Academic literature on the topic 'De novo Proteins'

Protein therapeutics are clinically developed and used as minorly engineered forms of their natural templates. This direct adoption of natural proteins in therapeutic contexts very frequently faces major challenges, including instability, poor solubility, and aggregation, which may result in undesired clinical outcomes. In contrast to classical protein engineering techniques, de novo protein design enables the introduction of radical sequence and structure manipulations, which can be used to address these challenges. In this work, we test the utility of two different design strategies to design novel granulopoietic proteins, using structural information from human granulocyte-colony stimulating factor (hG-CSF) as a template. The two strategies are: (1) An epitope rescaffolding where we migrate a tertiary structural epitope to simpler, idealised, proteins scaffolds (Fig. 1A-C), and (2) a topological refactoring strategy, where we change the protein fold by rearranging connections across the secondary structures and optimised the designed sequence of the new fold (Fig. 1A,D,E). Testing only eight designs, we obtained novel granulopoietic proteins that bind to the G-CSF receptor, have nanomolar activity in cell-based assays, and were highly thermostable and protease-resistant. NMR structure determination showed three designs to match their designed coordinates within less than 2.5 Å. While the designs possessed starkly different sequence and structure from the native G-CSF, they showed very specific activity in differentiating primary human haematopoietic stem cells into fully mature granulocytes. Morever, one design shows significant and specific activity in vivo in zebrafish and mice. These results are prospectively directing us to investigate the role of dimerisation geometry of G-GCSF receptor on activation magnitude and downstream signalling pathways. More broadly, the results also motivate our ongoing work on to design other heamatopoietic agents. In conclusion, our findings highlight the utility of computational protein design as a highly effective and guided means for discovering nover receptor modulators, and to obtain new mechanistic information about the target molecule. Figure 1. Two different strategies to generate superfolding G-CSF designs. (A) X-ray structure of G-CSF (orange) bound to its cognate receptor (red) through its binding epitope (blue). According to the epitope rescaffolding strategy, (B) the critical binding epitope residues were disembodied and used as a geometric search query against the entire Protein Data Bank (PDB) to retrieve structurally compatible scaffolds. The top six compatible scaffolds structures are shown in cartoon representation. (C) The top two templates chosen for sequence design, were a de novo designed coiled-coil and a four-helix bundle with unknown function. The binding epitopes were grafted, and the scaffolds were optimised to rigidly host the guest epitope. (D-E) According to the topological refactoring strategy (D) the topology of the native G-CSF was rewired from around the fixed binding epitope, and then was further mutated to idealise the core residues (blue volume (E)) and residues distal from the binding epitope (orange crust (E)). Both strategies aimed at simplifying the topology, reducing the size, and rigidifying the bound epitope conformation through alternate means. Figure 1 Disclosures No relevant conflicts of interest to declare.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 107-119).
Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, M13 bacteriophage libraries are engineered as a biochemical platform for de novo semisynthetic enzymes, functionally modular and widely stable. Carbonic anhydrase-inspired hydrolytic activity via Zn²+ coördination is first demonstrated. The phage clone identified hydrolyzes a range of carboxylic esters, is active from 25°C to 80°C, and displays greater catalytic efficacy in DMSO than in water. Reduction-oxidation activity is subsequently developed via heme and copper cofactors. Heme-phage complexes oxidize multiple peroxidase substrates in a pH-dependent manner. The same phage clone also binds copper(II) and oxidizes a catechol derivative, di-tert-butylcatechol, using atmospheric oxygen as a terminal oxidant. This clone could be purified from control phage via Cu-NTA columns, enabling future library selections for phage that coördinate Cu²+ ions. The M13 semisynthetic enzyme platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work could tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.
by John P. Casey, Jr.
Ph. D.

While the advances of the scientific community have enabled extraordinary improvements in the capabilities of synthetic biology, there is a continued desire in biotechnology for enhanced or entirely novel biological functions. As proteins are either directly or indirectly responsible for the vast majority of naturally occurring biological activities, the modification of peptide structures constitutes a promising approach to address the ambitions of biotechnology. Central to the work in this thesis is the recognition that naturally occurring protein structures are intangibly complex due to the relics of evolutionary processes, accumulated from years of blind natural selection. Chapter 1 introduces de novo protein design strategies that circumvent the use of naturally occurring peptide scaffolds, offering examples of tractable systems that have been generated to perform various biological functions, thus forming the justification for the experimental approach undertaken here. The experimental work detailed in chapters 3 and 4 aimed to develop a system that would enable the incorporation of carotenoids and acenes into the internal cavity of de novo-designed 'maquette' proteins by hydrophobic partitioning alone. The results of these sections demonstrated that the protein chassis had little or no effect in the photophysical properties of the incorporated chromophores, whilst providing enhanced stability and solubility in entirely aqueous solutions. Conversely, the experimental strategy outlined in chapter 5 aimed to introduce nuclei of high atomic mass into the maquette proteins in order to directly affect the photophysical properties of the bound chromophores through the spin-orbit coupling interaction. The results of the final experimental chapter demonstrated that de novo designed proteins could effectively interface with native biological systems and provide a mechanism to enable cofactor incorporation in vivo. Where appropriate, the results of each experimental section are discussed in relation to their impact on specific areas of research and potential applications in biotechnology.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

