Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.Comment: submitted to Physical Review

Investigation of Living Cells in the Nanometer Regime with the Scanning Force Microscope

Membrane structures of different types of cells are imaged in the nanometer regime by scanning force microscopy (SFM). The images are compared to those obtained with a scanning electron microscope (SEM). The SFM imaging can be done on the outer cell membrane under conditions that keep the cells alive in aqueous solutions. This opens up the possibility of observing the kinematics of the structures that determine the interaction of a cell with its environment. Therefore, STM observations, together with information obtained with the electron microscope, open up new ways of studying the development of biological structures. With the currently possible resolution, the SFM gives access to processes such as antibody binding or endo- and exocytosis, including processes correlated to the infection of cells by viruses

Laser operation of Ga(NAsP) lattice-matched to (001) silicon substrate

The lattice-matched growth of the direct band gap material Ga(NAsP) is a seminal concept for the monolithic integration of III/V laser on a silicon substrate. Here, we report on the growth, characterization, and lasing properties of Ga(NAsP)/(BGa)(AsP) multi quantum well heterostructures embedded in (BGa)P cladding layers which were deposited on an exactly oriented (001) Si substrate. Structural investigations confirm a high crystal quality without any indication for misfit or threading dislocation formation. Laser operation between 800 nm and 900 nm of these broad area device structures was achieved under optical pumping as well as electrical injection for temperatures up to 150 K. This “proof of principle” points to the enormous potential of Ga(NAsP) as an optical complement to Si microelectronics

Functional paper-based materials for diagnostics

Functional papers are the subject of extensive research efforts and have already become an irreplaceable part of our modern society. Among other issues, they enable fast and inexpensive detection of a plethora of analytes and simplify laboratory work, for example in medical tests. This article focuses on the molecular and structural fundamentals of paper and the possibilities of functionalization, commercially available assays and their production, as well as on current and future challenges in research in this field

Reading, Trauma and Literary Caregiving 1914-1918: Helen Mary Gaskell and the War Library

This article is about the relationship between reading, trauma and responsive literary caregiving in Britain during the First World War. Its analysis of two little-known documents describing the history of the War Library, begun by Helen Mary Gaskell in 1914, exposes a gap in the scholarship of war-time reading; generates a new narrative of "how," "when," and "why" books went to war; and foregrounds gender in its analysis of the historiography. The Library of Congress's T. W. Koch discovered Gaskell's ground-breaking work in 1917 and reported its successes to the American Library Association. The British Times also covered Gaskell's library, yet researchers working on reading during the war have routinely neglected her distinct model and method, skewing the research base on war-time reading and its association with trauma and caregiving. In the article's second half, a literary case study of a popular war novel demonstrates the extent of the "bitter cry for books." The success of Gaskell's intervention is examined alongside H. G. Wells's representation of textual healing. Reading is shown to offer sick, traumatized and recovering combatants emotional and psychological caregiving in ways that she could not always have predicted and that are not visible in the literary/historical record

Double sign reversal of the vortex Hall effect in YBa2Cu3O7-delta thin films in the strong pinning limit of low magnetic fields

Measurements of the Hall effect and the resistivity in twinned YBa2Cu3O7-delta thin films in magnetic fields B oriented parallel to the crystallographic c-axis and to the twin boundaries reveal a double sign reversal of the Hall coefficient for B below 1 T. In high transport current densities, or with B tilted off the twin boundaries by 5 degrees, the second sign reversal vanishes. The power-law scaling of the Hall conductivity to the longitudinal conductivity in the mixed state is strongly modified in the regime of the second sign reversal. Our observations are interpreted as strong, disorder-type dependent vortex pinning and confirm that the Hall conductivity in high temperature superconductors is not independent of pinning.Comment: 4 pages, 4 figure

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

The state-of-the-art determination of urinary nucleosides using chromatographic techniques “hyphenated” with advanced bioinformatic methods

Over the last decade metabolomics has gained increasing popularity and significance in life sciences. Together with genomics, transcriptomics and proteomics, metabolomics provides additional information on specific reactions occurring in humans, allowing us to understand some of the metabolic pathways in pathological processes. Abnormal levels of such metabolites as nucleosides in the urine of cancer patients (abnormal in relation to the levels observed in healthy volunteers) seem to be an original potential diagnostic marker of carcinogenesis. However, the expectations regarding the diagnostic value of nucleosides may only be justified once an appropriate analytical procedure has been applied for their determination. The achievement of good specificity, sensitivity and reproducibility of the analysis depends on the right choice of the phases (e.g. sample pretreatment procedure), the analytical technique and the bioinformatic approach. Improving the techniques and methods applied implies greater interest in exploration of reliable diagnostic markers. This review covers the last 11 years of determination of urinary nucleosides conducted with the use of high-performance liquid chromatography in conjunction with various types of detection, sample pretreatment methods as well as bioinformatic data processing procedures

Efficiency-limiting processes in Ga(NAsP)/GaP quantum well lasers

We report on the carrier recombination mechanisms in dilute nitride Ga(NAsP)/GaP quantum well lasers. Spontaneous emission measurements show that defect-related recombination in the devices is less significant compared with other GaAs-based dilute nitride lasers. From temperature dependent measurements, we find that the threshold current density, Jth is dominated by non-radiative recombination process(es), which account for at least 91% of Jth at room temperature. The characteristic temperature, T0 (T1) is measured to be ∼104 K (∼99 K) around 200 K, which drops to ∼58 K ( ∼37 K) around room temperature. Hydrostatic pressure measurements reveal a strong increase of threshold current with increasing pressure. This implies that current leakage dominates carrier recombination which is also responsible for their low T0 and T1 values at room temperature