Direct characterization of circulating DNA in blood plasma using μLAS technology

Circulating cell-free DNA (cfDNA) is a powerful cancer biomarker for establishing targeted therapies or monitoring patients' treatment. However, current cfDNA characterization is severely limited by its low concentration, requiring the extensive use of amplification techniques. Here we report that the μLAS technology allows us to quantitatively characterize the size distribution of purified cfDNA in a few minutes, even when its concentration is as low as 1 pg/μL. Moreover, we show that DNA profiles can be directly measured in blood plasma with a minimal conditioning process to speed up considerably speed up the cfDNA analytical chain

Laser-Evoked Vertex Potentials Predict Defensive Motor Actions

The vertex potential is the largest response that can be recorded in the electroencephalogram of an awake, healthy human. It is elicited by sudden and intense stimuli, and is composed by a negative-positive deflection. The stimulus properties that determine the vertex potential amplitude have been well characterized. Nonetheless, its functional significance remains elusive. The dominant interpretation is that it reflects neural activities related to the detection of salient stimuli. However, given that threatening stimuli elicit both vertex potentials and defensive movements, we hypothesized that the vertex potential is related to the execution of defensive actions. Here, we directly compared the salience and motoric interpretations by investigating the relationship between the amplitude of laser-evoked potentials (LEPs) and the response time of movements with different defensive values. First, we show that a larger LEP negative wave (N2 wave) predicts faster motor response times. Second, this prediction is significantly stronger when the motor response is defensive in nature. Third, the relation between the N2 wave and motor response time depends not only on the kinematic form of the movement, but also on whether that kinematic form serves as a functional defense of the body. Therefore, the N2 wave of the LEP encodes key defensive reactions to threats

On the functional anatomy of the urge-for-action

Several common neuropsychiatric disorders (e.g., obsessive-compulsive disorder, Tourette syndrome (TS), autistic spectrum disorder) are associated with unpleasant bodily sensations that are perceived as an urge for action. Similarly, many of our everyday behaviors are also characterized by bodily sensations that we experience as urges for action. Where do these urges originate? In this paper, we consider the nature and the functional anatomy of “urges-for-action,” both in the context of everyday behaviors such as yawning, swallowing, and micturition, and in relation to clinical disorders in which the urge-for-action is considered pathological and substantially interferes with activities of daily living (e.g., TS). We review previous frameworks for thinking about behavioral urges and demonstrate that there is considerable overlap between the functional anatomy of urges associated with everyday behaviors such as swallowing, yawning, and micturition, and those urges associated with the generation of tics in TS. Specifically, we show that the limbic sensory and motor regions—insula and mid-cingulate cortex—are common to all of these behaviors, and we argue that this “motivation-for-action” network should be considered distinct from an “intentional action” network, associated with regions of premotor and parietal cortex, which may be responsible for the perception of “willed intention” during the execution of goal-directed actions

Recognition without identification, erroneous familiarity, and déjà vu

Déjà vu is characterized by the recognition of a situation concurrent with the awareness that this recognition is inappropriate. Although forms of déjà vu resolve in favor of the inappropriate recognition and therefore have behavioral consequences, typical déjà vu experiences resolve in favor of the awareness that the sensation of recognition is inappropriate. The resultant lack of behavioral modification associated with typical déjà vu means that clinicians and experimenters rely heavily on self-report when observing the experience. In this review, we focus on recent déjà vu research. We consider issues facing neuropsychological, neuroscientific, and cognitive experimental frameworks attempting to explore and experimentally generate the experience. In doing this, we suggest the need for more experimentation and amore cautious interpretation of research findings, particularly as many techniques being used to explore déjà vu are in the early stages of development.PostprintPeer reviewe

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.Comment: Submitted versio

Rad51 Polymerization Reveals a New Chromatin Remodeling Mechanism

Rad51 protein is a well known protagonist of homologous recombination in eukaryotic cells. Rad51 polymerization on single-stranded DNA and its role in presynaptic filament formation have been extensively documented. Rad51 polymerizes also on double-stranded DNA but the significance of this filament formation remains unclear. We explored the behavior of Saccharomyces cerevisiae Rad51 on dsDNA and the influence of nucleosomes on Rad51 polymerization mechanism to investigate its putative role in chromatin accessibility to recombination machinery. We combined biochemical approaches, transmission electron microscopy (TEM) and atomic force microscopy (AFM) for analysis of the effects of the Rad51 filament on chromatinized templates. Quantitative analyses clearly demonstrated the occurrence of chromatin remodeling during nucleoprotein filament formation. During Rad51 polymerization, recombinase proteins moved all the nucleosomal arrays in front of the progressing filament. This polymerization process had a powerful remodeling effect, as Rad51 destabilized the nucleosomes along considerable stretches of DNA. Similar behavior was observed with RecA. Thus, recombinase polymerization is a powerful mechanism of chromatin remodeling. These remarkable features open up new possibilities for understanding DNA recombination and reveal new types of ATP-dependent chromatin dynamics

Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA

We have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences

Structural plasticity of single chromatin fibers revealed by torsional manipulation

Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.Comment: 18 pages, 7 figures, Supplementary information available at http://www.nature.com/nsmb/journal/v13/n5/suppinfo/nsmb1087_S1.htm

Fractal dimension of chromatin is an independent prognostic factor for survival in melanoma

<p>Abstract</p> <p>Background</p> <p>Prognostic factors in malignant melanoma are currently based on clinical data and morphologic examination. Other prognostic features, however, which are not yet used in daily practice, might add important information and thus improve prognosis, treatment, and survival. Therefore a search for new markers is desirable. Previous studies have demonstrated that fractal characteristics of nuclear chromatin are of prognostic importance in neoplasias. We have therefore investigated whether the fractal dimension of nuclear chromatin measured in routine histological preparations of malignant melanomas could be a prognostic factor for survival.</p> <p>Methods</p> <p>We examined 71 primary superficial spreading cutaneous melanoma specimens (thickness ≥ 1 mm) from patients with a minimum follow up of 5 years. Nuclear area, form factor and fractal dimension of chromatin texture were obtained from digitalized images of hematoxylin-eosin stained tissue micro array sections. Clark's level, tumor thickness and mitotic rate were also determined.</p> <p>Results</p> <p>The median follow-up was 104 months. Tumor thickness, Clark's level, mitotic rate, nuclear area and fractal dimension were significant risk factors in univariate Cox regressions. In the multivariate Cox regression, stratified for the presence or absence of metastases at diagnosis, only the Clark level and fractal dimension of the nuclear chromatin were included as independent prognostic factors in the final regression model.</p> <p>Conclusion</p> <p>In general, a more aggressive behaviour is usually found in genetically unstable neoplasias with a higher number of genetic or epigenetic changes, which on the other hand, provoke a more complex chromatin rearrangement. The increased nuclear fractal dimension found in the more aggressive melanomas is the mathematical equivalent of a higher complexity of the chromatin architecture. So, there is strong evidence that the fractal dimension of the nuclear chromatin texture is a new and promising variable in prognostic models of malignant melanomas.</p

Protein/DNA interactions in complex DNA topologies: expect the unexpected

DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology