scholarly journals Genetically flexible but conserved: a new essential motif in the C-ter domain of HIV-1 group M integrases

2020 ◽  
Author(s):  
Marine Kanja ◽  
Pierre Cappy ◽  
Nicolas Levy ◽  
Oyndamola Oladosu ◽  
Sylvie Schmidt ◽  
...  
Keyword(s):  
Amino Acids ◽  
Viral Evolution ◽  
Purifying Selection ◽  
The Other ◽  
Functional Motif ◽  
Multiple Functions ◽  
Per Se ◽  
Integration Levels ◽  
Infectious Cycle ◽  
Hiv 1

ABSTRACTUsing coevolution-network interference based on the comparison of two phylogenetically distantly related isolates, one from the main group M and the other from the minor group O of HIV-1, we identify, in the C-terminal domain (CTD) of integrase, a new functional motif constituted by four non-contiguous amino acids (N222K240N254K273). Mutating the lysines abolishes integration through decreased 3’-processing and inefficient nuclear import of reverse transcribed genomes. Solution of the crystal structures of wt and mutated CTDs shows that the motif generates a positive surface potential that is important for integration. The number of charges in the motif appears more crucial than their position within the motif. Indeed, the positions of the K could be permutated or additional K could be inserted in the motif, generally without affecting integration per se. Despite this potential genetic flexibility, the NKNK arrangement is strictly conserved in natural sequences, indicative of an effective purifying selection exerted at steps other than integration. Accordingly, reverse transcription was reduced even in the mutants that retained wt integration levels, indicating that specifically the wt sequence is optimal for carrying out the multiple functions integrase exerts. We propose that the existence of several amino acids arrangements within the motif, with comparable efficiencies of integration per se, might have constituted an asset for the acquisition of additional functions during viral evolution.IMPORTANCEIntensive studies on HIV-1 have revealed its extraordinary ability to adapt to environmental and immunological challenges, an ability that is also at the basis of antiviral treatments escape. Here, by deconvoluting the different roles of the viral integrase in the various steps of the infectious cycle, we report how the existence of alternative equally efficient structural arrangements for carrying out one function opens on the possibility of adapting to the optimisation of further functionalities exerted by the same protein. Such property provides an asset to increase the efficiency of the infectious process. On the other hand, though, the identification of this new motif provides a potential target for interfering simultaneously with multiple functions of the protein.

scholarly journals NKNK: a New Essential Motif in the C-Terminal Domain of HIV-1 Group M Integrases

2020 ◽  
Vol 94 (20) ◽  
Author(s):  
Marine Kanja ◽  
Pierre Cappy ◽  
Nicolas Levy ◽  
Oyndamola Oladosu ◽  
Sylvie Schmidt ◽  
...  
Keyword(s):  
Antiviral Treatment ◽  
Viral Evolution ◽  
Purifying Selection ◽  
The Other ◽  
Functional Motif ◽  
Multiple Functions ◽  
Terminal Domain ◽  
Per Se ◽  
Infectious Cycle ◽  
Hiv 1

ABSTRACT Using coevolution network interference based on comparison of two phylogenetically distantly related isolates, one from the main group M and the other from the minor group O of HIV-1, we identify, in the C-terminal domain (CTD) of integrase, a new functional motif constituted by four noncontiguous amino acids (N222K240N254K273). Mutating the lysines abolishes integration through decreased 3′ processing and inefficient nuclear import of reverse-transcribed genomes. Solution of the crystal structures of wild-type (wt) and mutated CTDs shows that the motif generates a positive surface potential that is important for integration. The number of charges in the motif appears more crucial than their position within the motif. Indeed, the positions of the K’s could be permutated or additional K’s could be inserted in the motif, generally without affecting integration per se. Despite this potential genetic flexibility, the NKNK arrangement is strictly conserved in natural sequences, indicative of an effective purifying selection exerted at steps other than integration. Accordingly, reverse transcription was reduced even in the mutants that retained wt integration levels, indicating that specifically the wt sequence is optimal for carrying out the multiple functions that integrase exerts. We propose that the existence of several amino acid arrangements within the motif, with comparable efficiencies of integration per se, might have constituted an asset for the acquisition of additional functions during viral evolution. IMPORTANCE Intensive studies of HIV-1 have revealed its extraordinary ability to adapt to environmental and immunological challenges, an ability that is also at the basis of antiviral treatment escape. Here, by deconvoluting the different roles of the viral integrase in the various steps of the infectious cycle, we report how the existence of alternative equally efficient structural arrangements for carrying out one function opens up the possibility of adapting to the optimization of further functionalities exerted by the same protein. Such a property provides an asset to increase the efficiency of the infectious process. On the other hand, though, the identification of this new motif provides a potential target for interfering simultaneously with multiple functions of the protein.

