Academic literature on the topic 'Position 2 in proteins'
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Journal articles on the topic "Position 2 in proteins"
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Javanbakht, Taraneh. "Optimization of Cdx Transcription Factors Characteristics." Journal of Engineering Sciences 10, no. 2 (2023): E1—E7. http://dx.doi.org/10.21272/jes.2023.10(2).e1.
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This study presents a new application of TOPSIS for the optimization of transcription factors characteristics. This application is essential as it can help compare the characteristics of these proteins and determine the optimized output of their comparison with this decision-making method. The hypothesis in this article was that according to the previous study of the Cdx transcription factors, as the Cdx2 transcription factor showed more robust characteristics than Cdx1 and Cdx4, the TOPSIS method would show a better rank position of these first proteins in comparison with the two other ones. Moreover, the engrailed repressor domain EnRCdx1 used in the plasmid showed the reduction of the pax3 gene expression in comparison with the induced regulation of the gene expression with the production of the Cdx1, Cdx2, and Cdx4 transcription factors using the corresponding plasmids, the worst rank position with TOPSIS was expected for this repressor domain. The results obtained with this ranking method showed that the rank positions of the transcription factors and the repressor domain corresponded to their compared properties. Moreover, the change in the weight values of the candidates showed the modification of their distances from the best and worst alternatives and closeness coefficients. However, as expected, the candidates’ rank positions were unchanged, and the Cdx2 transcription factor was still the best candidate. The results of this article can be used in computer engineering to improve biological applications of these proteins.
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Denesyuk, Alexander I., Sergei E. Permyakov, Mark S. Johnson, Konstantin Denessiouk, and Eugene A. Permyakov. "System Approach for Building of Calcium-Binding Sites in Proteins." Biomolecules 10, no. 4 (April 11, 2020): 588. http://dx.doi.org/10.3390/biom10040588.
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We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
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Skvortsov, V. S., N. N. Alekseychuk, Yu V. Miroshnichenko, and A. V. Rybina. "pIPredict Version 2: New Features and PTM Analysis." Biomedical Chemistry: Research and Methods 1, no. 2 (2018): e00009. http://dx.doi.org/10.18097/bmcrm00009.
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pIPredict was created as a tool for prediction of the isoelectric point of peptides and proteins. It can also generate virtual 2D electrophoresis maps. The method of pI prediction is based on the Henderson-Hasselbach equation. In a new version the ProMoST and our new scales of pKa values were added. The other added features included: correction of electrophoretic shift by analyzing amino acid composition of proteins and prediction of pI values for proteins with a new set of posttranslational and other chemical modifications. Prediction of pI for proteins with PTM can be used to predict position of modified proteoforms on the virtual 2D electrophoresis map or as the tool of identifying which particular proteoform was observed in the experiment.The program also includes several widely used pKa scales, that can partially calculate values for proteins with some post-translational modifications. pIPredict is created as JAVA application and is freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.
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Zhang, Xiaoqi, Paul L. Bishop, and Margaret J. Kupferle. "Measurement of polysaccharides and proteins in biofilm extracellular polymers." Water Science and Technology 37, no. 4-5 (February 1, 1998): 345–48. http://dx.doi.org/10.2166/wst.1998.0661.
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The structure of biofilm extracellular polymers (ECPs) was studied by measuring their polysaccharide and protein spatial distributions along biofilm depth. Biofilm was collected from two aerobic heterotrophic biofilm reactors, which were seeded with Sphingomonas sp. and Sphingomonas sp. plus mixed liquor, respectively, and operated under toxic organic (in this case, azo dye) degrading conditions. Complete mixing conditions in the two reactors were verified by measuring water content, and polysaccharide and protein quantities from three vertical sampling positions over time. Experimental results showed that: (1) the biofilm water content of either reactor did not change with sample position or biofilm age, with an average biofilm water content in both reactors of 97%; (2) polysaccharides and proteins in the ECPs did not change with sample position; (3) the profiles of polysaccharides and proteins along the biofilm depth showed a stratified biofilm structure, with their ratio (proteins/polysaccharides) being relatively stable over the depth. Oxygen and substrate transport and interactions among species were considered to be the main reasons for producing such a non-uniform biofilm structure; and (4) Sphingomonas sp. could not compete well with microorganisms derived from the mixed liquor of a wastewater treatment plant aeration basin.
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Miyaji, Akimitsu, Teppei Miyoshi, Ken Motokura, and Toshihide Baba. "Discrimination of the prochiral hydrogens at the C-2 position of n-alkanes by the methane/ammonia monooxygenase family proteins." Organic & Biomolecular Chemistry 13, no. 30 (2015): 8261–70. http://dx.doi.org/10.1039/c5ob00640f.
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The substrate binding site of AMO/pMMO family proteins can discriminate between the prochiral hydrogens at the C-2 position ofn-alkanes. We predict that at least one of the three amino acid residues at the di-copper site affects the discriminating ability of the family proteins.
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Moeller-Ehrlich, K., M. Ludlow, R. Beschorner, R. Meyermann, B. K. Rima, W. P. Duprex, S. Niewiesk, and J. Schneider-Schaulies. "Two functionally linked amino acids in the stem 2 region of measles virus haemagglutinin determine infectivity and virulence in the rodent central nervous system." Journal of General Virology 88, no. 11 (November 1, 2007): 3112–20. http://dx.doi.org/10.1099/vir.0.83235-0.
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Rodent brain-adapted measles virus (MV) strains, such as CAM/RB and recombinant MVs based on the Edmonston strain containing the haemagglutinin (H) of CAM/RB, cause acute encephalitis after intracerebral infection of newborn rodents. We have demonstrated that rodent neurovirulence is modulated by two mutations at amino acid positions 195 and 200 in the H protein, one of these positions (200) being a potential glycosylation site. In order to analyse the effects of specific amino acids at these positions, we introduced a range of individual and combined mutations into the open reading frame of the H gene to generate a number of eukaryotic expression plasmids. The functionality of the mutant H proteins was assessed in transfected cells and by generating recombinant viruses. Interestingly, viruses caused acute encephalitis only if the amino acid Ser at position 200 was coupled with Gly at position 195, whereas viruses with single or combined mutations at these positions, including glycosylation at position 200, were attenuated. Neurovirulence was associated with virus spread and induction of neuronal apoptosis, whereas attenuated viruses failed to infect brain cells. Similar results were obtained by using primary brain-cell cultures. Our findings indicate that a structural alteration in the stem 2 region of the H protein at position 195 or 200 interferes with infectivity of rodent neurons, and suggest that the interaction of the viral attachment protein with cellular receptors on neurons is affected.
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Nufer, Oliver, Svend Guldbrandsen, Martin Degen, Felix Kappeler, Jean-Pierre Paccaud, Katsuko Tani, and Hans-Peter Hauri. "Role of cytoplasmic C-terminal amino acids of membrane proteins in ER export." Journal of Cell Science 115, no. 3 (February 1, 2002): 619–28. http://dx.doi.org/10.1242/jcs.115.3.619.
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Export of membrane proteins from the ER is believed to be selective and require transport signals, but the identity of such signals has remained elusive. The recycling type I membrane protein ERGIC-53 carries a C-terminal diphenylalanine motif that is required for efficient ER export. Here we show that this motif can be functionally substituted by a single phenylalanine or tyrosine at position -2, two leucines or isoleucines at position -1 and -2 or a single valine at position -1. These motifs are common among mammalian type I membrane proteins. A single C-terminal valine, but none of the other motifs,accelerates transport of inefficiently exported reporter constructs and hence operates as an export signal. The valine signal is position, but not context,dependent. All transport motifs mediate COPII binding in vitro with distinct preferences for the COPII subunits Sec23p, Sec24Bp, Sec24Cp and p125. These results suggest that cytoplasmic C-terminal amino-acid motifs, either alone or in conjunction with other transport determinants, accelerate ER export of numerous type I and probably polytopic membrane proteins by mediating interaction with COPII coat components.
