Search results for "QM"
showing 10 items of 284 documents
An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era
2017
Introduction: Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies. They also provide an omics perspective, pointing out many unsettled aspects of the most relevant families of metallo-drugs at an ep…
Synchronizing eye tracking and optical motion capture : How to bring them together
2018
Both eye tracking and motion capture technologies are nowadays frequently used in human sciences, although both technologies are usually used separately. However, measuring both eye and body movements simultaneously would offer great potential for investigating cross- modal interaction in human (e.g. music and language-related) behavior. Here we combined an Ergoneers Dikablis head mounted eye tracker with a Qualisys Oqus optical motion cap- ture system. In order to synchronize the recordings of both devices, we developed a gener- alizable solution that does not rely on any (cost-intensive) ready-made / company-provided synchronization solution. At the beginning of each recording, the partic…
Indexing a sequence for mapping reads with a single mismatch
2014
Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the s…
Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
2021
AbstractRibozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries…
Bone Fusion in Normal and Pathological Development is Constrained by the Network Architecture of the Human Skull
2016
The premature fusion of cranial bones, craniosynostosis, affects the correct development of the skull producing morphological malformations in newborns. To assess the susceptibility of each craniofacial articulation to close prematurely, we used a network model of the skull to quantify the link reliability (an index based on stochastic block modeling and Bayesian inference) of each articulation. We show that, of the 93 human skull articulations at birth, the few articulations that are associated with nonsyndromic craniosynostosis conditions have statistically significant lower reliability scores than the others. In a similar way, articulations that close during the normal postnatal developm…
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges
2017
International audience; Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evol…
Complete Genome Sequence of “Candidatus Portiera aleyrodidarum” BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia ta…
2012
ABSTRACT The genome of “ Candidatus Portiera aleyrodidarum,” the primary endosymbiont of the whitefly Bemisia tabaci (Mediterranean species), is reported. It presents a reduced genome (357 kb) encoding the capability to synthetize, or participate in the synthesis of, several amino acids and carotenoids, being the first insect endosymbiont capable of supplying carotenoids.
A multiplex RTi-PCR reaction for simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus on fresh, minimally pr…
2007
In this work, a new multiplex single-tube real-time PCR approach is presented for the detection of Escherichia coli O157:H7, Salmonella spp. and Staphylococcus aureus, three of the more frequent food-borne bacterial pathogens that are usually investigated in a variety of food matrices. The study includes the design and specificity testing, of a new primer and probe specific for Salmonella spp. Reaction conditions were adjusted for the simultaneous amplification and detection of specific fragments in the beta-glucuronidase (uidA, E. coli) and Thermonulease (nuc, Sta. aureus) genes, and in the replication origin sequence (oriC, Salmonella spp.). Melting-curve analysis using a SYBR Green I RTi…
A TaqMan-based real-time PCR assay for the specific detection and quantification ofLeuconostoc mesenteroidesin meat products
2007
A new real-time PCR procedure was developed for the specific detection and quantification of Leuconostoc mesenteroides in meat products. It is a TaqMan assay based on 23S rRNA gene targeted primers and probe. Specificity was evaluated using purified DNA from 132 strains: 102 lactic acid bacteria (LAB), including 57 reference strains and 46 food isolates, belonging to genus Leuconostoc and related genera, and 30 non-LAB strains. Quantification was linear over at least 5 log units using both serial dilutions of purified DNA and calibrated cell suspensions from Leuconostoc mesenteroides ssp. dextranicum CECT 912T. This assay was able to detect at least five genomic equivalents, using purified …
PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food.
2006
Aims: To evaluate the specificity of nuc targeted primers for PCR detection of Staphylococcus aureus in different food matrices and to establish a RTQ-PCR procedure suitable for the routine detection and quantification of this pathogen in food. Methods and Results: Specificity of nuc targeted primers (Pri1–Pri2 and the newly designed RTQ-PCR primers) was tested on a total of 157 strains of genetically confirmed identity, including reference and food isolates. PCR detection on artificially inoculated beef samples by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) showed a sensitivity value around 103 CFU g−1. The two RTQ-PCR systems, incorporating SYBR-Green I and T…