Analysis of high-identity segmental duplications in the grapevine genome

<p>Abstract</p> <p>Background</p> <p>Segmental duplications (SDs) are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (<it>Vitis vinifera</it>) genome (PN40024).</p> <p>Results</p> <p>We demonstrate that recent SDs (> 94% identity and >= 10 kb in size) are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence). We detected mitochondrial and plastid DNA and genes (10% of gene annotation) in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress.</p> <p>Conclusions</p> <p>These data show the great influence of SDs and organelle DNA transfers in modeling the <it>Vitis vinifera </it>nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.</p

gSeaGen: The KM3NeT GENIE-based code for neutrino telescopes

Program summary Program Title: gSeaGen CPC Library link to program files: http://dx.doi.org/10.17632/ymgxvy2br4.1 Licensing provisions: GPLv3 Programming language: C++ External routines/libraries: GENIE [1] and its external dependencies. Linkable to MUSIC [2] and PROPOSAL [3]. Nature of problem: Development of a code to generate detectable events in neutrino telescopes, using modern and maintained neutrino interaction simulation libraries which include the state-of-the-art physics models. The default application is the simulation of neutrino interactions within KM3NeT [4]. Solution method: Neutrino interactions are simulated using GENIE, a modern framework for Monte Carlo event generators. The GENIE framework, used by nearly all modern neutrino experiments, is considered as a reference code within the neutrino community. Additional comments including restrictions and unusual features: The code was tested with GENIE version 2.12.10 and it is linkable with release series 3. Presently valid up to 5 TeV. This limitation is not intrinsic to the code but due to the present GENIE valid energy range. References: [1] C. Andreopoulos at al., Nucl. Instrum. Meth. A614 (2010) 87. [2] P. Antonioli et al., Astropart. Phys. 7 (1997) 357. [3] J. H. Koehne et al., Comput. Phys. Commun. 184 (2013) 2070. [4] S. Adrián-Martínez et al., J. Phys. G: Nucl. Part. Phys. 43 (2016) 084001.The gSeaGen code is a GENIE-based application developed to efficiently generate high statistics samples of events, induced by neutrino interactions, detectable in a neutrino telescope. The gSeaGen code is able to generate events induced by all neutrino flavours, considering topological differences between tracktype and shower-like events. Neutrino interactions are simulated taking into account the density and the composition of the media surrounding the detector. The main features of gSeaGen are presented together with some examples of its application within the KM3NeT project.French National Research Agency (ANR) ANR-15-CE31-0020Centre National de la Recherche Scientifique (CNRS)European Union (EU)Institut Universitaire de France (IUF), FranceIdEx program, FranceUnivEarthS Labex program at Sorbonne Paris Cite ANR-10-LABX-0023 ANR-11-IDEX-000502Paris Ile-de-France Region, FranceShota Rustaveli National Science Foundation of Georgia (SRNSFG), Georgia FR-18-1268German Research Foundation (DFG)Greek Ministry of Development-GSRTIstituto Nazionale di Fisica Nucleare (INFN)Ministry of Education, Universities and Research (MIUR)PRIN 2017 program Italy NAT-NET 2017W4HA7SMinistry of Higher Education, Scientific Research and Professional Training, MoroccoNetherlands Organization for Scientific Research (NWO) Netherlands GovernmentNational Science Centre, Poland 2015/18/E/ST2/00758National Authority for Scientific Research (ANCS), RomaniaMinisterio de Ciencia, Innovacion, Investigacion y Universidades (MCIU): Programa Estatal de Generacion de Conocimiento, Spain (MCIU/FEDER) PGC2018-096663-B-C41 PGC2018-096663-A-C42 PGC2018-096663-BC43 PGC2018-096663-B-C44Severo Ochoa Centre of Excellence and MultiDark Consolider (MCIU), Junta de Andalucia, Spain SOMM17/6104/UGRGeneralitat Valenciana: Grisolia, Spain GRISOLIA/2018/119GenT, Spain CIDEGENT/2018/034La Caixa Foundation LCF/BQ/IN17/11620019EU: MSC program, Spain 71367

Cationic Antimicrobial Peptides\u2014The Defensins

The term defensin relates different families of host defense peptides (HDPs) in vertebrates, invertebrates, plants, and molds that display structural similarities based on a cystine stabilized antiparallel b-sheet core, with an N-terminal a-helical stretch in many members. Despite structural and functional similarities, invertebrate/ plant and vertebrate defensins belong to two distinct phylogenetic groups, and whether a unified relationship exists is controversial. Most defensins show a direct, salt- and medium-sensitive antimicrobial activity in vitro, with varying spectra, which requires interaction with the microbial membrane, although the mode of action differs markedly for defensins both within and from different families. A regulatory role in innate and adaptive immunity has also been observed for mammalian defensins

Development of pseudopeptide inhibitors of HIV-1 aspartic protease: analysis and tuning of the subsite specificity

HIV-1 aspartic protease (PR) is a promising target for acquired immunodeficiency syndrome (AIDS) therapy, and the development of PR inhibitors can be accelerated by computer-aided design methods. We describe an approach for the design of new inhibitors, based on the modification of a known reference inhibitor, and the calculation of relative binding energies, taking into account contributions from all species in the binding equilibrium (inhibitor, PR and inhibitor/PR complex), as well as their solvation. This allows for a rational selection of new structures that are likely to have increased inhibition potency. We have analyzed reduced amide bond hexapeptides (Ac-P3-P2-P1-phi[CH2-NH]-P1'-P2-P3'-NH2), based on the structure of the known inhibitor MVT-101. A maximum gain in binding energy (approximately -55 kcal/mol) is observed when Phe or Tyr are present in positions P1 and P1', Glu in position P2' and aromatic residues (Phe, Trp or Tyr) in positions P3 and P3', while, in general, the presence of positively charged residues is destabilizing. This specificity is explained in terms of the interaction of individual inhibitor residues with proximal and distal PR residues. The validity of this computational approach has been confirmed by solid-phase synthesis of several of the designed pseudopeptides, followed by in vitro enzyme inhibition assaying. The best candidate structures show IC50 values in the low nanomolar range

Computational design of highly selective antimicrobial peptides.