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Black, Katherine A., and Patricia C. Dos Santos. "Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis." Journal of Bacteriology 197, no. 11 (March 30, 2015): 1952–62. http://dx.doi.org/10.1128/jb.02625-14.
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ABSTRACTThe 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine, and lysine tRNA molecules serves to stabilize the anticodon structure, improving ribosomal binding and overall efficiency of the translational process. Biosynthesis of s2U inEscherichia colirequires a cysteine desulfurase (IscS), a thiouridylase (MnmA), and five intermediate sulfur-relay enzymes (TusABCDE). TheE. coliMnmA adenylates and subsequently thiolates tRNA to form the s2U modification.Bacillus subtilislacks IscS and the intermediate sulfur relay proteins, yet its genome contains a cysteine desulfurase gene,yrvO, directly adjacent tomnmA. The genomic synteny ofyrvOandmnmAcombined with the absence of the Tus proteins indicated a potential functionality of these proteins in s2U formation. Here, we provide evidence that theB. subtilisYrvO and MnmA are sufficient for s2U biosynthesis. A conditionalB. subtilisknockout strain showed that s2U abundance correlates with MnmA expression, andin vivocomplementation studies inE. coliIscS- or MnmA-deficient strains revealed the competency of these proteins in s2U biosynthesis.In vitroexperiments demonstrated s2U formation by YrvO and MnmA, and kinetic analysis established a partnership between theB. subtilisproteins that is contingent upon the presence of ATP. Furthermore, we observed that the slow-growth phenotype ofE. coliΔiscSand ΔmnmAstrains associated with s2U depletion is recovered byB. subtilis yrvOandmnmA. These results support the proposal that the involvement of a devoted cysteine desulfurase, YrvO, in s2U synthesis bypasses the need for a complex biosynthetic pathway by direct sulfur transfer to MnmA.IMPORTANCEThe 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine, and lysine tRNA is conserved in all three domains of life and stabilizes the anticodon structure, thus guaranteeing fidelity in translation. The biosynthesis of s2U inEscherichia colirequires seven proteins: the cysteine desulfurase IscS, the thiouridylase MnmA, and five intermediate sulfur-relay enzymes (TusABCDE).Bacillus subtilisand most Gram-positive bacteria lack a complete set of biosynthetic components. Interestingly, themnmAcoding sequence is located adjacent toyrvO, encoding a cysteine desulfurase. In this work, we provide evidence that theB. subtilisYrvO is able to transfer sulfur directly to MnmA. Both proteins are sufficient for s2U biosynthesis in a pathway independent of the one used inE. coli.
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Hay, D. I., A. Bennick, D. H. Schlesinger, K. Minaguchi, G. Madapallimattam, and S. K. Schluckebier. "The primary structures of six human salivary acidic proline-rich proteins (PRP-1, PRP-2, PRP-3, PRP-4, PIF-s and PIF-f)." Biochemical Journal 255, no. 1 (October 1, 1988): 15–21. http://dx.doi.org/10.1042/bj2550015.
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Human glandular salivary secretions contain several acidic proline-rich phosphoproteins (PRPs). These proteins have important biological functions related to providing a protective environment for the teeth, and appear to possess other activities associated with modulation of adhesion of bacteria to oral surfaces. These functions and activities depend on the primary structures of the PRPs. Previously determined amino acid sequences of two 150-residue molecules, PRP-1 and PRP-2, and two related 106-residue proteins, PRP-3 and PRP-4, indicated that residue 4 was Asn in PRP-1 and PRP-3, and Asp in PRP-2 and PRP-4, and position 50 was Asn in all four proteins. Recent data from cDNA sequence studies and further structural studies, however, showed that the previously proposed sequences cannot be completely correct. The present work has shown that the protein previously designated as PRP-1 actually consisted of two positional isomers, PIF-s, which has Asn and Asp at positions 4 and 50 respectively, and authentic PRP-1, which has the reverse arrangement. The same isomerism is present in the smaller proteins, PIF-f and PRP-3. Since the isomeric pairs have identical compositions and charges, their presence was not previously detected. Also, by using a more highly purified preparation, it has been found that position 50 in PRP-2 and PRP-4 is Asp, rather than Asn previously reported. These new findings for the six PRPs define their complete primary structures, which are now consistent with those proposed for PRP-1 and PIF-s from cDNA data, and are also consistent with the chromatographic and electrophoretic behaviours of the six PRPs and their derived peptides. These corrected structures are important for understanding the biological functions and activities of these unusual proteins.
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Boguszewska, A., R. Szyszka, and N. Grankowski. "The phosphorylation sites of ribosomal P proteins from Saccharomyces cerevisiae cells by endogenous CK-2, PK60S and RAP protein kinases." Acta Biochimica Polonica 44, no. 2 (June 30, 1997): 191–200. http://dx.doi.org/10.18388/abp.1997_4413.
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The phosphorylation sites of ribosomal acidic proteins (P proteins) from Saccharomyces cerevisiae were studied in vivo and in vitro by using CK-2, PK60S and RAP protein kinases. The three enzymes phosphorylate the last serine residues located in a highly conserved carboxyl end of the polypeptide chains. This was established by two-dimensional analysis of tryptic phosphopeptides from 32P-labelled proteins YP1 alpha, YP1 beta, YP2 alpha and YP2 beta, and by kinetic studies of the protein kinases with synthetic peptides corresponding to the fragments of endogenous ribosomal acidic polypeptides. In experiments with both endogenous P proteins and synthetic peptides as substrates protein kinase PK60S demonstrated unusual substrate specificity. In contrast to CK-2 and RAP protein kinases, PK60S phosphorylates predominantly two of the four P proteins, YP1 alpha and YP2 beta, with kinetic constants dependent on the primary structure of the N-terminal region of the polypeptide containing the target residue. The neutral amino acid, alanine, at position 3 in the peptide AAEESDDD (polypeptide fragments of YP1 beta and YP2 alpha) decreases the K(m) value more than 10-fold by comparison with the basic lysine residue at the same position in the peptide AKEESDDD (polypeptide fragments of YP1 alpha and YP2 beta).
Dissertations / Theses on the topic "Position 2 in proteins"
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El, Barbry Houssam. "Découverte du rôle crucial du résidu en position 2 des séquences MTS d’adressage mitochondrial." Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS035.
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Les mitochondries sont des organites complexes impliquant un millier de protéines, la plupart codées dans le génome nucléaire. Leur biogenèse a nécessité au cours de l’évolution la mise en place de systèmes efficaces d’adressage et d’import protéique, et des défaillances de ces systèmes sont associées à des pathologies graves, neuropathies, troubles cardiovasculaires, myopathies, maladies neurodégénératives ainsi que cancers. De nombreuses protéines mitochondriales possèdent en N-terminal une séquence d’adressage appelée MTS (Mitochondrial Targeting sequence) qui forme une hélice alpha amphiphile essentielle pour leur import mitochondrial. La séquence des divers MTSs est néanmoins très variables et leur caractéristiques critiques ne sont pas encore bien comprises. Le point de départ de ma thèse est la découverte, chez les levures, d’une surreprésentation en position 2 des séquences MTSs de 4 acides aminés hydrophobes (F, L, I, W). Au cours de mes années de thèse, j’ai pu confirmer, par des expériences de mutagenèse dirigée, le rôle critique de la nature du résidu en position 2 des MTSs. En effet, grâce au développement d’un système novateur de criblage des défauts d’import basé sur le sauvetage fonctionnel de la toxicité d’une protéine mitochondriale, j’ai pu observer que seuls les résidus surreprésentés en position 2 des protéines mitochondriales permettaient un import efficace. Mon travail a ainsi démontré l'existence de fortes contraintes évolutives s’exerçant au niveau de la position 2 des MTSs dont la compréhension pourrait à terme être utile pour optimiser l’adressage mitochondrial de protéines thérapeutiques chez des patients atteints de maladies mitochondrialesMitochondria are complex organelles involving a thousand proteins, most of which are encoded in the nuclear genome. Their biogenesis has required the evolutionary development of efficient protein addressing and import systems, and failures of these systems are associated with serious pathologies, neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancers.Many mitochondrial proteins have an N-terminal addressing sequence called MTS (Mitochondrial Targeting Sequence) which forms an amphiphilic alpha helix essential for their mitochondrial import. However, the sequence of the various MTSs is highly variable and their critical characteristics are not yet well understood. The starting point of my thesis was the discovery in yeast of an overrepresentation of 4 hydrophobic amino acids (F, L, I, W) at position 2 of the MTSs sequences. During my thesis, I was able to confirm the critical role of the nature of the residue in position 2 of the MTSs through directed mutagenesis experiments. Indeed, thanks to the development of an innovative system for screening import defects based on the functional rescue of the toxicity of a mitochondrial protein, I was able to observe that only residues overrepresented at position 2 of mitochondrial proteins allowed efficient import. My work has thus demonstrated the existence of strong evolutionary constraints at position 2 of MTSs, the understanding of which could ultimately be useful for optimising the mitochondrial addressing of therapeutic proteins in patients suffering from mitochondrial diseases
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Mayack, Shane Renee. "The role of Janus Kinase 3 in CD4+ T Cell Homeostasis and Function: A Dissertation." eScholarship@UMMS, 2004. https://escholarship.umassmed.edu/gsbs_diss/94.