Inhibition of protein synthesis serves as a general measure of cellular consequences of chemical stress. A few proteins are translated selectively and influence cell fate. How these proteins can bypass the general control of translation remains unknown. We found that low to mild doses of oxidants induce de novo translation of the NRF2 protein. Here we demonstrate the presence of a G-quadruplex structure in the 5' untranslated region (UTR) of NRF2 mRNA, as measured by circular dichroism, nuclear magnetic resonance, and dimethylsulfate footprinting analyses. Such a structure is important for 5'-UTR activity, since its removal by sequence mutation eliminated H2O2-induced activation of the NRF2 5' UTR. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed elongation factor 1 alpha (EF1a) as a protein binding to the G-quadruplex sequence. Cells responded to H2O2 treatment by increasing the EF1a protein association with NRF2 mRNA, as measured by RNA-protein interaction assays. The EF1a interaction with small and large subunits of ribosomes did not appear to change due to H2O2 treatment, nor did post translational modifications, as measured by two-dimensional (2-D) Western blot analysis. Since NRF2 encodes a transcription factor essential for protection against tissue injury, our data have revealed a novel mechanism of cellular defense involving de novo NRF2 protein translation governed by the EF1a interaction with the G-quadruplex in the NRF2 5' UTR during oxidative stress.

The ability to design, synthesize and characterize de novo proteins can help facilitate the understanding of how individual amino acids contribute to the stability and structure of a protein. The de novo approach can be extended to include the use of templates, which assist in the organization of the peptides to form predetermined three-dimensional structures. These template assembled de novo proteins have been named "caviteins" (cavitand + protein).[See thesis for diagram]. One of the challenges in this area of research is the ability to design and synthesize native-like de novo proteins. Previously two caviteins, LG2 and LG3, had shown some nativelike characteristics, although the evidence for a completely native-like structure remained debatable. The approach to identify a native-like structure was to design a corresponding protein that would exhibit non native-like properties. The leucine residues of LG2 and LG3 were replaced with norleucine residues in NG2 and NG3, respectively. The norleucine-based caviteins were less native-like in structure, as speculated, than their leucine-based counterparts. In the past, the designed caviteins were limited to having only one type of peptide sequence attached within one bundle. Here, the design of a hetero-TASP, i.e. two different sequences within one bundle, was explored, and provided a means to create various de novo proteins, including an anti-parallel four-helix bundle. The hetero-TASPs were characterized and found to exhibit different native-like properties depending on the attached peptide sequences, and helix orientations. Lastly, the N - and C-capping efficiency of glycine was examined. Caviteins having, peptides linked to the cavitand template via their N - and C-termini, and with and without glycine caps were synthesized and characterized. It was found that the caviteins lacking glycine caps at their respective helix termini were comparable in stability with their capped-counterparts, which was contrary to what was hypothesized. It has been shown that subtle changes in the peptide sequence, linker and helix orientation have dramatic effects on the overall cavitein structure and stability. Since many of the factors underlying the stability and structure of four-helix bundles are now well understood, it would be exciting to undertake the challenges of designing caviteins with specific applications.
Science, Faculty of
Chemistry, Department of
Graduate

Redox cofactors and amino-acid free radicals play important roles in biology. Although many of the same cofactors and amino acids that form these radicals are found across a broad range of biological systems, identical cofactors can have different reduction potentials. The local environment plays a role in defining these redox potentials. An understanding of this local-environment effect can shed more light on how redox chemistry works in nature. Our laboratory has developed a library of model proteins that are well suited to study amino-acid radicals. a3X is a de novo designed protein that is composed of 67 residues. It forms a three-helix bundle connected by two glycine loops. The radical site is located at position 32 on the central a-helix. The a3X protein is designed to be well-folded and thermodynamically stable across a broad pH range. Paper 1 describes the structural and electrochemical characterization of a3Y, a tyrosine variant of a3X. We were able to obtain a unique Faradaic response from Y32 at both low and high pH, using differential pulse voltammetry. In addition, we successfully redesigned α3Y by introducing a histidine in close proximity to Y32, creating a tyrosine/histidine pair. Our goal in creating this pair was to study proton-coupled electron transfer (PCET) in a well-structured and solvent-sequestered protein environment.  In paper 2 we illustrated the redox reversibility of Y32 and produced the first ever Pourbaix diagram for a tyrosine radical in a protein. The formal potential of the Y32-OŸ/Y32-OH redox couple was determined to be 918 ± 2 mV vs. the normal hydrogen electrode (NHE) at pH 8.40.  While at pH 5.52, the formal potential of the Y32-OŸ/Y32-OH redox couple was recorded at 1.07 V. Papers 3 and 4 utilize a3W to study cation-π interactions. In paper 3, we showed how solvation can affect the strength of these interactions by -0.9 kcal/mol. In Paper 4, we were able to monitor the disruption of the cation-π interaction with the use of high-pressure fluorescence and were able to calculate the interaction energy for a solvent exposed cation-π. The aim of the work described in this thesis was to use model proteins to study tyrosine radicals to gain a broader perspective and better understanding of the versatility of biological electron transfer and to measure cation-π interactions and how they behave in different environments.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

The kidney is central to acid–base homeostasis. Major processes are reabsorption of filtered bicarbonate, de novo synthesis of bicarbonate from ammoniagenesis, and net excretion of protons. The latter requires buffers such as ammonium, phosphate, citrate and other bases binding protons (so-called titratable acids). The proximal tubule is the major site of bicarbonate reabsorption and only site of ammoniagenesis. The thick ascending limb and the distal convoluted tubule handle ammonia/ammonium and complete bicarbonate reabsorption. The collecting duct system excretes protons and ammonium, but may switch to net bicarbonate secretion. The kidney displays a great plasticity to adapt acid or bicarbonate excretion. Angiotensin II, aldosterone and endothelin are involved in regulating these processes, and they induce morphological changes along the nephron. Inborn and acquired disorders of renal acid–base handling are caused by mutations in acid–base transport proteins or by dysregulation of adaptive mechanisms.