We have created a structure-selectivity database (AMPad) of frog-derived, helical antimicrobial peptides (AMPs), in which the selectivity was determined as a therapeutic index (TI), and then used the novel concept of sequence moments to study the lengthwise asymmetry of physicochemical peptide properties. We found that the cosine of the angle between two sequence moments obtained with different hydrophobicity scales, defined as the D-descriptor, identifies highly selective peptide antibiotics. We could then use this descriptor to predict TI changes after point mutations in known AMPs, and to aid the prediction of TI for de novo designed AMPs. In combination with an amino acid selectivity index, a motif regularity index and other statistical rules extracted from AMPad, the D-descriptor enabled construction of the AMP-Designer algorithm. A 23 residue, glycine-rich, peptide suggested by the algorithm was synthesized and the activity and selectivity tested. This peptide, adepantin 1, is less than 50% identical to any other AMP, has a potent antibacterial activity against the reference organism, E. coli, and has a significantly greater selectivity (TI > 200) than the best AMP present in the AMPad database (TI = 125)

Efficient inhibition of HIV-1 aspartic protease by synthetic, computer designed peptide mimetics

Inhibitors of HIV-1 aspartic protease, an enzyme which is essential for viral processing and maturation, represent an important new type of anti-AIDS drug. To be effective, these must be potent and selec tive, must present a suitable pharmacological profile with respect to drug uptake and clearance, and should also be synthesizeable in good yields. We have developed a design method based on computer aided modification of a reference compound for which the crystal structure of the complex with the enzyme is known. After relaxation of the new structures to an optimized geometry, the complexation energy is calculated, relative to that of the reference inhibitor, taking into account all aspects of the interaction, including solvation. This affords a numerical prediction of the putative effectiveness of the new structure as an inhibitor, relative to that of the reference structure, and thus allows us to rapidly evaluate modifications that could result in increased potency and reduce the number of compounds that it is actually necessary to synthesize so as to obtain useful lead compounds for drug development. In an initial study, we have determined the role of flanking residues in modulating inhibition, for hexapeptide mimetics with a central, reduced amide non-cleavable bond. The structure was based on that of the reference inhibitor MVT-101. We have found that by tuning the residues flanking the central bond, the complexation energy could be markedly improved, and have determined that the putatively optimal structure should contain an aromatic residue (Phe or Tyr) at positions p1 and p1', immediately flanking the central bond, a hydrophobic residue at P2, a glutamic acid residue at P2', and an aromatic residue (Phe, Tyr or Trp) at positions P3 and P3', most distant from the central bond. Synthesis of a series of inhibitors containing these modifications was carried out entirely in the solid phase, using Fmoc type chemistry, on a polyethylene glycol/polystyrene resin, and in vitro enzyme inhibition assays have confirmed the computer-based predictions. In particular, it was possible to obtain several inhibitors with potency in the low nanomolar range, an improvement of several orders of magnitude with respect to the parent compound

Native oligomerization determines the mode of action and biological activities of human cathelicidin LL-37

LL-37 is a multifunctional component of innate immunity, with a membrane-directed antimicrobial activity and receptor-mediated pleiotropic effects on host cells. Sequence variations in its primate orthologues suggest two types of functional features have evolved; human LL-37-like peptides form amphipathic helical structures and self-assemble under physiological conditions, while rhesus RL-37-like ones only adopt this structure in the presence of bacterial membranes. The first type of peptide has a lower and more medium-sensitive antimicrobial activity than the second, but an increased capacity to stimulate host cells. Oligomerization strongly affects the mode of interaction with biological membranes and consequently both cytotoxicity and receptor-mediated activities. In this work we explored the effects of LL-37 self-association by using obligate, disulfide-linked dimers with either parallel or anti-parallel orientations. These had an increased propensity to form stacked helices in bulk-solution and when in contact with either anionic or neutral model membranes. The antimicrobial activity against Gram-positive or Gram-negative bacteria, as well as the cytotoxic effects on host cells, strongly depended on the type of dimerization. To investigate the extent of native oligomerization we replaced Phe5 with the photoactive residue p-Benzoyl-L-Phenylalanine (Bpa), which on UV irradiation enabled covalent cross-linking and allowed us to assess the extent of oligomerization in both physiological solution and in model membrane

Flexible synthesis of symmetric and non-symmetric hiv-1 protease inhibitors based on all-s-diaminodiol isosteres

C2 symmetric and non-symmetric pseudopeptide inhibitors of HIV-1 protease, containing a S,S,S,S-diaminodiol isostere have been obtained by a synthetic strategy designed to couple a high degree of stereochemical control with complete flexibility in the choice of residues in the central core and flanking chains. Using this approach, inhibitors with IC50 values in the low nanomolar range were assembled from readily available aminoacids and carboxylic acids, chosen with the aid of molecular modelling