DIP-STR: Highly Sensitive Markers for the Analysis of Unbalanced Genomic Mixtures.

Samples containing highly unbalanced DNA mixtures from two individuals commonly occur both in forensic mixed stains and in peripheral blood DNA microchimerism induced by pregnancy or following organ transplant. Because of PCR amplification bias, the genetic identification of a DNA that contributes trace amounts to a mixed sample represents a tremendous challenge. This means that standard genetic markers, namely microsatellites, also referred as short tandem repeats (STR), and single-nucleotide polymorphism (SNP) have limited power in addressing common questions of forensic and medical genetics. To address this issue, we developed a molecular marker, named DIP-STR that relies on pairing deletion-insertion polymorphisms (DIP) with STR. This novel analytical approach allows for the unambiguous genotyping of a minor component in the presence of a major component, where DIP-STR genotypes of the minor were successfully procured at ratios up to 1:1,000. The compound nature of this marker generates a high level of polymorphism that is suitable for identity testing. Here, we demonstrate the power of the DIP-STR approach on an initial set of nine markers surveyed in a Swiss population. Finally, we discuss the limitations and potential applications of our new system including preliminary tests on clinical samples and estimates of their performance on simulated DNA mixtures

From Bloch model to the rate equations II: the case of almost degenerate energy levels

Bloch equations give a quantum description of the coupling between an atom and a driving electric force. In this article, we address the asymptotics of these equations for high frequency electric fields, in a weakly coupled regime. We prove the convergence towards rate equations (i.e. linear Boltzmann equations, describing the transitions between energy levels of the atom). We give an explicit form for the transition rates. This has already been performed in [BFCD03] in the case when the energy levels are fixed, and for different classes of electric fields: quasi or almost periodic, KBM, or with continuous spectrum. Here, we extend the study to the case when energy levels are possibly almost degenerate. However, we need to restrict to quasiperiodic forcings. The techniques used stem from manipulations on the density matrix and the averaging theory for ordinary differential equations. Possibly perturbed small divisor estimates play a key role in the analysis. In the case of a finite number of energy levels, we also precisely analyze the initial time-layer in the rate aquation, as well as the long-time convergence towards equilibrium. We give hints and counterexamples in the infinite dimensional case

One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera

Recent molecular studies of symbiotic dinoflagellates (genus Symbiodinium) from a wide array of invertebrate hosts have revealed exceptional fine-scale symbiont diversity whose distribution among hosts, regions and environments exhibits significant biogeographic, ecological and evolutionary patterns. Here, similar molecular approaches using the internal transcribed spacer-2 (ITS-2) region were applied to investigate cryptic diversity in Symbiodinium inhabiting soritid foraminifera. Approximately 1,000 soritid specimens were collected and examined during a 12-month period over a 40m depth gradient from a single reef in Guam, Micronesia. Out of 61 ITS-2 types distinguished, 46 were novel. Most types found are specific for soritid hosts, except for three types (C1, C15 and C19) that are common in metazoan hosts. The distribution of these symbionts was compared with the phylotype of their foraminiferal hosts, based on soritid small subunit ribosomal DNA sequences, and three new phylotypes of soritid hosts were identified based on these sequences. Phylogenetic analyses of 645 host-symbiont pairings revealed that most Symbiodinium types associated specifically with a particular foraminiferal host genus or species, and that the genetic diversity of these symbiont types was positively correlated with the genetic diversity found within each of the three host genera. Compared to previous molecular studies of Symbiodinium from other locations worldwide, the diversity reported here is exceptional and suggests that Micronesian coral reefs are home to a remarkably large Symbiodinium assemblag

Colloidal brazil nut effect in sediments of binary charged suspensions

Equilibrium sedimentation density profiles of charged binary colloidal suspensions are calculated by computer simulations and density functional theory. For deionized samples, we predict a colloidal ``brazil nut'' effect: heavy colloidal particles sediment on top of the lighter ones provided that their mass per charge is smaller than that of the lighter ones. This effect is verifiable in settling experiments.Comment: 4 pages, 4 figure

Evidence for ideal insulating/conducting state in a 1D integrable system

Using numerical diagonalization techniques we analyze the finite temperature/frequency conductance of a one dimensional model of interacting spinless fermions. Depending on the interaction, the observed finite temperature charge stiffness and low frequency conductance indicate a fundamental difference between integrable and non-integrable cases. The integrable systems behave as ideal conductors in the metallic regime and as ideal insulators in the insulating one. The non-integrable systems are, as expected, generic conductors in the metallic regime and activated ones in the insulating regime.Comment: revtex file, followed by 5 uuencoded postscript figure

Touch DNA collection - Performance of four different swabs.