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This dissertation addresses the role for Janus Kinase 3 (Jak3) in CD4+ T cell homeostasis and function. Jak3 is a protein tyrosine kinase whose activity is essential for signals mediated by the γc dependent cytokines IL-2, -4, -7, -9, -15, and -21. Previous data have demonstrated that peripheral CD4+ T cells from Jak3-deficient mice have a memory phenotype and are functionally impaired in both proliferative and IL-2 responses in vitro. Interestingly, Jak3/γc activity has been previously shown to play a role in the prevention of T cell anergy.
These studies were initiated to more precisely define the role for Jak3/γc cytokines in the prevention of T cell anergy and the maintenance of functional CD4+ T cell responses. We began to address this question by assessing global gene expression changes between wild type and Jak3-/- CD4+ T cells. These data indicate that Jak3-/- CD4+ T cells have an increase in gene expression levels of inhibitory surface receptors as well as immunosuppressive cytokines.
Further analyses confirmed that Jak3-deficient T cells express high levels of PD-1, secrete a Trl-type cytokine profile following direct ex vivo activation, and suppress the proliferation of wild type T cells in vitro. These characteristics indicate that CD4+ Jak3-/- T cells share properties with regulatory T cell subsets that have an important role in peripheral tolerance and the prevention of autoimmunity.
We next addressed whether these regulatory characteristics were T cell intrinsic or rather the result of expanding in a Jak3-deficient microenvironment characterized by a number of immune abnormalities and a disrupted splenic architecture. Jak3-/- CD4+ T cells proliferate in vivoin a lymphopenic environment and selectively acquire regulatory T cell characteristics in the absence of any additional activation signals. While the precise mechanism by which Jak3-deficient T cells acquire these characteristics remains unclear, our data indicate that one important component is a T cell-intrinsic requirement for Jak3 signaling.
These findings indicate several interesting aspects of T cell biology. First, these studies, demonstrate that the homeostatic proliferation of CD4+ T cells is not dependent on signaling via γc-dependent cytokine receptors. And, second, that the weak activation signals normally associated with homeostatic expansion are sufficient to drive Jak3-/- T cells into a non-conventional differentiation program. Previous data indicate that, for wild type T cells, signaling through both the TCR as well as γc-dependent cytokine receptors promote the homeostatic proliferation of T cells in lymphopenic hosts. Since Jak3-/- T cells are unable to receive these cytokine signals, their proliferation is likely to be wholly dependent on TCR signaling. As a consequence of this TCR signaling, Jak3-/- T cells proliferate, but in addition, are induced to up regulate PD-1 and to selectively activate the IL-10 locus while shutting off the production of IL-2. Since this fate does not occur for wild type T cells in a comparable environment, it is likely that the unique differentiation pathway taken by Jak3-/- T cells reflects the effects of TCR signaling in the absence of γc-dependent cytokine signaling.
Interestingly, wild type T cells undergoing homeostatic expansion in lymphopenic hosts show many common patterns of gene expression to freshly-purified unmanipulated Jak3-/- T cells. For instance, micro array analysis of gene expression in wild type CD4+ T cells after lymphopenia induced homeostatic expansion show a similar pattern of upregulation in surface markers (PD-1 and LAG-3), and cytokine signaling molecules (IL-10 and IFN-γ cytokine, receptors, and inducible gene targets) to that of Jak3-/- CD4+ T cells immediately ex vivo. These data suggest that the process of homeostatic proliferation normally induces immune attenuation and peripheral tolerance mechanisms, but that full differentiation into a regulatory T cell phenotype is prevented by γc-dependent cytokine signals.
Taken together these data suggest that Jak3 plays an important role in tempering typical immune attenuation mechanisms employed to maintain T cell homeostasis and peripheral tolerance.
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Bishop, Kenneth D. "Egr-2 and PD-1 Are Required for Induction and Maintenance of T Cell Anergy: A Dissertation." eScholarship@UMMS, 2005. https://escholarship.umassmed.edu/gsbs_diss/354.
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The prevalence of diabetes is approaching epidemic proportions worldwide. There is currently no cure for type 1 diabetes, and successful treatment requires constant monitoring of blood sugars and use of exogenous insulin to prevent hyperglycemia. Diabetes will be curable when pancreatic β-islet cells can be transplanted into diabetes patients without requiring long-term immunosuppression. This will require learning more about the induction of functional tolerance, a state that maintains the competence of the immune system to most antigens but protects graft-specific antigens from immune rejection, permitting transplantation. One known mechanism of peripheral tolerance is T cell anergy, a phenotype of hypo-reponsiveness in CD4+ T cells. The focus of this thesis is a description of factors shown to be specific to the induction and maintenance of T cell anergy, whose loss reverses the anergic phenotype, restoring the ability of the cells to proliferate in response to antigen. The first of these is Egr-2, a zinc-finger transcription factor, whose presence is required for the induction of anergy induced in T cell clones by TCR stimulation in the absence of costimulation. Egr-2 is shown to be important to anergy induction but not anergy maintenance. In contrast, a negative costimulation receptor, PD-1, is shown to be necessary for the maintenance of anergy. It is possible that learning more about the genetic factors that orchestrate T cell anergy will prove useful in the development of tolerance-based protocols for organ and tissue transplantation without the use of long-term immunosuppression.
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Genet, Roger. "La l-tryptophane 2',3'-oxydase de chromobacterium violaceum : purification, caracterisation et clonage du gene. l'introduction d'une double liaison en position c alpha-c beta des residus tryptophanyles, au sein des peptides et des proteines." Paris 11, 1992. http://www.theses.fr/1992PA112391.
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Chromobacterium violaceum possede la capacite de metaboliser le carboxybenzoyl-l-tryptophane en un compose insature, possedant une double liaison entre ses carbones alpha et beta (davis et al. , bba (1975) 385:133-144). A partir de cette souche, nous avons purifie une nouvelle enzyme, nommee l-tryptophane 2,3-oxydase (trpox) ou l-tryptophane: oxygene 2,3-oxydoreductase (e. C. 1. 3. 3. X), qui catalyse specifiquement la formation d'une double liaison en position c alpha-c beta du l-tryptophane. Les caracteristiques structurales de l'enzyme ont ete etablies, et une etude des proprietes fonctionnelles nous a permis de preciser les interactions stabilisatrices du substrat au site actif. La trpox n'agit pas seulement sur le l-tryptophane et ses derives, mais catalyse egalement la deshydrogenation des residus tryptophanyles au sein des peptides et des proteines. Sa stabilite en conditions reductrices et denaturantes, et sa thermostabilite, font de cette enzyme un outil particulierement performant pour la synthese de dehydropeptides et de dehydroproteines. Une etude genetique des conditions d'expression de l'activite enzymatique chez c. Violaceum, nous a permis de mettre en evidence une correlation avec la biosynthese d'un pigment, la violaceine, et la presence d'un plasmide de 27 megadaltons, prg100, isole au laboratoire. L'un des genes specifiant la trpox a ete localise sur prg100. Nous disposons aujourd'hui d'un faisceau d'arguments en faveur d'une participation de cette enzyme au processus de biosynthese du pigment de c. Violaceum
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Vincent, Karla Kristine. "Transactivation of Beta 2 Adrenergic Receptor by Bradykinin type 2 Receptor via heterodimerization." Diss., Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/37117.