O vírus da dengue (DENV), o vírus da Zika (ZIKV) e o vírus da chikungunya (CHIKV) são espécies que apresentam relevância clínica para a saúde pública. Porém, ainda não existe um tratamento específico ou vacina disponível para esses arbovírus. Nesse contexto, é fundamental encontrar novos alvos terapêuticos que possam auxiliar estratégias e tratamentos mais eficientes. A metodologia de codon usage tem demonstrado bons resultados para encontrar alvos para terapias que visam inibidores de tradução. Este estudo buscou analisar o uso de códons e o equilíbrio entre a abundância relativa dos RNAs transportadores (tRNAs) para encontrar alvos terapêuticos que irão estimular novas alternativas de tratamento para infecções causadas pelos DENV, ZIKV e CHIKV. Para tanto, foi replicada uma estratégia computacional, assumindo uma terapia hipotética de inibição seletiva de tRNA (Selective Transport RNA Inhibition Therapy - STRIT), onde foi estabelecido um índice de potencial terapêutico (T-score) para encontrar potenciais espécies de tRNA que poderiam ser inibidas seletivamente para atenuar a replicação viral na célula hospedeira. Foram identificados os cinco códons com maior frequência relativa vírus/hospedeiro (mais relevantes para o vírus) nas seis espécies de arbovírus, notando que todos terminam com purinas A ou G. Os códons GGA (Glicina), AGA (Arginina) e ATA (Isoleucina) são relevantes em todos os flavivirus (ZIKV, DENV-1, DENV-2, DENV-3, DENV-4), mas não no alphavirus CHIKV, onde os códons ACG (Treonina) e CCG (Prolina) são os mais relevantes. Posteriormente, selecionando os cinco códons com maiores T-score nas seis espécies virais (30 códons em total) encontramos apenas 11 códons diferentes, todos terminados com A ou G. Agrupados segundo o nucleotídeo na primeira posição do códon estes 11 códons são: (AGA, ACA, ATA, ACG), (GGA, GCA, GTA, GCG), (CTA, CCG) e (TGG). No agrupamento, notamos outro fato intrigante: que 10 dos 11 códons mais bem ranqueados por T-score, terminam com GA, CA, TA ou CG. Nosso método identificou as espécies de tRNA (através da identificação do códon cognato com maior T-score), cuja inibição funcional por qualquer método específico a anticódon, poderia ter potenciais efeitos terapêuticos em células infectadas pelo vírus da Dengue, Zika e Chikungunya causando a inibição da tradução das proteínas do vírus sem ter um efeito deletério na sobrevivência das células hospedeiras durante o período da infeção. A predominância absoluta dos nucleotídeos A e G na terceira posição dos 11 códons com maior T-score, que por sua vez indica uma preferência dos arbovírus por 11 espécies de tRNA com C ou T na primeira posição do anticódon, abre um novo espaço de pesquisa na interação vírus-hospedeiro.

esistance features a selection of overtly non-conformist positions in the contemporary visual art scene of Albania vis-à-vis the most recent social, political, and economic turmoils in the Western Balkans – a region marked by the dark side of political governances that have remained “democratic” in their outward appearance (especially toward the European Union), while dramatically leaning toward autocratic regimes in the eyes of their own citizens. Regardless of their citizens’ primary interests, and despite some positive signals surfacing in the international media, almost every attempt to establish lasting conditions for democratic governance in the Western Balkans has been shrouded in the veil of profit-driven political scandals, personal greed for more and more power over the people’s rights, and the extinction of public property in pursuit of social elite’s corporate and private interests. Additionally, and more specifically related to Tirana, artists and citizens have, over the years, been involved in various types of revolt, expressing their disagreements with the ongoing destruction of public property in the name of “modernization and development”: a movement led by local political powers through financially and strategically motivated processes of architectural cannibalism – not only at the expense of erasing Albanian cultural heritage or long-term residents’ habitats, but also at the expense of taking human lives under the pretext of “urbanization.” The most obvious instance of this economy of destruction was the complex of buildings linked to the National Theater of Albania in downtown Tirana that has served as a symbolic and material place of citizens’ resistance: for more than two years, together with local artists, they have been opposing the government’s plans to demolish the old complex in order to build a new one – until this finally happened in Spring 2020, in the midst of the ongoing COVID19 pandemic. Rooted in the atmosphere of the National Theater Protests in Tirana, RESISTANCE was conceived in Summer 2019 by ZETA Center for Contemporary Art as the International Artists-in-Residence Program, in cooperation with three partner organizations from Kosovo, Serbia and North Macedonia (Stacion – Center for Contemporary Art in Prishtina; Ilija & Mangelos Foundation in Novi Sad; and Faculty of Things That Can’t Be Learned in Bitola) and supported by Swiss Cultural Fund in Albania, a project of the Swiss Agency for Development and Cooperation. Gradually, the project expanded into an exhibition (Heterotopias of Resistance, curated by Blerta Hoçia and featuring works by Lori Lako, Fatlum Doçi, Edona Kryeziu, Nina Galiç, Darko Vukiç, Nikola Slavevski, and Natasha Nedelkova) and a series of interviews and panel discussions (with contributions by Lindita Komani, Edmond Budina, Ervin Goci, Ergin Zaloshnja, Pleurad Xhafa, Gentian Shkurti, Stefano Romano, Luçjan Bedeni, HAVEIT, Leonard Qylafi, Jonida Gashi, and Fatmira Nikolli). The results of both have been collected and presented in the format of a publication that, besides serving as an indispensable reading material concerning visual arts and politics in contemporary Albania, especially to those abroad, functions by itself as a form of resistance against contagious cultural policies in weak post-socialist “democracies” in Southeastern Europe.

