand its scope to piping components including elbows, reducers, branch tees and gate valve body ends. This paper provides three application examples of the Code Case implementation based on US plant operating experience. Specifically, detailed evaluations of through-wall leakage in straight pipe, a piping elbow and gate valve body end are provided. These examples will help facilitate Code Case implementation by future users.

Abstract In the framework of fatigue assessment of Nuclear Power Plant (NPP) components, Environmentally Assisted Fatigue (EAF) is nowadays receiving an increased level of attention by regulatory bodies, code committees and utilities worldwide. This concerns particularly the Long Term Operation (LTO) of NPPs, where EAF may impact significantly the stress reports that are revised for Periodic Safety Reviews (PSRs), but also nuclear new builds in some cases. In this context, several guidance documents were developed and issued, the most well-known example being the NUREG/CR-6909 report [1] prepared in the US, which prescribes inter alia an update of the Cumulative Usage Factor (CUF) through an environmental correction factor “Fen” that accounts for the detrimental effect of Light-Water Reactor (LWR) coolant environments on fatigue life and besides the water chemistry mainly depends on the temperature and the strain rate. Several nuclear codes have already incorporated this type of approach, including the AFCEN RCC-M code since its 2016 edition [2][3] through the introduction of two code cases or “Rules in Probationary Phase” (RPPs), entitled “RPP-2” and “RPP-3”. RPP-2 consists of an update of the design fatigue curve for austenitic and cast duplex stainless steels as well as Nickel based alloys, and is also a prerequisite for RPP-3 which provides guidelines for incorporating an Fen factor in fatigue usage factor calculations. RPP-3 describes a different method to consider EAF in fatigue analysis, that applies to austenitic and cast duplex stainless steel locations subjected to a Pressurized Water Reactor (PWR) primary circuit environment. It is an alternative to the straightforward application of the NUREG/CR-6909 methodology, where the Fen factor is alleviated by a factor of 3. This allowance, also known as the “Fen-integrated” approach, is possible because of an over-conservative quantification of the effect of surface finish under a PWR environment, which is accounted for through the design fatigue curve. This has been demonstrated on the basis of numerous fatigue tests led in a PWR primary circuit environment, on small scale fatigue specimens with a rough surface finish [4][5][6][7]. While RPPs 2 and 3 have been applied in several stress report calculations for the fourth decennial inspection of the 900 MWe French PWRs fleet, these rules are still a novelty and could be further improved in their practical implementation. From this perspective, AFCEN has then launched a benchmark exercise at the end of 2019, involving several nuclear stakeholders in Europe and China. This benchmark consisted in solving a sample problem really close to one already used in an earlier EPRI benchmark [8] which aimed at the implementation of the ASME code case N-792 [9]. The geometry studied represents a vessel nozzle with an attached piping, and the structure is exemplarily subjected to three thermal and mechanical transients. The sample problem has been solved through Finite Element Analysis (FEA) calculations with various Finite Element (FE) software packages. The benchmark was divided into two stages. The first step consisted in achieving thermal and mechanical FE calculations, which were kept as simple as possible in such a way as to avoid discrepancies between participants’ results. On the basis of the stresses obtained, the remaining part of the first phase consisted in calculating a CUF in air according to the RCC-M methodology. The second step was related to the calculation of a CUF in PWR primary circuit environment using the RPP-3, and more particularly to the calculation of Fen factors for the transient combinations identified during the previous stage. Since there is no mandatory rule (only guidance) in RPP-3 for calculating an equivalent strain rate, and since strain rate calculation constitutes a crucial step in the EAF concept, this is the area where discrepancies could be expected between participants’ results. Based on these results, improvements could be proposed to the content of RPP-3, or additional guidelines could be added.

ASME Code Case N-513, Evaluation Criteria for Temporary Acceptance of Flaws in Moderate Energy Class 2 or 3 Piping, provides evaluation rules for the temporary acceptance of flaws, including through-wall flaws, in moderate energy Class 2 or 3 piping without performing repair/replacement activities. The Code Case has gone through three revisions with the latest approved by ASME Section XI being N-513-2. The Code Case allows for evaluation of both planar and nonplanar flaws. The planar flaw evaluation uses the rules in Appendix C of ASME Section XI. The nonplanar flaw evaluation uses the procedure provided in Code Case N-480. This Code Case has been used widely in the nuclear industry ever since it was published. Its use is expected to grow with plant aging and especially since Revision 2 was recently endorsed by the NRC in Regulatory Guide 1.147 without condition. The paper describes three specific applications of the Code Case to accept leaking flaws in piping components for continued operation till the end of the operating cycle when repairs could be performed. The use of this Code Case thus avoided costly and unnecessary shutdown of the plants in these cases. The evaluation procedures using this Code Case for these instances are described in the paper.