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Although a long standing convention maintained that G Protein Coupled Receptors (GPCRs) exist in the plasma membrane solely as monomers, substantial work over the last two decades has demonstrated that these ubiquitous receptors can and in many cases, preferentially, exist as homodimers, heterodimers, or higher order oligomers. Often, two GPCRs of the same class heterodimerize; it is less common for two GPCRs of different signaling pathways to interact. The work presented here studied the physical and functional interaction of two GPCRs from discrete classes, the Beta 2 Adrenergic Receptor (β2AR), a Gαs-coupled receptor, and Bradykinin type 2 Receptor (Bk2R), a Gαq coupled receptor. These data show that Bk2R and β2AR are physically coupled when heterologously expressed in Xenopus oocytes, and in pheochromocytoma (PC12) cells and in freshly isolated murine ventricular myocytes, two systems that endogenously express these receptors. This physical coupling led to functional consequences in heterologous and endogenous expression systems, as Bk2R was able to transactivate β2AR signaling via its direct interaction with the receptor. Furthermore, coexpression of Bk2R shifted the dose response curve of β2AR for its selective agonist rightward in Xenopus oocyte electrophysiology experiments, suggesting the presence of Bk2R negatively affected β2AR native pharmacology. Up to thirty minutes of either bradykinin (BK) or isoproterenol exposure did not change the relative amount of Bk2R/β2AR heterodimer in PC12 cells, a rat adrenal medulla tumor cell line that endogenously expresses these receptors. Despite the obvious signaling consequences, the Bk2R/β2AR heterodimer accounted for only 10% of the total β2AR protein detected and 20% of the total Bk2R protein detected. When other Bk2R-specific ligands were also tested to examine the extent of β2AR transactivation, our data showed that both Lys-des-Arg-Bradykinin, a Bk2R partial agonist and NPC 567, a Bk2R antagonist, transactivated β2AR to the same extent as BK. Taken together, our data provide a novel mode of receptor regulation and signaling via Bk2R/β2AR heterodimerization. Because a large percentage of therapeutics target GPCRs, a greater understanding of how a GPCR heterodimer functions could be beneficial for targeting new drugs and refining existing drugs. Understanding the Bk2R/β2AR heterodimer provides a new perspective on the myriad of fucntional consequences that occur when a GPCR is activated.
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Reed, Eric Christopher. "Improvement of MPEG-2 compression by position-dependent encoding." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/38823.
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Ozkaya, Tugba. "Hezbollah And Its Position Towards Israel." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/2/12611119/index.pdf.
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This thesis analyses how Hezbollah has perceived Israel since its establishment. In
this study it is argued that Israel is the main enemy of and source of hatred for
Hezbollah. The references of this overall statement are the ideology and political,
social and military history of Hezbollah. The armed struggle of Hezbollah against
Israel started with the 1982 Israeli invasion of Lebanon evolved into both a
political participation with the continued armed militia in the period between 1982
to today. During this period, in addition to its armed conflict with Israel,
Hezbollah came on the stage with social services for Lebanese society and
political propaganda in Lebanese elections. The intersection point of these three
identities is the endless encouragement of Hezbollah for a determined resistance
against Israel. While on the one hand Hezbollah defines Israel to be the most
dangerous threat for the world, in addition to being a prominent enemy for the
Arab and Muslim communityon the other hand Israel regards Hezbollah to be the highest impact menace. Consequently, the thesis is finalized with outputs and predictions taking all historical and ideological aspects into concern.
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FREVILLE-HERENTHALS, STEPHANIE. "Synthese enantioselective d'alcaloides monosubstitues en position 2 et disubstitues en positions 2 et 6." Paris 6, 1996. http://www.theses.fr/1996PA066557.
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La these presentee porte sur l'elaboration de nouvelles syntheses enantioselectives d'alcaloides piperidiniques monosubstitues en position 2 et disubstitues en positions 2 et 6. Le travail a pour point de depart un substrat bicyclique oxazolopiperidonique, lui-meme issu de la condensation du phenylglycinol et d'un -cetoacide dont une nouvelle methode de preparation a ete developpee. Ce bicycle possede en et de l'atome d'azote des reactivites potentielles: fonction carbonyle du lactame et fonction iminium aminal masquee. Une ouverture stereoelectronique en (cycle oxazolidinique) conduit aux lactames n-proteges. Trois voies sont alors envisagees: la premiere donne acces aux 2-alkylpiperidines apres une reaction d'extrusion d'oxygene et une elimination de la partie chirale. La deuxieme conduit aux lactames chiraux par debenzylation. Ces derniers sont des synthons-cles permettant l'acces direct aux 2-alkylpiperidines apres une reaction d'extrusion d'oxygene et aux 2,6-dialkylpiperidines trans ou cis par une suite de reactions stereoselectives effectuee en de la fonction carbonyle. Une inversion de configuration du carbone portant la fonction hydroxyle de l'un de ces derives conduit au (-)-pinidinol. C'est la premiere synthese enantioselective de ce compose. La derniere voie conduit aux oxazolopiperidines par action d'organomagnesiens sur la fonction carbonyle du lactame. L'ouverture ulterieure du cycle oxazolopiperidinique et la debenzylation conduisent stereoselectivement aux 2,6-dialkylpiperidines trans. La plupart des composes obtenus sont des produits naturels et presentent un interet biologique
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Roy, Guylaine. "Characterization of PABP-interacting proteins 1 and 2." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84317.
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The 3' poly(A) tail of eukaryotic mRNAs and the poly(A) binding protein (PABP) play key roles in the regulation of translation. Recently, our group identified two human PABP-interacting proteins (Paip), Paip1 and Paip2, which stimulate and repress translation, respectively. Paip2 also inhibits the binding of PABP to the poly(A) tail and competes with Paip1 for binding to PABP. My research project was divided into two parts to allow me to gain a greater understanding of the roles of these two PABP-interacting proteins. First, in order to study the mechanism of interaction of Paip1 and PABP, their binding sites were mapped by Far Western and GST pull-downs experiments. The Paip1-PABP interaction involves two distinct binding regions in each protein. The PABP interacting motif-1 (PAM1) of Paip1 is rich in acidic amino acids and is located in the C-terminus (a.a. 440--479). PAM1 interacts with the RNA recognition motifs (RRMs) 1 and 2 of PABP. PAM2 consists of a 15 amino acid stretch residing in the N-terminus of Paip1 (a.a. 123--137) and interacts with the C-terminal domain of PABP. In addition, the stoichiometry and the kinetic and thermodynamic constants for the Paip1-PABP interaction were determined using a Surface Plasmon Resonance (SPR)-biosensor. Paip1 interacts with PABP with an apparent KD of 1.9 nM and with a 1:1 stoichiometry. In the second part of my thesis research, the Drosophila Paip2 (dPaip2) was isolated and characterized in order to ascertain a biological role for Paip2. dPaip2 was found to be the bona fide homologue of human Paip2 since it interacts with the Drosophila PABP (dPABP) via two independent binding sites, interferes with the ability of dPABP to bind to poly(A), and represses translation. Ectopic overexpression of dPaip2 in wings resulted in a size reduction phenotype, which was due to a decrease in the cell number but not to a difference in cell size. Clones of cells overexpressing dPaip2 in wing discs also contai
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Kimura, Atsuko. "Isolation and identification of imidazoline-2 binding proteins." Thesis, University of Bristol, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399960.