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.

Tetranectin (Mr = 68,000) is a tetrameric blood plasma protein, which binds to plasminogen and also to the lysine-binding site of the isolated kringle 4 from plasminogen. Its four polypeptide chains, which are non-covalently bound, each consists of 181 amino acid residues. We have determined the complete amino acid sequence and the disulfide bonds. Each position corresponds to a single amino acid residue except 34 which contains Ala and Ser and 37 which contains Val and Met in equimolar amounts. The three disulfide bonds connect Cys-50 to Cys-60, Cys-77 to Cys-176 and Cys-152 to Cys-168. The sequence of tetranectin was found to be homologous, to an extent indicating common ancestry, with the extracellular part of the asialoglyco-protein receptors and with the C-terminal globular domain of the cartilage proteoglycan core protein. Conserved residues include the six half-cystines of tetranectin. Therefore, we can now propose disulfide bond patterns for the proteins homologous with tetranectin. Supported by NIH-grant HL-16238 (S.M.), the Danish Science and Medical Research Councils, the Danish Cancer Society and NOVO Foundation.

Gas vesicles are low-density, gas-filled protein organelles found inside various microorganisms. They have a lipid-free membrane with an average thickness of 2 nm and provide their hosts with buoyancy. In this study we characterized gas vesicle proteins synthesized by the Halobacterium sp. NRC-1 strain making use of molecular modeling methods and molecular dynamics (MD) simulations. The tertiary structure of GvpA protein, the major constituent of the gas vesicle membrane, was predicted using the De Novo computational design method available in the Rosetta Suite 2.3.1 software and was found to be in agreement with experimental data available from previous studies conducted by others and the consensus of different secondary structure prediction web servers. Optimization of the predicted structure was first carried out by energy minimization and simulated annealing. Subsequently, the mechanical properties of GvpA were investigated via constant pressure and temperature (NPT) aqueous MD simulations, in which two approaches were used to study the isothermal compressibility: quantification of the fluctuations in protein volume at constant pressure and temperature, and quantification of the volume changes induced through changes in the simulation pressure. Long term we plan to incorporate this information into multi-scale models of whole gas vesicles.

Fibrous proteins, such as collagen and elastin, form the underlying structure of many soft tissues. These proteins form micrometer-scale networks of varying topology that play a role in governing the mechanics of tissues at larger length scales [1]. The relationship between a network’s topology and its mechanics, however, are poorly understood. This disconnect presents an important challenge in constructing realistic multiscale models of tissues informed by collagen network micrographs and subsequently reconstructed networks [2]. Accurate multiscale simulations may require thousands to millions of such unique networks. It is imperative that a method be developed to generate random networks that are functionally similar to ones derived experimentally. In the current study, we present a probabilistic method for generating de novo networks that mimic the mechanical properties of previously characterized networks. We chose Delaunay and Voronoi networks as model targets because they have been used successfully to model the mechanics of collagenous tissues [3] and since their topologies are well characterized. Understanding the role of topology in network mechanics is fundamental to building improved models of the mechanics of fibrous soft tissues — models that can aid in the rational design of engineered tissues or that can help assess the mechanical impact of damage or disease on native tissues.

Self-assembly of β-sheet forming peptides into filaments has drawn great interests in biomedical applications [1,2]; Hydrogels formed by filaments self-assembled from de novo designed peptides possess potential applications for cell culture scaffolds [3]. On the other hand, peptides derived from amyloidogenic proteins in neurodegenerative diseases such as Alzheimer’s and Parkinson’s also form similar β-sheet filaments in vitro. They share little sequence homology, yet filaments formed by these self-assembling peptides commonly have the cross-β structure, the key signature of the amyloid fibril. Detailed structural information of the self-assembled β-sheet filaments has been limited partly due to the difficulty in preparing ordered filament samples, and it has been only recently that solid-state nuclear magnetic resonance and x-ray techniques have revealed their molecular structure at the atomic level [4,5]. Although molecular structures of amyloid fibrils are becoming available, physical principles governing their self-assembly and the properties of the filaments are not well-understood, for which computational as well as theoretical approaches are desirable [6].

Vascularization is critical for success of tissue engineering applications. Previous studies by us and others have shown that self-assembling peptide nanoscaffold RAD16-II promotes de novo capillary formation (angiogenesis) in vitro and neovascularization in vivo, and is a promising material for tissue engineering applications [1, 2]. However, the molecular mechanisms for cell interactions with this material are not known. Angiogenesis is mediated via interactions between integrins, which are expressed on the surface of activated endothelial cells (ECs), and extracellular matrix proteins. Among several integrins, αvβ3 is the most abundant and influential receptor regulating angiogenesis [3]. The αvβ3 integrin binds to its ligands via Arg-Gly-Asp (RGD) biding motif. However, there are no RGD motifs on RAD 16-II peptide. Instead, it contains three RAD motifs. Studies have shown that non-specific binding of αvβ3 with RAD can be retained through R and D sides [4]. The objective of this study, therefore, is to elucidate the underlying molecular mechanisms of RAD16-II nanoscaffold interactions with microvascular endothelial cells. We hypothesize that non-specific interactions between RAD16-II peptide nanoscaffold and αvβ3 integrin result in phosphorylations of β3 cytoplasmic domain, which then activate downstream angiogenic signaling pathways and promote angiogenesis.