A collaborative study conducted by three police forensic units, a DNA laboratory, and a forensic academic institute was undertaken in order to compare the performance of four different swabs in controlled and quasi-operational conditions. For this purpose, a reference swab (Prionics cardboard evidence collection kit) currently used within the police forensic units and 3 challenger swabs (COPAN 4N6FLOQSwabs™ (Genetics variety), Puritan FAB-MINI-AP and Sarstedt Forensic Swab) were used for collecting DNA traces from previously used items (referred as "touch DNA" in this article) including on 60 collars, 60 screwdrivers and 60 steering wheels obtained from volunteers. For each comparison, the surface considered was divided into two equal components; one was sampled with the reference swab and the other with one of the three challenger swabs. This lead to a total of 360 samples. Conclusions were consistent within the four operational partners. From a practical point of view, the COPAN 4N6FLOQSwabs™ (Genetics variety) was judged the most convenient to use. Furthermore, it allowed the recovery of significantly more DNA from collars (0.65 vs 0.13 ng/μL) and steering wheels (2.82 vs 1.77 ng/μL), and a similar amount of DNA from screwdrivers (0.032 vs 0.026 ng/μL) compared with the Prionics reference swab. The two other challenger swabs provided results that were not significantly different from the reference swab, except for the Puritan swab, whose performance was significantly lower for steering wheels (0.37 vs 0.58 ng/μL). As part of a conservation study, 50 μL of a blood dilution (1/4 with PBS) was deposited on a total of 105 COPAN (Genetics and Crime Scene varieties), Prionics and Sarstedt swabs. They were stored within a cupboard at room temperature. The integrity of the recovered DNA was evaluated with NGM SElect™ DNA profiles after different time-spans ranging from 1 day to 12 months by comparing the height difference of the peaks occurring at the shortest and longest loci, respectively. DNA seemed to remain stable, except when using the COPAN 4N6FLOQSwabs™ treated with an antimicrobial agent (Crime scene variety), which resulted in significant DNA degradation. Following these tests, the COPAN 4N6FLOQSwabs™ (Genetics variety), a model with a desiccant, was selected for further testing in fully operational conditions

Finite temperature mobility of a particle coupled to a fermion environment

We study numerically the finite temperature and frequency mobility of a particle coupled by a local interaction to a system of spinless fermions in one dimension. We find that when the model is integrable (particle mass equal to the mass of fermions) the static mobility diverges. Further, an enhanced mobility is observed over a finite parameter range away from the integrable point. We present a novel analysis of the finite temperature static mobility based on a random matrix theory description of the many-body Hamiltonian.Comment: 11 pages (RevTeX), 5 Postscript files, compressed using uufile

Electron spin resonance in high-field critical phase of gapped spin chains

Motivated by recent experiments on Ni(C_{2}H_{8}N_{2})_{2}Ni(CN)_{4} (commonly known as NENC), we study the electron spin resonance in the critical high-field phase of the antiferromagnetic S=1 chain with strong planar anisotropy and show that the ESR spectra exhibit several peculiarities in the critical phase. Possible relevance of those results for other gapped spin systems is discussed.Comment: 8 revtex pages, 1 eps figure include

Coherent Control for a Two-level System Coupled to Phonons

The interband polarizations induced by two phase-locked pulses in a semiconductor show strong interference effects depending on the time tau_1 separating the pulses. The four-wave mixing signal diffracted from a third pulse delayed by tau is coherently controlled by tuning tau_1. The four-wave mixing response is evaluated exactly for a two-level system coupled to a single LO phonon. In the weak coupling regime it shows oscillations with the phonon frequency which turn into sharp peaks at multiples of the phonon period for a larger coupling strength. Destructive interferences between the two phase-locked pulses produce a splitting of the phonon peaks into a doublet. For fixed tau but varying tau_1 the signal shows rapid oscillations at the interband-transition frequency, whose amplitude exhibits bursts at multiples of the phonon period.Comment: 4 pages, 4 figures, RevTex, content change