Full textBooks on the topic "Position 2 in proteins"
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Ramløv, Hans, and Dennis Steven Friis, eds. Antifreeze Proteins Volume 2. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-41948-6.
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Gavathiotis, Evripidis, ed. BCL-2 Family Proteins. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-8861-7.
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Sellers, James R. Motor proteins 2: myosin. London: Academic Press, 1995.
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Coalition, Northern Ireland Women's. Position on Strands 1, 2, and 3. Belfast: Women's Coalition, 1998.
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McKay, William F. The rhBMP-2 reference guide. St. Louis, Mo: Quality Medical Pub., 2002.
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Brazil, Derek P. Regulation of phospholipase C-[beta]2 by G protein [beta] [gamma] subunits. Dublin: University College Dublin, 1996.
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Wittinghofer, Alfred, ed. Ras Superfamily Small G Proteins: Biology and Mechanisms 2. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-07761-1.
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BCL-2 protein family: Essential regulators of cell death. New York: Springer Science+Business Media, 2010.
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Garcia Fruitós, Elena, and Anna Arís Giralt, eds. Insoluble Proteins. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1859-2.
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Sharma, Mayank, ed. Fluorescent Proteins. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2667-2.
Full textBook chapters on the topic "Position 2 in proteins"
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Schirra, Claudia, Nadia Alawar, Ute Becherer, and Hsin-Fang Chang. "Separation of Single Core and Multicore Lytic Granules by Subcellular Fractionation and Immunoisolation." In The Immune Synapse, 159–67. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3135-5_11.
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AbstractSubcellular fractionation is an important tool used to separate intracellular organelles, structures or proteins. Here, we describe a stepwise protocol to isolate two types of lytic granules, multicore (MCG), and single core (SCG), from primary murine CTLs. We used cell disruption by nitrogen cavitation followed by separation of organelles via discontinuous sucrose density gradient centrifugation. Immunoisolation with a Synaptobrevin 2 antibody attached to magnetic beads was then used to harvest Synaptobrevin 2 positive granules for immunoblotting, mass spectrometry, electron, and light microscopy.
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Riley, William W. "Plant Proteins." In Alternative Proteins, 17–47. Boca Raton: CRC Press, 2021. http://dx.doi.org/10.1201/9780429299834-2.
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Sotoudehnia, Maral. "An uncomfortable position." In Writing Intimacy into Feminist Geography, 33–40. Abingdon, Oxon ; New York, NY : Routledge, [2017]: Routledge, 2017. http://dx.doi.org/10.4324/9781315546186-2.
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Johansen, Ken. "Root Position Triads." In Harmony at the Piano, 4–19. New York: Routledge, 2023. http://dx.doi.org/10.4324/9781003333289-2.
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Nyce, David S. "Specifications." In Understanding Position Sensors, 17–76. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9781003368991-2.
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Monk, Alex. "The Curse Position (2)." In Trauma and the Supernatural in Psychotherapy, 54–67. London: Routledge, 2023. http://dx.doi.org/10.4324/9781003168027-5.
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Vicker, Lauren A., and Harriette J. Royer. "Profile and Position Descriptions." In The Complete Academic Search Manual, 9–19. New York: Routledge, 2023. http://dx.doi.org/10.4324/9781003447719-2.
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Ebert, Susanne, and Thorsten Veith. "review your position." In Systemisch beraten und steuern live 2, 9–22. Göttingen: Vandenhoeck & Ruprecht, 2011. http://dx.doi.org/10.13109/9783666403361.9.
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Ranz, Thomas. "Initial Position—Solutionprocess." In Linear Elasticity of Elastic Circular Inclusions Part 2/Lineare Elastizitätstheorie bei kreisrunden elastischen Einschlüssen Teil 2, 9–10. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-62852-9_2.
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Rothman, Stephen. "An indifferent student." In Proteins Crossing Membranes, 5–8. Boca Raton : Taylor & Francis, 2019.: CRC Press, 2019. http://dx.doi.org/10.1201/9780429020810-2.
Full textConference papers on the topic "Position 2 in proteins"
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Petrich, J. W., J. W. Longworth, and G. R. Fleming. "Electron Transfer in Homologous Azurins." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1986. http://dx.doi.org/10.1364/up.1986.tuf7.
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Using time correlated single photon counting, we have studied electron transfer rates, kET in the homologous blue-copper proteins, azurins, obtained from Pseudomonas aeruginosa (Pae) and Alcaligenes faecalis (Afe). The salient difference between these proteins lies in the position of their single tryptophan residues. The tryptophan in azurin Pae, W48, is buried in the hydrophobic core of the protein while the tryptophan in azurin Afe, W118, lies on the protein surface, exposed to the solvent [1]. kET for the reaction W* + Az-Cu (II)→W*+·+Az-Cu(I) was determined to be 1 × 1010 s−1 and 0.5 × 1010s−1 for Pae and Afe, respectively ; i.e. kET(W48)/kET(W118) = 2.
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Yonashiro, Kan, and Kouichi Hirata. "Trim Distance between Positions in Nucleotide Sequences for Structural Proteins of SARS-CoV-2." In 2021 10th International Congress on Advanced Applied Informatics (IIAI-AAI). IEEE, 2021. http://dx.doi.org/10.1109/iiai-aai53430.2021.00006.
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Wasielewski, Michael R., David M. Tiede, and Harry A. Frank. "Ultrafast Electron and Energy Transfer in Reaction Center and Antenna Proteins from Photosynthetic Bacteria." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1986. http://dx.doi.org/10.1364/up.1986.wb2.
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The recent crystal structure of the reaction center protein from Rps. viridis reveals that a BChl b molecule occupies a position between the primary (BChl b)2 donor, P960 and the BPheo b primary acceptor molecule. There is a great deal of uncertainty as to whether the primary acceptor in Rps. viridis is the intermediary BChl b, the BPheo b, or a supermolecule consisting of both of these chromophores.
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Yonashiro, Kan, Yuichi Shimaya, and Kouichi Hirata. "Finding Correlated Mutations of Positions among Structural Proteins in SARS-CoV-2 Amino Acid Sequences." In 2022 12th International Congress on Advanced Applied Informatics (IIAI-AAI). IEEE, 2022. http://dx.doi.org/10.1109/iiaiaai55812.2022.00022.
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Ny, T., L. Hansson, and B. Åstedt. "ISOLATION OF cDNA FOR TYPE-2 PLASMINOGEN ACTIVATOR INHIBITOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642855.
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The placental type plasminogen activator inhibitor (PAI-2) has been purified from extracts of human placenta and from a histiocytic lymphoma cell line. It is mainly an uPA inhibitor but it also inhibits the two-chain form of tPA.In order to determine the factors regulating PAI-2 gene expression and thereby clarify the physiological role of PAI-2 we have undertaken the molecular cloning of PAI-2 cDNA. A λgt11 expression library prepared from placental mRNA, was screened, immunologically using a monoclonal antibody probe developed against PAI-2 purified from human placenta. When 1.7×105 recombinant phages were screened six positive clones were obtained. Hybridization experiments and comparison of restriction enzyme cleavege pattern revealed that the DNA inserts of the six clones were, related. To identify the clones as coding for PAI-2, a lysogen made from one of them was induced, and the proteins were separated by SDS-PAGE. In immuno-blotting wxperiments the recombinant fusion protein and purified PAI-2 were recognized by the monoclonal antibody and a monospecific polyclonal antibody against PAI-2, revealing an immunological similarity. The nucleotide sequence of the largest cDNA was determined. It was found to code for a protein with extensive sequence homology with members of the serine protease inhibitor family (serpins) Alignment of the active center region with other serpins indicates that PAI-2 is an arg-serpin, as expected for an inhibitor of plasminogen activators.
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Gralnick, H. R., L. M. Magurder, K. Hansmann, M. Vail, G. Marti, R. McEver, and S. Williams. "THE SURFACE EXPRESSION OF ALPHA GRANULE PROTEINS FOLLOWING THROMBIN STIMULATION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643859.