New data were presented for the first time on the intestinal transcriptome of the intestines (posterior section) of the Baikal omul Coregonus migratorius Georgi, 1775 (Salmoniformes: Coregonidae) belonging to the deep water bottom morphological group (Lake Baikal) infected with parasites of various systematic groups: cestodes Dibothriocephalus dendriticus, Proteocephalus longicollis, Eubothrium crassum, and nematode Contracaecum osculatum baicalensis. Sequencing of the transcriptomics libraries was performed on an Illumina NextSeq550 sequencer using the NextSeq® 550 High Output Kit v2. Based on the obtained data, de-novo transcriptome assembly was performed. Conserved domains and their associated Gene Ontology annotations were predicted using Blast2Go. As a result, it was found that in the posterior section of the intestine enriched with lymphoid tissue (GALT), expression of functional proteins was observed that were primarily associated with enzymatic activity, with the development of specialized tissues, with cellular, metabolic and secretory processes. It should be noted that a significant proportion of gene ontology terms is associated with the functioning of the immune system, and with the cellular response to stress, which, under conditions of sensitization by the metabolic end products of helminths and their traumatic and antigenic effects, is quite understandable. The identified transcriptome may provide new information for understanding the functions of lymphoid organs in salmonids with parasitosis.

Coagulation factor V (FV), is a single chain, multifunctional glycoprotein of Mr 350,000 which interacts with a variety of hemostatic proteins such as factor Xa, prothrombin, thrombin and protein C, on the surface of platelets and vascular endothelial cells. FV serves as both a cofactor and substrate in the generation of thrombin and plays a critical regulatory role in both physiologic hemostasis and pathologic thrombosis. The biosynthesis of FV and its subsequent expression are therefore expected to be precisely controlled and may differ in the three sites of synthesis - hepatocytes, endothelial cells, and megakaryocytes (MK). We have previously demonstrated that each guinea pig MK contains 500 times as much FV as in a platelet, as quantified by a competitive enzyme-linked-immunosorbent assay and expresses FV by cytoimmunofluorescence. De novo biosynthesis was demonstrated by incorporation of S-methionine into FV purified on a immunoaffinity column. The purified MK protein exhibited both FV coagulant activity and antigenicity. However, MK FV was more slowly activated by thrombin, more stable in the absence of Ca and exhibited a slightly higher M of 380,000 compared to plasma FV. Similar studies have documented biosynthesis in human MK. In addition, all morphologically recognizable MK enriched by elutriation from human bone marrow contained FV as documented by both monospecific polyclonal and monoclonal antibodies (MAb) to FV. All these cells bound FV since a murine MAb reacting with the light chain of FV (B38) labeled all cells. In contrast, 68% of cells synthesized FV since B10, a MAb to the activation peptide recognizing FV but not FVa, labeled this fraction. To determine whether immature nonnorphologically recognizable MK expressed FV, we identified these cells with an antiserum to human platelet glycoproteins and then probed them with B38. Seventy percent (70%) of such small cells expressed FV. In contrast, no small cells in MK colonies cloned in FV deficient medium expressed FV while only 40% of such colonies contained cells which expressed FV.To further probe the regulation of FV in MK we attempted to correlate the synthesis of FV as probed by MAb B10 with geometric mean cell diameter, stage and ploidy. No significant correlation of FV with any of these indicators of MK maturation. In contrast, preliminary studies suggest that low doses of tetradecanoyl phorbol acetate augment both the number of MK containing FV and the level of FV expressed by individual cells. Thus, FV synthesis may be regulated independent of size, stage, or ploidy and protein kinase C may play a role.To further define the molecular nature of FV in MK we found that purified FV was converted from a monomer to high Mr multimers by an enzyme derived from MK. These multimers resulting from covalent crosslinking since they were stable to SDS, 100° C and reducing agents. The responsible enzyme appeared to be MK FXIIIa since it required C, was inhibited by agents which react with the active site thiol group and was blocked by pseudoamine donor substrates such as putrescine. In addition, FXIIIa was directly demonstrated in guinea pig MK by a specific activity stain. Other investigators have established that FV became irreversibly associated with platelet cytoskeletons after exposure to thrombin. tested whether FXIIIa might mediate this association by performing ligand blotting of platelet membrane proteins using 125I-FV(FV*). Only actin of all the membrane proteins was detected by radioautography. The binding of FV* to the cytoskeleton was dependent in the presence of Ca and FXIIIa. In purified systems crosslinked complexes containing FV* or radiolabeled actin were detected in separate experiments. In whole platelets, the formation of the heteropolymer, after thrombin stimulation, was inhibited by antibodies to FXIII a chain, FV activation peptide (B10) or actin. Endogenous platelet FV was also dependent on FXIII for incorporation into the platelet cytoskeleton after thrombin stimulation. When thrombin-treated FV was crosslinked to actin only the activation peptide (150 kDa) was crosslinked. The light chain or heavy chain of FVa were not involved. Thus FXIIIa play an important role in the binding of FV in platelets to the cytoskeleton during activation and secretion.Further studies of FV in megakaryocytes are necessary to define the regulation of biosynthesis and the control of expression which dictate its critical role in hemostasis and thrombosis.