Crime, Responsibility, Culpability, and Wrongdoing

2021 ◽  
pp. 3-25
Author(s):  
A P Simester
Keyword(s):  
Criminal Justice ◽  
Moral Responsibility ◽  
Criminal Justice System ◽  
Criminal Law ◽  
Justice System ◽  
The Other ◽  
Multiple Functions ◽  
Primary Function ◽  
Per Se ◽  
Theoretical Overview

This chapter provides a theoretical overview of criminal law, claiming that it has multiple functions. Among other things, the criminal law operates to prevent certain kinds of wrongs, and to punish them when they occur. Those functions are compatible; but they are often thought to be in tension. Whether preventive, interrogative, or punitive, all parts of the criminal justice system need justification. The chapter then briefly introduces at five foundational principles for criminal law: culpability, legitimate enactment, moral responsibility, wrongdoing, and ascriptive responsibility. Culpability is served by moral responsibility, and it is entwined with wrongdoing: but the latter principles, and the doctrines they govern, are independently significant. The principle of ascriptive responsibility, on the other hand, is related more closely to wrongdoing and legitimate enactment than to culpability per se. Its primary function is to moderate the state’s generic prohibition by identifying those defendants who fall within its scope. As such, it is primarily a criminalization principle.

The Problem of the Typology of Rationality in Muslim Culture

2019 ◽  
Vol 62 (6) ◽  
pp. 88-99
Author(s):  
Andrey A. Lukashev
Keyword(s):  
Modern Philosophy ◽  
Theoretical Basis ◽  
Theoretical Models ◽  
The Other ◽  
Common Denominator ◽  
Islamic Culture ◽  
The Common ◽  
Per Se ◽  
The One ◽  
Muslim Culture

The typology of rationality is one of major issues of modern philosophy. In an attempt to provide a typology to Oriental materials, a researcher faces additional problems. The diversity of the Orient as such poses a major challenge. When we say “Oriental,” we mean several cultures for which we cannot find a common denominator. The concept of “Orient” involves Arabic, Indian, Chinese, Turkish and other cultures, and the only thing they share is that they are “non-Western.” Moreover, even if we focus just on Islamic culture and look into rationality in this context, we have to deal with a conglomerate of various trends, which does not let us define, with full confidence, a common theoretical basis and treat them as a unity. Nevertheless, we have to go on trying to find common directions in thought development, so as to draw conclusions about types of rationality possible in Islamic culture. A basis for such a typology of rationality in the context of the Islamic world was recently suggested in A.V. Smirnov’s logic of sense theory. However, actual empiric material cannot always fit theoretical models, and the cases that do not fit the common scheme are interesting per se. On the one hand, examination of such cases gives an opportunity to specify certain provisions of the theory and, on the other hand, to define the limits of its applicability.

Genetic Flexibility of the NKNK Motif in HIV-1 Integrases Allows Its Involvement in Multiple Functions During Infection

2018 ◽  
Author(s):  
Marine Kanja ◽  
Pierre Cappy ◽  
Guillermo Blanco-Rodriguez ◽  
Nicolas Levy ◽  
Oyndamola Oladosu ◽  
...  
Keyword(s):  
Multiple Functions ◽  
Hiv 1

Natural Vulcanization Accelerators in Hevea Latex

1948 ◽  
Vol 21 (4) ◽  
pp. 853-859
Author(s):  
R. F. A. Altman
Keyword(s):  
Amino Acids ◽  
Experimental Results ◽  
The Other ◽  
Active Nitrogen ◽  
Nitrogen Bases ◽  
Other Hand ◽  
Decomposition Processes ◽  
Volatile Products ◽  
Nitrogenous Substances ◽  
The One