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We have studied the platelet glycoproteins (GP) GPIb and the GPIIb/IIIa and the expression of alpha granule proteins (AGP) on the platelet (P) surface following thrombin (T) stimulation. The platelets were separated from plasma proteins on a arabinogalactan gradient. The P were stimulated with purified alpha T 0.1u/108p. Either monospecific polyclonal or murine monoclonal antibodies were used to detect the P glycoprotein and AGP. The platelets were analyzed on an EPICS V Flow Cytometer. Resting P had small amounts of AGP (2-8%) present on their surface. Within 1-3 min. after T stimulation significantly increased amounts of PF4 (26%) vWf (8%) Ig (10%) and the 140 kD alpha granule membrane (70%) were present on the P surface. The peak expression of all the AGP occurred within 5 mins. The 140 kD activation protein remained stable over 3-60 mins, in contrast the PF4 and the vWf expression peaked at 5 mins. and then decreased to near baseline levels. The GPIb and GPIIb/IIIa showed different patterns after activation. The GPIb intensity and number of positive cells decreased over time, while the GPIIb/ IIIa increased in flourescent intensity and the number of positive cells. These studies indicate that T stimulation of AGP on the P surface. vWf and P4 have a transient appearance on the P surface while Ig and the 140 kD activation protein both appear to become stable components of the P plasma membrane. This technique of detecting platelet activation is a specific, sensitive, and rapid method.
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Stoicescu, Ramona, Razvan-Alexandru Stoicescu, Codrin Gheorghe, Adina Honcea, and Iulian Bratu. "CONSIDERATIONS ON SARS-COV-2 DIAGNOSIS IN THE LABORATORY OF UNIVERSITY EMERGENCY CLINICAL HOSPITAL OF CONSTANTA." In GEOLINKS Conference Proceedings. Saima Consult Ltd, 2021. http://dx.doi.org/10.32008/geolinks2021/b1/v3/07.
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Coronaviruses are members of the Coronaviridae family. They are enveloped, non-segmented, positive-sense, single-stranded RNA viruses. Their genome size is about 30 kilobases (kb) which consist, at the 5’ end, of non-structural open reading frames (ORFs: ORF1a, ORF 1b) which code for 16 non structural proteins, and at the 3’ end the genes which code for four structural proteins including membrane (M), envelope (E), spike (S), and nucleocapsid (N) proteins. Due to the rapid spread of COVID-19, a reliable detection method is needed for patient diagnosis especially in the early stages of the disease. WHO has recommended nucleic acid amplification tests such as real-time reverse transcription-polymerase chain reaction (RT-PCR). The assay detects three SARS-CoV-2 RNA targets: the envelope (E) gene, the nucleocapsid (N) gene and a region of the open reading frame (ORF1) of the RNA-dependent RNA polymerase (RdRp) gene from SARS-CoV-2 virus isolate Wuhan-Hu-1. Our study was made in the first 3 months of the year 2021 using the real-time RT PCR results obtained in the Cellular Biology ward of the University Emergency Clinical Hospital. In our lab we are testing the inpatients from the hospital wards (Neurology, Pediatrics, Surgery, Internal medicine, ICU, Cardiology, etc.); we are also testing the outpatients from Dialysis and Oncology, 2 days prior to their therapy; we also test the health care personnel. The number of tests we performed was: in January 1456, with 399 positive results (27.4%), 33 deaths; in February 1273 tests, 221 positive (17.36%), 16 deaths; in March 1471 tests, 373 positive (25.36%), 37 deceased.
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Chang, Jeng-Shian, Chih-Kai Yang, Sheng D. Chao, and Kuang-Chong Wu. "Finite-Element Simulation on Electrothermal Effects for Immuno-Biosensors." In ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer. ASMEDC, 2008. http://dx.doi.org/10.1115/mnht2008-52195.
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For a diffusion-limited protein, the diffusion boundary layer of the analyte formed on the reaction surface hinders the binding reaction from association and dissociation. With a non-uniform AC electric field, the electrothermal force generates a pair of stirring vortices to increase the transport of the analytes to the reaction surface and thus to enhance the association or dissociation of analyte-ligand complex. This work simulates a 2-dimensional full scale finite element analysis of the binding reaction kinetics of two commonly used proteins, CRP and IgG, by applying a non-uniform AC electric field. In addition to the electrothermal stirring effect, the blocking effect of the flow field due to the existence of the reaction surface at different positions of the micro-channel could cause different degrees of enhancement to the association and the dissociation. The largest enhancement is found at the position near the negative electrode. The initial slope of the curve of the analyte-ligand complex versus time can be raised up to 5.166 times for CRP and 1.934 times for IgG in association; and 3.744 times for CRP and 1.277 times for IgG in dissociation, respectively, with a field 15 Vrms peak-to-peak and operating frequency 100 kHz.
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Brusco, Lauren, Ines Barone, Guowei Gu, Kyle Covington, Amanda Beyer, and Suzanne Fuqua. "Abstract 2280: Increased activity of the Rho family of proteins results in a tamoxifen-resistant phenotype in ERα-positive breast cancer cells." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-2280.
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Shimaya, Yuichi, and Kouich Hirata. "Correlated Mutations of Positions Among Structural Proteins in Delta and Omicron Variants for SARS-CoV-2 Amino Acid Sequences." In 12th International Conference on Pattern Recognition Applications and Methods. SCITEPRESS - Science and Technology Publications, 2023. http://dx.doi.org/10.5220/0011676000003411.
Full textReports on the topic "Position 2 in proteins"
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Sadot, Einat, Christopher Staiger, and Zvi Kam Weizmann. functional genomic screen for new plant cytoskeletal proteins and the determination of their role in actin mediated functions and guard cells regulation. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7587725.bard.
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The original objectives of the approved proposal were: 1. To construct a YFP fused Arabidopsis cDNA library in a mammalian expression vector. 2. To infect the library into a host fibroblast cell line and to screen for new cytoskeletal associated proteins using an automated microscope. 3. Isolate the new genes. 4. Characterize their role in plants. The project was approved as a feasibility study to allow proof of concept that would entail building the YFP library and picking up a couple of positive clones using the fluorescent screen. We report here on the construction of the YFP library, the development of the automatic microscope, the establishment of the screen and the isolation of positive clones that are plant cDNAs encoding cytoskeleton associated proteins. The rational underling a screen of plant library in fibroblasts is based on the high conservation of the cytoskeleton building blocks, actin and tubulin, between the two kingdoms (80-90% homology at the level of amino acids sequence). In addition, several publications demonstrated the recognition of mammalian cytoskeleton by plant cytoskeletal binding proteins and vice versa. The major achievements described here are: 1. The development of an automated microscope equipped with fast laser auto-focusing for high magnification and a software controlling 6 dimensions; X, Y position, auto focus, time, color, and the distribution and density of the fields acquired. This system is essential for the high throughput screen. 2. The construction of an extremely competent YFP library efficiently cloned (tens of thousands of clones collected, no empty vectors detected) with all inserts oriented 5't03'. These parameters render it well representative of the whole transcriptome and efficient in "in-frame" fusion to YFP. 3. The strategy developed for the screen allowing the isolation of individual positive cDNA clones following three rounds of microscopic scans. The major conclusion accomplished from the work described here is that the concept of using mammalian host cells for fishing new plant cytoskeletal proteins is feasible and that screening system developed is complete for addressing one of the major bottlenecks of the plant cytoskeleton field: the need for high throughput identification of functionally active cytoskeletal proteins. The new identified plant cytoskeletal proteins isolated in the pilot screen and additional new proteins which will be isolated in a comprehensive screen will shed light on cytoskeletal mediated processes playing a major role in cellular activities such as cell division, morphogenesis, and functioning such as chloroplast positioning, pollen tube and root hair elongation and the movement of guard cells. Therefore, in the long run the screen described here has clear agricultural implications.