The aim of this research project was to obtain information on the role of the cytochrome b559 in the function of Photosystem-II (PSII) with special emphasis on the light induced photo inactivation of PSII and turnover of the photochemical reaction center II protein subunit RCII-D1. The major goals of this project were: 1) Isolation and sequencing of the Chlamydomonas chloroplast psbE and psbF genes encoding the cytochrome b559 a and b subunits respectively; 2) Generation of site directed mutants and testing the effect of such mutation on the function of PSII under various light conditions; 3) To obtain further information on the mechanism of the light induced degradation and replacement of the PSII core proteins. This information shall serve as a basis for the understanding of the role of the cytochrome b559 in the process of photoinhibition and recovery of photosynthetic activity as well as during low light induced turnover of the D1 protein. Unlike in other organisms in which the psbE and psbF genes encoding the a and b subunits of cytochrome b559, are part of an operon which also includes the psbL and psbJ genes, in Chlamydomonas these genes are transcribed from different regions of the chloroplast chromosome. The charge distribution of the derived amino-acid sequences of psbE and psbF gene products differs from that of the corresponding genes in other organisms as far as the rule of "positive charge in" is concerned relative to the process of the polypeptide insertion in the thylakoid membrane. However, the sum of the charges of both subunits corresponds to the above rule possibly indicating co-insertion of both subunits in the process of cytochrome b559 assembly. A plasmid designed for the introduction of site-specific mutations into the psbF gene of C. reinhardtii. was constructed. The vector consists of a DNA fragment from the chromosome of C. reinhardtii which spans the region of the psbF gene, upstream of which the spectinomycin-resistance-conferring aadA cassette was inserted. This vector was successfully used to transform wild type C. reinhardtii cells. The spectinomycin resistant strain thus obtained can grow autotrophically and does not show significant changes as compared to the wild-type strain in PSII activity. The following mutations have been introduced in the psbF gene: H23M; H23Y; W19L and W19. The replacement of H23 involved in the heme binding to M and Y was meant to permit heme binding but eventually alter some or all of the electron transport properties of the mutated cytochrome. Tryptophane W19, a strictly conserved residue, is proximal to the heme and may interact with the tetrapyrole ring. Therefore its replacement may effect the heme properties. A change to tyrosine may have a lesser affect on the potential or electron transfer rate while a replacement of W19 by leucine is meant to introduce a more prominent disturbance in these parameters. Two of the mutants, FW19L and FH23M have segregated already and are homoplasmic. The rest are still grown under selection conditions until complete segregation will be obtained. All mutants contain assembled and functional PSII exhibiting an increased sensitivity of PSII to the light. Work is still in progress for the detailed characterization of the mutants PSII properties. A tobacco mutant, S6, obtained by Maliga and coworkers harboring the F26S mutation in the b subunit was made available to us and was characterized. Measurements of PSII charge separation and recombination, polypeptide content and electron flow indicates that this mutation indeed results in light sensitivity. Presently further work is in progress in the detailed characterization of the properties of all the above mutants. Information was obtained demonstrating that photoinactivation of PSII in vivo initiates a series of progressive changes in the properties of RCII which result in an irreversible modification of the RCII-D1 protein leading to its degradation and replacement. The cleavage process of the modified RCII-D1 protein is regulated by the occupancy of the QB site of RCII by plastoquinone. Newly synthesized D1 protein is not accumulated in a stable form unless integrated in reassembled RCII. Thus the degradation of the irreversibly modified RCII-D1 protein is essential for the recovery process. The light induced degradation of the RCII-D1 protein is rapid in mutants lacking the pD1 processing protease such as in the LF-1 mutant of the unicellular alga Scenedesmus obliquus. In this case the Mn binding site of PSII is abolished, the water oxidation process is inhibited and harmful cation radicals are formed following light induced electron flow in PSII. In such mutants photo-inactivation of PSII is rapid, it is not protected by ligands binding at the QB site and the degradation of the inactivated RCII-D1 occurs rapidly also in the dark. Furthermore the degraded D1 protein can be replaced in the dark in absence of light driven redox controlled reactions. The replacement of the RCII-D1 protein involves the de novo synthesis of the precursor protein, pD1, and its processing at the C-terminus end by an unknown processing protease. In the frame of this work, a gene previously isolated and sequenced by Dr. Pakrasi's group has been identified as encoding the RCII-pD1 C-terminus processing protease in the cyanobacterium Synechocystis sp. PCC 6803. The deduced sequence of the ctpA protein shows significant similarity to the bovine, human and insect interphotoreceptor retinoid-binding proteins. Results obtained using C. reinhardtii cells exposes to low light or series of single turnover light flashes have been also obtained indicating that the process of RCII-D1 protein turnover under non-photoinactivating conditions (low light) may be related to charge recombination in RCII due to back electron flow from the semiquinone QB- to the oxidised S2,3 states of the Mn cluster involved in the water oxidation process.

