Search results for "Fragmentation"

New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples

2021

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Poliz…

A TDDFT-based Study on the Proton-DNA Collision

2019

The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3' atoms responsible for the attachment. The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitr…

N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.

2014

The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affect…

Cationic Nanohydrogel Particles as Potential siRNA Carriers for Cellular Delivery

2012

Oligonucleotides such as short, double-stranded RNA (siRNA) or plasmid DNA (pDNA) promise high potential in gene therapy. For pharmaceutical application, however, adequate drug carriers are required. Among various concepts progressing in the market or final development, nanosized hydrogel particles may serve as novel transport media especially for siRNA. In this work, a new concept of synthesizing polymeric cationic nanohydrogels was developed, which offers a promising strategy to complex and transport siRNA into cells. For this purpose, amphiphilic reactive ester block copolymers were synthesized by RAFT polymerization of pentafluorophenyl methacrylate as reactive ester monomer together wi…

Effect of protonation and deprotonation on the gas phase reactivity of fluorinated 1,2,4-triazines

2008

Positive and negative electrospray mass spectrometry (MS), in-time and in-space MS n experiments, high-resolution and accurate mass measurements obtained with an Orbitrap, together with density functional theory calculations have been used to study the gas-phase ion chemistry of a series of fluorinated 1,2,4-triazines. As a result of low-energy collision-induced dissociations, occurring in an ion trap and in a triple quadrupole, their protonated and deprotonated molecules show interesting features depending on the nature and structure of the precursor ions. The occurrence of elimination/hydration reactions produced by positive ions in the ion trap is noteworthy. Decompositions of deprotonat…

Caspase-mediated apoptosis in sponges: cloning and function of the phylogenetic oldest apoptotic proteases from Metazoa

2003

AbstractSponges (phylum Porifera) represent the phylogenetically oldest metazoan phylum. These animals have complex cell adhesion and powerful immune systems which allow the formation of a distinct body plan. Consequently, an apoptotic machinery has to be predicted that allows sponges to eliminate unwanted cells accumulating during development. With the marine sponge Geodia cydonium, it is shown that allografts of these animals undergo apoptosis as demonstrated by apoptotic DNA fragmentation. Extracts from allografts contain an enzymic activity characteristic for caspases; as substrate to determine the cleavage activity, Ac-DEVD-AMC was applied. cDNAs encoding predicted caspase-3-related pr…

Spontaneous fragmentation of multiply charged metal clusters.

1987

Does fragmentation of wetlands affect gene flow in sympatric Acrocephalus warblers with different migration strategies?

2015

Wetlands are naturally patchy habitats, but patchiness has been accentuated by the extensive wetlands loss due to human activities. In such a fragmented habitat, dispersal ability is especially important to maintain gene flow between populations. Here we studied population structure, genetic diversity and demographic history of Iberian and North African populations of two wetland passerines, the Eurasian reed warbler Acrocephalus scirpaceus and the moustached warbler Acrocephalus melanopogon. These species are closely related and sympatric in our study sites, but the reed warbler is a long-distance migrant and widespread bird while the moustached warbler is resident or migrates over short d…

Low effective population sizes and limited connectivity inxerothermic beetles: implications for the conservation ofan endangered habita

2014

Fragmentation and isolation may have detrimental effects on the viability of populations. Xerothermic grasslands, which are extra-zonal analogues of steppes, are among Europe's most endangered natural environments. Information about connectivity between the remaining habitat patches is critical for effective conservation planning. However, very little is known about the actual levels of isolation of individual xerothermic patches at the inter-regional and local scale. In this study, 16 microsatellite loci were used to investigate genetic diversity, structuring, effective sizes (Ne), and connectivity among populations of the weevil Centricnemus leucogrammus at various geographic scales. Anal…

Neurotoxicity in Rat Cortical Cells Caused by N-Methyl-D-Aspartate (NMDA) and gp120 of HIV-1: Induction and Pharmacological Intervention

1996

Incubation of highly enriched neurons from rat cerebral cortex with the human immunodeficiency virus type 1 (HIV-1) coat protein gpl20 for 18 h results in fragmentation of DNA at internucleosomal linkers, a feature of apoptosis. We report that neurons respond to exposure to gp120 with an increased release of arachidonic acid via activation of phospholipase A2. This process is not inhibited by antagonists of the N-methyl-D-aspartate (NMDA) receptor channels. To investigate the influence of arachidonic acid on the sensitivity of NMDA receptor towards its aganist, low concentrations of NMDA were coadministered with arachidonic acid. Under these conditions the NMDA-mediated cytotoxicity was enh…