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Brice, Jeremy. Investment, power and protein in sub-Saharan Africa. Edited by Tara Garnett. TABLE, October 2022. http://dx.doi.org/10.56661/d8817170.
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The place of protein in sub-Saharan Africa’s food system is changing rapidly, raising complex international development, global health and environmental sustainability issues. Despite substantial growth in the region’s livestock agriculture sector, protein consumption per capita remains low, and high levels of undernourishment persist. Meanwhile sub-Saharan Africa’s population is growing and urbanising rapidly, creating expectations that demand for protein will increase rapidly over the coming decades and triggering calls for further investment in the expansion and intensification of the region’s meat and dairy sector. However, growing disquiet over the environmental impacts of further expansion in livestock numbers, and growing sales of alternative protein products in the Global North, has raised questions about the future place of plant-based, insect and lab-grown proteins in African diets and food systems. This report examines financial investment in protein production in sub-Saharan Africa. It begins from the position that investors play an important role in shaping the development of diets and food systems because they are able to mobilise the financial resources required to develop new protein products, infrastructures and value chains, or to prevent their development by withholding investment. It therefore investigates which actors are financing the production in sub-Saharan Africa of: a) animal proteins such as meat, fish, eggs and dairy products; b) ‘protein crops’ such as beans, pulses and legumes; and c) processed ‘alternative proteins’ derived from plants, insects, microbes or animal cells grown in a tissue culture. Through analysing investment by state, philanthropic and private sector organisations – as well as multilateral financial institutions such as development banks – it aims to establish which protein sources and stages of the value chain are financed by different groups of investors and to explore the values and goals which shape their investment decisions. To this end, the report examines four questions: 1. Who is currently investing in protein production in sub-Saharan Africa? 2. What goals do these investors aim to achieve (or what sort of future do they seek to bring about) through making these investments? 3. Which protein sources and protein production systems do they finance? 4. What theory of change links their investment strategy to these goals? In addressing these questions, this report explores what sorts of protein production and provisioning systems different investor groups might be helping to bring into being in sub-Saharan Africa. It also considers what alternative possibilities might be marginalised due to a lack of investment. It thus seeks to understand whose priorities, preferences and visions for the future of food might be informing the changing place of protein in the region’s diets, economies and food systems.
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Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.
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Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.
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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.
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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.
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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Wang, X. F., and M. Schuldiner. Systems biology approaches to dissect virus-host interactions to develop crops with broad-spectrum virus resistance. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134163.bard.
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More than 60% of plant viruses are positive-strand RNA viruses that cause billion-dollar losses annually and pose a major threat to stable agricultural production, including cucumber mosaic virus (CMV) that infects numerous vegetables and ornamental trees. A highly conserved feature among these viruses is that they form viral replication complexes (VRCs) to multiply their genomes by hijacking host proteins and remodeling host intracellular membranes. As a conserved and indispensable process, VRC assembly also represents an excellent target for the development of antiviral strategies that can be used to control a wide-range of viruses. Using CMV and a model virus, brome mosaic virus (BMV), and relying on genomic tools and tailor-made large-scale resources specific for the project, our original objectives were to: 1) Identify host proteins that are required for viral replication complex assembly. 2) Dissect host requirements that determine viral host range. 3) Provide proof-of-concept evidence of a viral control strategy by blocking the viral replication complex-localized phospholipid synthesis. We expect to provide new ways and new concepts to control multiple viruses by targeting a conserved feature among positive-strand RNA viruses based on our results. Our work is going according to the expected timeline and we are progressing well on all aims. For Objective 1, among ~6,000 yeast genes, we have identified 96 hits that were possibly play critical roles in viral replication. These hits are involved in cellular pathways of 1) Phospholipid synthesis; 2) Membrane-shaping; 3) Sterol synthesis and transport; 4) Protein transport; 5) Protein modification, among many others. We are pursuing several genes involved in lipid metabolism and transport because cellular membranes are primarily composed of lipids and lipid compositional changes affect VRC formation and functions. For Objective 2, we have found that CPR5 proteins from monocotyledon plants promoted BMV replication while those from dicotyledon plants inhibited it, providing direct evidence that CPR5 protein determines the host range of BMV. We are currently examining the mechanisms by which dicot CPR5 genes inhibit BMV replication and expressing the dicot CPR5 genes in monocot plants to control BMV infection. For Objective 3, we have demonstrated that substitutions in a host gene involved in lipid synthesis, CHO2, prevented the VRC formation by directing BMV replication protein 1a (BMV 1a), which remodels the nuclear membrane to form VRCs, away from the nuclear membrane, and thus, no VRCs were formed. This has been reported in Journal of Biological Chemistry. Based on the results from Objective 3, we have extended our plan to demonstrate that an amphipathic alpha-helix in BMV 1a is necessary and sufficient to target BMV 1a to the nuclear membrane. We further found that the counterparts of the BMV 1a helix from a group of viruses in the alphavirus-like superfamily, such as CMV, hepatitis E virus, and Rubella virus, are sufficient to target VRCs to the designated membranes, revealing a conserved feature among the superfamily. A joint manuscript describing these exciting results and authored by the two labs will be submitted shortly. We have also successfully set up systems in tomato plants: 1) to efficiently knock down gene expression via virus-induced gene silencing so we could test effects of lacking a host gene(s) on CMV replication; 2) to overexpress any gene transiently from a mild virus (potato virus X) so we could test effects of the overexpressed gene(s) on CMV replication. In summary, we have made promising progress in all three Objectives. We have identified multiple new host proteins that are involved in VRC formation and may serve as good targets to develop antiviral strategies; have confirmed that CPR5 from dicot plants inhibited viral infection and are generating BMV-resistance rice and wheat crops by overexpressing dicot CPR5 genes; have demonstrated to block viral replication by preventing viral replication protein from targeting to the designated organelle membranes for the VRC formation and this concept can be further employed for virus control. We are grateful to BARD funding and are excited to carry on this project in collaboration.
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Sessa, Guido, and Gregory Martin. MAP kinase cascades activated by SlMAPKKKε and their involvement in tomato resistance to bacterial pathogens. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7699834.bard.
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The research problem: Pseudomonas syringae pv. tomato (Pst) and Xanthomonas campestrispv. vesicatoria (Xcv) are the causal agents of tomato bacterial speck and spot diseases, respectively. These pathogens colonize the aerial parts of the plant and cause economically important losses to tomato yield worldwide. Control of speck and spot diseases by cultural practices or chemicals is not effective and genetic sources of resistance are very limited. In previous research supported by BARD, by gene expression profiling we identified signaling components involved in resistance to Xcvstrains. Follow up experiments revealed that a tomato gene encoding a MAP kinase kinase kinase (MAPKKKe) is required for resistance to Xcvand Pststrains. Goals: Central goal of this research was to investigate the molecular mechanisms by which MAPKKKεand associated MAP kinase cascades regulate host resistance. Specific objectives were to: 1. Determine whether MAPKKKεplays a broad role in defense signaling in plants; 2. Identify components of MAP kinase cascades acting downstream of MAPKKKε; 3. Determine the role of phosphorylation-related events in the function of MAPKKKε; 4. Isolate proteins directly activated by MAPKKKε-associatedMAPK modules. Our main achievements during this research program are in the following major areas: 1. Characterization of MAPKKKεas a positive regulator of cell death and dissection of downstream MAP kinase cascades (Melech-Bonfil et al., 2010; Melech-Bonfil and Sessa, 2011). The MAPKKKεgene was found to be required for tomato resistance to Xcvand Pstbacterial strains and for hypersensitive response cell death triggered by different R gene/effector gene pairs. In addition, overexpression analysis demonstrated that MAPKKKεis a positive regulator of cell death, whose activity depends on an intact kinase catalytic domain. Epistatic experiments delineated a signaling cascade downstream of MAPKKKεand identified SIPKK as a negative regulator of MAPKKKε-mediated cell death. Finally, genes encoding MAP kinase components downstream of MAPKKKεwere shown to contribute to tomato resistance to Xcv. 2. Identification of tomato proteins that interact with MAPKKKεand play a role in plant immunity (Oh et al., 2011). We identified proteins that interact with MAPKKKε. Among them, the 14-3-3 protein TFT7 was required for cell death mediated by several R proteins. In addition, TFT7 interacted with the MAPKK SlMKK2 and formed homodimersin vivo. Thus, TFT7 is proposed to recruit SlMKK2 and MAPKKK client proteins for efficient signal transfer. 3. Development of a chemical genetic approach to identify substrates of MAPKKKε-activated MAP kinase cascades (Salomon et al., 2009, 2011). This approach is based on engineering the kinase of interest to accept unnatural ATP analogs. For its implementation to identify substrates of MAPKKKε-activated MAP kinase modules, we sensitized the tomato MAP kinase SlMPK3 to ATP analogs and verified its ability to use them as phosphodonors. By using the sensitized SlMPK3 and radiolabeled N6(benzyl)ATP it should be possible to tag direct substrates of this kinase. 4. Development of methods to study immunity triggered by pathogen-associated molecular patterns (PAMPs) in tomato and N. benthamiana plants (Kim et al., 2009; Nguyen et al. 2010). We developed protocols for measuring various PTI-associatedphenotypes, including bacterial populations after pretreatment of leaves with PAMPs, induction of reporter genes, callose deposition at the cell wall, activation of MAP kinases, and a luciferase-based reporter system for use in protoplasts. Scientific and agricultural significance: Our research activities discovered and characterized a signal transduction pathway mediating plant immunity to bacterial pathogens. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease. In addition, we successfully developed new biochemical and molecular methods that can be implemented in the study of plant immunity and other aspects of plant biology.