The avian influenza virus, subtype H9N2 subtype, defined as having a low pathogenicity, causes extensive economical losses in commercial flocks, probably due to management and synergism with other pathogens. AIV H9N2 was first identified in Israel in the year 2000, and since then it became endemic and widespread in Israel. Control by vaccination of commercial flocks with an inactivated vaccine has been introduced since 2007. In face of the continuous H9N2 outbreaks, and the application of the vaccination policy, we aimed in the present study to provide a method of differentiating naturally infected from vaccinated animals (DIVA). The aim of the assay would be detect only antibodies created by a de-novo infection, since the inactivated vaccine virus is not reproducing, and might provide a simple tool for mass detection of novel infections of commercial flocks. To fulfill the overall aim, the project was designed to include four operational objectives: 1. Evaluation of the genetic evolution of AIV in Israel; 2. Assessment of the diagnostic value of an NS1 ELISA; 3. NS1 ELISA as evaluation criteria for measuring the efficacy of vaccination against H9N2 AIV; 4. Development of an AIV H9 subtype specific ELISA systems. Major conclusion and implications drawn from the project were: 1. A continuous genetic change occurred in the collection of H9N2 isolates, and new introductions were identified. It was shown thatthe differences between the HA proteins of viruses used for vaccine productionand local fieldisolatesincreasedin parallelwith the durationand intensity ofvaccine use, therefore, developing a differential assay for the vaccine and the wild type viruses was the project main aim. 2. To assess the diagnostic value of an NS1 ELISA we first performed experimental infection trials using representative viruses of all introductions, and used the sera and recombinant NS1 antigens of the same viruses in homologous and heterologous NS1 ELISA combination. The NS1 ELISA was evidently reactive in all combinations, and did not discriminate significantly between different groups. 3. However, several major drawbacks of the NS1 ELISA were recognized: a) The evaluation of the vaccination effect in challenged birds, showed that the level of the NS1 antibodies dropped due to the vaccination-dependent virus level drop; b) the applicability of the NS1-ELISA was verified on sera of commercial flocks and found to be unusable due to physico-chemical composition of the sera and the recombinant antigen, c) commercial sera showed non-reactivity that might be caused by many factors, including vaccination, uncertainty regarding the infection time, and possibly low antigen avidity, d) NS1 elevated antibody levels for less than 2 months in SPF chicks. Due to the above mentioned reasons we do not recommend the application of the DIVA NS1 ELISA assay for monitoring and differentiation AIV H9N2 naturally-infected from vaccinated commercial birds.

Plant species synthesize a multitude of specialized compounds 10 help ward off pests. and these in turn may well serve as an alternative to synthetic pesticides to reduce environmental damage and health risks to humans. The general goal of this research was to perform a genetic and biochemical dissection of the natural-insecticides methylketone pathway that is specific to the glandular trichomes of the wild species of tomato, Solanumhabrochaites f. glabratum (accession PI126449). Previous study conducted by us have demonstrated that these compounds are synthesized de novo as a derivate pathway of the fatty acid biosynthesis, and that a key enzyme. designated MethylketoneSynthase 1 (MKS 1). catalyzes conversion of the intermediate B-ketoacyl- ACPs to the corresponding Cn-1 methylketones. The approach taken in this proposed project was to use an interspecific F2 population. derived from the cross between the cultivated lV182 and the wild species PIl26449. for three objectives: (i) Analyze the association between allelic status of candidate genes from the fatty acid biosynthesis pathway with the methylketone content in the leaves (ii) Perform bulk segregant analysis of genetic markers along the tomato genome for identifying genomic regions that harbor QTLs for 2TD content (iii) Apply differential gene expression analysis using the isolated glands of bulk segregant for identifying new genes that are involved in the pathway. The genetic mapping in the interspecific F2 population included app. 60 genetic markers, including the candidate genes from the FAS pathway and SSR markers spread evenly across the genome. This initial; screening identified 5 loci associated with MK content including the candidate genes MKS1, ACC and MaCoA:ACP trans. Interesting observation in this genetic analysis was the connection between shape and content of the glands, i.e. the globularity of the four cells, typical to the wild species. was associated with increased MK in the segregating population. In the next step of the research transcriptomic analysis of trichomes from high- and 10w-MK plants was conducted. This analysis identified a new gene, Methy1ketone synthase 2 (MKS2), whose protein product share sequence similarity to the thioesterase super family of hot-dog enzymes. Genetic analysis in the segregating population confirmed its association with MK content, as well as its overexpression in E. coli that led to formation of MK in the media. There are several conclusions drawn from this research project: (i) the genetic control of MK accumulation in the trichomes is composed of biochemical components in the FAS pathway and its vicinity (MKS 1 and MKS2). as well as genetic factors that mediate the morphology of these specialized cells. (ii) the biochemical pathway is now realized different from what was hypothesized before with MKS2 working upstream to I\1KS 1 and serves as the interface between primary (fatty acids) and secondary (MK) metabolism. We are currently testing the possible physical interactions between these two proteins in vitro after the genetic analysis showed clear epistatic interactions. (iii) the regulation of the pathway that lead to specialized metabolism in the wild species is largely mediated by transcription and one of the achievements of this project is that we were able to isolate and verify the specificity of the MKS1 promoter to the trichomes which allows manipulation of the pathways in these cells (currently in progress). The scientific implications of this research project is the advancement in our knowledge of hitherto unknown biochemical pathway in plants and new leads for studying a new family in plants (hot dog thioesterase). The agricultural and biotechnological implication are : (i) generation of new genetic markers that could assist in importing this pathway to cultivated tomato hence enhancing its natural resistance to insecticides, (ii) the discovery of MKS2 adds a new gene for genetic engineering of plants for making new fatty acid derived compounds. This could be assisted with the use of the isolated and verified MKS1 promoter. The results of this research were summarized to a manuscript that was published in Plant Physiology (cover paper). to a chapter in a proceeding book. and one patent was submitted in the US.