Abstract As numerous investigators have shown, some of the nonrubber components of Hevea latex have a decided accelerating action on the process of vulcanization. A survey of the literature on this subject points to the validity of certain general facts. 1. Among the nonrubber components of latex which have been investigated, certain nitrogenous bases appear to be most important for accelerating the rate of vulcanization. 2. These nitrogen bases apparently occur partly naturally in fresh latex, and partly as the result of putrefaction, heating, and other decomposition processes. 3. The nitrogen bases naturally present in fresh latex at later stages have been identified by Altman to be trigonelline, stachhydrine, betonicine, choline, methylamine, trimethylamine, and ammonia. These bases are markedly active in vulcanization, as will be seen in the section on experimental results. 4. The nitrogenous substances formed by the decomposition processes have only partly been identified, on the one hand as tetra- and pentamethylene diamine and some amino acids, on the other hand as alkaloids, proline, diamino acids, etc. 5. It has been generally accepted that these nitrogenous substances are derived from the proteins of the latex. 6. Decomposition appears to be connected with the formation of a considerable amount of acids. 7. The production of volatile nitrogen bases as a rule accompanies the decomposition processes. These volatile products have not been identified. 8. The active nitrogen bases, either already formed or derived from complex nitrogenous substances, seem to be soluble in water but only slightly soluble in acetone.

METABOLISM OF AROMATIC COMPOUNDS IN HEALTHY AND RUST-INFECTED PRIMARY LEAVES OF WHEAT: II. STUDIES WITH L-PHENYLALANINE-U-14C, L-TYROSINE-U-14C, AND FERULATE-U-14C

1967 ◽  
Vol 45 (11) ◽  
pp. 2137-2153 ◽  
Author(s):  
A. Fuchs ◽  
R. Rohringer ◽  
D. J. Samborski
Keyword(s):  
Amino Acids ◽  
Stem Rust ◽  
Aromatic Compounds ◽  
The Other ◽  
Major Portion ◽  
Insoluble Residue ◽  
Resistant Reaction ◽  
Wheat Leaves

Wheat leaves infected with stem rust, especially those of susceptible plants, contained more phenylalanine and tyrosine than healthy leaves. The utilization of phenylalanine was increased in both the susceptible and resistant reaction, but the utilization of tyrosine was increased only in the susceptible reaction. No evidence of interconversion of these amino acids was obtained.In n-butanol extracts, which contained glycosides, many constituents were labelled after feeding of L-phenylalanine-U-14C. Most of the n-butanol extractives from resistant-reacting leaves contained more label than those from susceptible-reacting leaves or from healthy leaves. However, one of the n-butanol extractives from susceptible-reacting leaves was 5–10 times as active as that isolated from the other tissues.With L-phenylalanine-U-14C and ferulate-U-14C as precursors, more activity was recovered in insoluble than in soluble esters (of ferulate and p-coumarate). With L-tyrosine-U-14C as precursor, the reverse was observed. After infection, the proportion of label in insoluble esters increased more in resistant leaves than it did in susceptible leaves, regardless of the precursor used.A major portion of the activity from these precursors was recovered in the insoluble residue that contained protein and other polymers. In the experiment with L-phenylalanine-U-14C, this residue was fractionated into protein and non-hydrolyzable material. Susceptible-reacting leaves contained equal amounts of activity in these fractions, while resistant-reacting leaves incorporated 2.5 times as much activity into the non-hydrolyzable material as into protein.

scholarly journals Amino acid transport in normal and glutathione-deficient sheep erythrocytes

1976 ◽  
Vol 154 (1) ◽  
pp. 43-48 ◽  
Author(s):  
J D Young ◽  
J C Ellory ◽  
E M Tucker
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Transport ◽  
Cell Types ◽  
The Other ◽  
Acid Transport ◽  
Sheep Erythrocytes ◽  
Uptake Rates

1. Uptake rates for 23 amino acids were measured for both normal (high-GSH) and GSH-deficient (low-GSH) erythrocytes from Finnish Landrace sheep. 2. Compared with high-GSH cells, low-GSH cells had a markedly diminished permeability to D-alanine, L-alanine, α-amino-n-butyrate, valine, cysteine, serine, threonine, asparagine, lysine and ornithine. Smaller differences were observed for glycine and proline, whereas uptake of the other amino acids was not significantly different in the two cell types.

scholarly journals Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection

2015 ◽  
Vol 89 (20) ◽  
pp. 10303-10318 ◽  
Author(s):  
Justine E. Sunshine ◽  
Brendan B. Larsen ◽  
Brandon Maust ◽  
Ellie Casey ◽  
Wenje Deng ◽  
...  
Keyword(s):  
T Cell ◽  
Viral Evolution ◽  
T Cell Responses ◽  
Fitness Cost ◽  
Viral Population ◽  
Cell Responses ◽  
Founder Virus ◽  
Ctl Escape ◽  
The Impact ◽  
Hiv 1

ABSTRACTTo understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24gagwere generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response (r= 0.43;P= 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack.IMPORTANCERapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens.