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Delwiche, Michael, Boaz Zion, Robert BonDurant, Judith Rishpon, Ephraim Maltz, and Miriam Rosenberg. Biosensors for On-Line Measurement of Reproductive Hormones and Milk Proteins to Improve Dairy Herd Management. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7573998.bard.
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The original objectives of this research project were to: (1) develop immunoassays, photometric sensors, and electrochemical sensors for real-time measurement of progesterone and estradiol in milk, (2) develop biosensors for measurement of caseins in milk, and (3) integrate and adapt these sensor technologies to create an automated electronic sensing system for operation in dairy parlors during milking. The overall direction of research was not changed, although the work was expanded to include other milk components such as urea and lactose. A second generation biosensor for on-line measurement of bovine progesterone was designed and tested. Anti-progesterone antibody was coated on small disks of nitrocellulose membrane, which were inserted in the reaction chamber prior to testing, and a real-time assay was developed. The biosensor was designed using micropumps and valves under computer control, and assayed fluid volumes on the order of 1 ml. An automated sampler was designed to draw a test volume of milk from the long milk tube using a 4-way pinch valve. The system could execute a measurement cycle in about 10 min. Progesterone could be measured at concentrations low enough to distinguish luteal-phase from follicular-phase cows. The potential of the sensor to detect actual ovulatory events was compared with standard methods of estrus detection, including human observation and an activity monitor. The biosensor correctly identified all ovulatory events during its testperiod, but the variability at low progesterone concentrations triggered some false positives. Direct on-line measurement and intelligent interpretation of reproductive hormone profiles offers the potential for substantial improvement in reproductive management. A simple potentiometric method for measurement of milk protein was developed and tested. The method was based on the fact that proteins bind iodine. When proteins are added to a solution of the redox couple iodine/iodide (I-I2), the concentration of free iodine is changed and, as a consequence, the potential between two electrodes immersed in the solution is changed. The method worked well with analytical casein solutions and accurately measured concentrations of analytical caseins added to fresh milk. When tested with actual milk samples, the correlation between the sensor readings and the reference lab results (of both total proteins and casein content) was inferior to that of analytical casein. A number of different technologies were explored for the analysis of milk urea, and a manometric technique was selected for the final design. In the new sensor, urea in the sample was hydrolyzed to ammonium and carbonate by the enzyme urease, and subsequent shaking of the sample with citric acid in a sealed cell allowed urea to be estimated as a change in partial pressure of carbon dioxide. The pressure change in the cell was measured with a miniature piezoresistive pressure sensor, and effects of background dissolved gases and vapor pressures were corrected for by repeating the measurement of pressure developed in the sample without the addition of urease. Results were accurate in the physiological range of milk, the assay was faster than the typical milking period, and no toxic reagents were required. A sampling device was designed and built to passively draw milk from the long milk tube in the parlor. An electrochemical sensor for lactose was developed starting with a three-cascaded-enzyme sensor, evolving into two enzymes and CO2[Fe (CN)6] as a mediator, and then into a microflow injection system using poly-osmium modified screen-printed electrodes. The sensor was designed to serve multiple milking positions, using a manifold valve, a sampling valve, and two pumps. Disposable screen-printed electrodes with enzymatic membranes were used. The sensor was optimized for electrode coating components, flow rate, pH, and sample size, and the results correlated well (r2= 0.967) with known lactose concentrations.
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Dubcovsky, Jorge, Tzion Fahima, and Ann Blechl. Positional cloning of a gene responsible for high grain protein content in tetraploid wheat. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7695875.bard.
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High Grain Protein Content (GPC) is a desirable trait in breadmaking and pasta wheat varieties because of its positive effects on quality and nutritional value. However, selection for GPC is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. The long-term goal of this project is to provide a better understanding of the genes controlling GPC in wheat. The specific objectives of this project were: a) to develop a high-density genetic map of the GPC gene in tetraploid wheat, b) to construct a T. turgidum Bacterial Artificial Chromosome (BAC) library, c) to construct a physical map of the GPC gene and identify a candidate for the GPC gene. A gene with a large effect on GPC was detected in Triticum turgidum var. dicoccoides and was previously mapped in the short arm of chromosome 6B. To define better the position of the Gpc-B1 locus we developed homozygous recombinant lines with recombination events within the QTL region. Except for the 30-cM region of the QTL these RSLs were isogenic for the rest of the genome minimizing the genetic variability. To minimize the environmental variability the RSLs were characterized using 10 replications in field experiments organized in a Randomized Complete Block Design, which were repeated three times. Using this strategy, we were able to map this QTL as a single Mendelian locus (Gpc-B1) on a 2.6-cM region flanked by RFLP markers Xcdo365 and Xucw67. All three experiments showed that the lines carrying the DIC allele had an average absolute increase in GPC of 14 g/kg. Using the RFLP flanking markers, we established the microcolinearity between a 2.l-cM region including the Gpc-B1 gene in wheat chromosome 6BS and a 350-kb region on rice chromosome 2. Rice genes from this region were used to screen the Triticeae EST collection, and these ESTs were used to saturate the Gpc-B1 region with molecular markers. With these new markers we were able to map the Gpc-B1 locus within a 0.3-cM region flanked by PCR markers Xucw83 and Xucw71. These flanking markers defined a 36-kb colinear region with rice, including one gene that is a potential candidate for the Gpc-B1 gene. To develop a physical map of the Gpc-B1 region in wheat we first constructed a BAC library of tetraploid wheat, from RSL#65 including the high Gpc-B1 allele. We generated half- million clones with an average size of l3l-kb (5.1 X genome equivalents for each of the two genomes). This coverage provides a 99.4% probability of recovering any gene from durum wheat. We used the Gpc-BI flanking markers to screen this BAC library and then completed the physical map by chromosome walking. The physical map included two overlapping BACs covering a region of approximately 250-kb, including two flanking markers and the Gpc-B1 gene. Efforts are underway to sequence these two BACs to determine if additional wheat genes are present in this region. Weare also developing new RSLs to further dissect this region. We developed PCR markers for flanking loci Xucw79andXucw71 to facilitate the introgression of this gene in commercial varieties by marker assisted selection (httQ://maswheat.ucdavis.edu/ orotocols/HGPC/index.hlm). Using these markers we introgressed the Gpc-B1 gene in numerous pasta and common wheat breeding lines.