Salmonella enterica is a worldwide food-borne pathogen, which regularly causes large outbreaks of food poisoning. Recent outbreaks linked to consumption of contaminated foods with low water-activity, have raised interest in understanding the factors that control fitness of this pathogen to dry environment. Consequently, the general objective of this study was to extend our knowledge on desiccation tolerance and long-term persistence of Salmonella. We discovered that dehydrated STm entered into a viable-but-nonculturable state, and that addition of chloramphenicol reduced bacterial survival. This finding implied that adaptation to desiccation stress requires de-novo protein synthesis. We also discovered that dried STm cells develop cross-tolerance to multiple stresses that the pathogen might encounter in the agriculture/food environment, such as high or low temperatures, salt, and various disinfectants. These findings have important implications for food safety because they demonstrate the limitations of chemical and physical treatments currently utilized by the food industry to completely inactivate Salmonella. In order to identify genes involved in desiccation stress tolerance, we employed transcriptomic analysis of dehydrated and wet cells and direct screening of knock-out mutant and transposon libraries. Transcriptomic analysis revealed that dehydration induced expression of ninety genes and down-regulated seven. Ribosomal structural genes represented the most abundant functional group with a relatively higher transcription during dehydration. Other large classes of induced functional groups included genes involved in amino acid metabolism, energy production, ion transport, transcription, and stress response. Initial genetic analysis of a number of up-regulated genes was carried out). It was found that mutations in rpoS, yahO, aceA, nifU, rpoE, ddg,fnr and kdpE significantly compromised desiccation tolerance, supporting their role in desiccation stress response.

Original objectives: The basic goal of the present project was to increase our understanding of the cellular mechanisms operating during the gravitropic response of cut flowers, for solving their bending problem without affecting flower quality. Thus, several elements operating at the 3 levels o the gravity-induced signal transduction pathway, were proposed to be examined in snapdragon stems according to the following research goals: 1) Signaling: characterize the signal transduction pathway leading to the gravitropic response, regarding the involvement of [Ca2+]cyt as a mediator of IAA movement and sensitivity to auxin. 2) Transduction by plant hormones: a) Examine the involvement of auxin in the gravitropic response of flower stems with regard to: possible participation of auxin binding protein (ABP), auxin redistribution, auxin mechanism of action (activation of H+-ATPase) mediation by changes in [Ca2+]cyt and possible regulation of auxin-induced Ca2+ action b: calmodulin-activated or Ca2+-activated protein kinases (PK). b) Examine the involvement of ethylene in the gravitropic response of flower stems with regard to auxin-induced ethylene production and sensitivity of the tissue to ethylene. 3) Response: examine the effect of gravistimulation on invertase (associated with growth and elongation) activity and invertase gene expression. 4) Commercial practice: develop practical and simple treatments to prevent bending of cut flowers grown for export. Revisions: 1) Model systems: in addition to snapdragon (Antirrhinum majus L.), 3 other model shoe systems, consisting of oat (Avena sativa) pulvini, Ornithogalun 'Nova' cut flowers and Arabidopsis thaliana inflorescence, were targeted to confirm a more general mechanism for shoot gravitropism. 2 Research topics: the involvement of ABP, auxin action, PK and invertase in the gravitropic response of snapdragon stems could not be demonstrated. Alternatively, the involvement in the gravity signaling cascade of several other physiological mediators apart of [Ca2+]cyt such as: IP3, protein phosphorylation and actin cytoskeleton, was shown. Additional topics introduced: starch statolith reorientation, differential expression of early auxin responsive genes, and differential shoot growth. Background to the topic: The gravitropic bending response of flowering shoots occurring upon their horizontal placement during shipment exhibits a major horticultural problem. In spite of extensive studies in various aboveground organs, the gravitropic response was hardly investigated in flowering shoots. Being a complex multistep process that requires the participation of various cellular components acting in succession or in parallel, analysis of the negative gravitropic response of shoot includes investigation of signal transduction elements and various regulatory physiological mediators. Major achievements: 1) A correlative role for starch statoliths as gravireceptors in flowering shoot was initially established. 2) Differentially phosphorylated proteins and IP3 levels across the oat shoe pulvini, as well as a differential appearance of 2 early auxin-responsive genes in snapdragon stems were all detected within 5-30 minutes following gravistimulation. 3) Unlike in roots, involvement of actin cytoskeleton in early events of the gravitropic response of snapdragon shoots was established. 4) An asymmetric IAA distribution, followed by an asymmetric ethylene production across snapdragon stems was found following gravistimulation. 5) The gravity-induced differential growth in shoots of snapdragon was derived from initial shrinkage of the upper stem side and a subsequent elongation o the lower stem side. 6) Shoot bending could be successfully inhibited by Ca2+ antagonists (that serve as a basis for practical treatments), kinase and phosphatase inhibitors and actin-cytoskeleton modulators. All these agents did not affect vertical growth. The essential characterization of these key events and their sequence led us to the conclusion that blocking gravity perception may be the most powerful means to inhibit bending without hampering shoot and flower growth after harvest. Implications, scientific and agriculture: The innovative results of this project have provided some new insight in the basic understanding of gravitropism in flower stalks, that partially filled the gap in our knowledge, and established useful means for its control. Additionally, our analysis has advanced the understanding of important and fundamental physiological processes involved, thereby leading to new ideas for agriculture. Gravitropism has an important impact on agriculture, particularly for controlling the bending of various important agricultural products with economic value. So far, no safe control of the undesired bending problem of flower stalks has been established. Our results show for the first time that shoot bending of cut flowers can be inhibited without adverse effects by controlling the gravity perception step with Ca2+ antagonists and cytoskeleton modulators. Such a practical benefit resulting from this project is of great economic value for the floriculture industry.