Difunctional enols of N-protected amino acids as low molecular weight and novel inhibitors of HIV-1 protease.

1993 ◽  
Vol 3 (6) ◽  
pp. 1169-1174 ◽  
Author(s):  
Marc Vaillancourt ◽  
Benoit Vanasse ◽  
Eric Cohen ◽  
Gilles Sauv
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Low Molecular Weight ◽  
Hiv 1

Nutritional factors associated with seasonal population increase of cacao thrips, Selenothrips rubrocinctus (Giard) (Thysanoptera), on cashew, Anacardium occidentale

1963 ◽  
Vol 53 (4) ◽  
pp. 681-713 ◽  
Author(s):  
R. G. Fennah
Keyword(s):  
Amino Acids ◽  
Water Stress ◽  
Amino Acid ◽  
Acid Concentration ◽  
Leaf Tissue ◽  
The Other ◽  
Amino Acid Concentration ◽  
Population Increase ◽  
Bearing Surface ◽  
Wet Season

The feeding of the cacao thrips, Selenothrips rubrocinctus (Giard), on cashew, Anacardium occidentale, one of its host plants in Trinidad, West Indies, is considered in relation to the annual period of maximum population increase on this host and to the choice of feeding sites on individual leaves. On trees observed for three years, populations regularly increased during the dry season, from a low level in December and January to a peak in April or May, and then rapidly declined during the wet season. Even when thrips were most abundant, some trees were free from attack, and this could not be attributed to protective morphological features, to specific repellent substances in the leaf, or to chance. S. rubrocinctus was found to feed on leaves that were subjected to water-stress and to breed only on debilitated trees: the evidence suggested that the adequacy of its supply of nutrients depends on the induction of suitable metabolic conditions within the leaf by water-stress.Both nymphs and adults normally feed on the lower, stomata-bearing surface of the leaf, but in a very humid atmosphere only a weak preference is shown for this surface and if, under natural conditions, it is exposed to insolation by inversion of the leaf, the insects migrate to the other surface. Since the thrips were shown to be indifferent to bodily posture, the observation suggests that their behaviour is governed primarily by avoidance of exposure to undue heat or dryness and only secondarily by the attractiveness of the stomata-bearing surface.Leaves of cashew tend not to become infested while still immature, and become most heavily infested, if at all, soon after they have hardened. Breeding does not occur on senescent leaves. The positions of feeding thrips are almost random on leaves under abnormal water-stress, but otherwise conform to certain patterns that mainly develop in fixed sequence. On reversal of an undetached leaf and consequent transfer of thrips from one surface to the other, there is no appreciable change in their distribution pattern or the apparent acceptability of the substrate. Changes of pattern were readily induced by injury to the plant during a period of water-stress and less easily, or not at all, when water-stress was low. Injury of areas of the leaf by heat was followed by their colonisation by thrips, and partial severance of branches by increased attack on their leaves.Leaves detached from uninfested trees invariably became acceptable for feeding within four hours. During this period, leaf water-content declined and the ratios of soluble-carbohydrate content and α-amino acids to fresh-leaf weight fell slightly and rose considerably, respectively. In the field, the latter ratio was invariably higher for infested than for uninfested leaf tissue, even on portions of the same leaf. If the nutrient value of leaf tissue is determined by the rate at which α-amino acids are extractable through a stylet puncture, the observed change in acceptability for feeding following plucking may be accounted for by the increase in α-amino-acid concentration. Feeding that is restricted on any one tree to the margins of local leaf injuries during prolonged high water-stress and totally absent when stress is low can be correlated with an α-amino-acid content in the living marginal tissue that is high or low, respectively. The ability of thrips to establish themselves and breed on leaves of a particular tree in the dry season and their failure to do so on leaves of the same tree in the wet season conforms with the greater or less amino-acid concentration occurring in the leaf at these respective times.

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