Code Case N-513 provides evaluation rules and criteria for temporary acceptance of flaws, including through-wall flaws, in moderate energy piping. The application of the Code Case is restricted to moderate energy, Class 2 and 3 systems, so that safety issues regarding short-term, degraded system operation are minimized. The first version of the Code Case was published in 1997. Since then, there have been four revisions to augment and clarify the evaluation requirements and acceptance criteria of the Code Case that have been published by ASME. The technical bases for the original version of the Code Case and the four revisions have been previously published [1, 2, and 3]. There is currently work underway to incorporate additional changes to the Code Case and this paper provides the technical basis for the changes proposed in a fifth revision. These changes include clarification for buried piping, investigation of various radii used in the Code Case, removal of the 0.1 limit on the flexibility characteristic for elbow flaw evaluation, and an update of the stress intensity factor parameters for circumferential through-wall flaws. In addition, a new flaw evaluation procedure is given for through-wall flaws in gate valve body ends. This procedure evaluates flaws in the end of the valve body as if in straight pipe. These changes and their technical bases are described in this paper. Clarifications and changes deemed editorial are not documented in this paper.

During the past 30 years the main rules for fatigue analysis of pressure vessels were based on elastic approaches in order to evaluate cyclic strain amplitude and compare with an S-N fatigue curve for the corresponding material. After review of some rules in different Nuclear and Non-Nuclear Codes, like ASME Boiler & Pressure Vessel Code Section III, French RCC-M and RCC-MRx, European Standards EN 13445, the major conservatisms and uncertainties of different rules are discussed. All these Codes propose simple rules to evaluate the strain amplitude based on elastic approaches and simplified correction factors (Ke and Kν), transient combination rules and damage cumulating procedure. In the other hand, the material properties are based on standard fatigue tests done on the material associated to reduction factors to consider some particular effects like scatter, scale, surface roughness, mean stress or environmental effects to transfer them from small specimen to real structures. Concerned components in this paper are mainly piping systems. No existing Code covers all the aspects of fatigue with similar conservatisms that can affect the in-service inspection programs and the remaining life assessment of the corresponding components. After the review of different rules, key factors that affect the results and predictions will be identified. Some proposals will be issued to progress in the near future. Finally, a first set of recommendation on fatigue analysis will be presented to improve existing codes on harmonized way, associated to material properties needed, as fatigue curves associated to reduction factors.

During the past 30 years the main rules for fatigue analysis of pressure vessels were based on elastic approaches in order to evaluate a cyclic strain amplitude and compare with an S-N fatigue curve for the corresponding material. After review of some rules in different Nuclear and Non Nuclear Codes, like ASME Boiler & Pressure Vessel Code Section III, French RCC-M and RCC-MRx, European Standards EN 13445, the major conservatisms and uncertainties of different rules are discussed. All these Codes propose simple rules to evaluate the strain amplitude based on elastic approaches and simplified correction factors (Ke and Kv), transient combination rules and damage cumulating procedure. In the other hand, the material properties are based on standard fatigue tests done on the material associated to reduction factors to consider some particular effects like scatter, scale, surface roughness, mean stress or environmental effects to transfer them from small specimen to real structures. Concerned components are mainly piping systems. No existing Code covers all the aspects of fatigue with similar conservatisms that can affect the in-service inspection programs and the remaining life assessment of the corresponding components. After the review of different rules, key factors that affect the results and predictions will be identified. Some proposals will be issued to progress in the near future. Finally, a first set of recommendation on fatigue analysis will be presented to improve existing codes on an harmonized way, associated to material properties needed, as fatigue curves associated to reduction factors.

The present paper describes the behaviour of chain segments that are subjected to pretension and a rotation angle at the segment end. The behaviour such segments has been investigated both experimentally and by finite element modelling. The purpose is to carry out fatigue life predictions. A full scale test with a studless chain segment with a diameter of 125 mm has been carried out to shed more light on the behaviour. The test corroborated the assumption that the chain segment behaves semi-rigidly under the given conditions due to locking of the inter-link hinge mechanism. The influence of various important parameters on the bending effect was studied. The chain segment has a significant flexural stiffness and an intra-link bending curvature for links that are in a flat position with respect to the inflicted end rotation. The associated Out of Plane Bending (OPB) stresses are significant for critical links close to the end hang-off. This effect must be taken into account when carrying out fatigue life predictions. There is still no guidance given in rules and regulations for this case. In the present work it is suggested that a hot spot method is applied for fatigue life predictions. Under a combined loading mode, defined by tension and OPB, the maximum principal stress range in the link bend area must be determined by refined finite element analysis. Subsequently, the fatigue life can be predicted by using an appropriate hot spot S-N curve. The paper points out how a good fatigue design of the hang-off area can reduce the effect of OPB. A Buoy Turret Loading (BTL) is used as a case study to demonstrate both the design proposal and the fatigue life prediction methodology.