Statistical Theory of Force Induced Unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the stiffness of single strand of DNA and the potential depth $D$. We used constant extension ensemble to calculate the average force needed to stretch a base pair $y$ distance apart. A very large peak around $y = 1 {\rm \AA}$ is found. The value of $F(y)$ needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance. The effect of mismatching in the base pairs on the peak height and position is investigated. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of "an eye" when a base pair far from ends is stretched are investigated.Comment: Minor changes in figures, published versio

Orbital changes, variation in solar activity and increased anthropogenic activities: controls on the Holocene flood frequency in the Lake Ledro area, Northern Italy

International audienceTwo lacustrine sediment cores from Lake Ledro in northern Italy were studied to produce chronologies of floodevents for the past 10 000 yr. For this purpose, we have developed an automatic method that objectively identifies the sedimentary imprint of river floods in the downstream lake basin. The method was based on colour data extracted from processed core photographs, and the count data were analysed to capture the flood signal. Flood frequency and reconstructed sedimentary dynamics were compared with lake-level changes and pollen inferred vegetation dynamics. The results suggest a record marked by low flood frequency during the early and middle Holocene (10 000–4500 cal BP). Only modest increases during short intervals are recorded at ca. 8000, 7500, and 7100 cal BP. After 4500–4000 cal BP, the record shows a shift toward increased flood frequency. With the exception of two short intervals around 2900–2500 and 1800–1400 cal BP, which show a slightly reduced number of floods, the trend of increasing flood frequency prevailed until the 20th century, reaching a maximum between the 16th and the 19th centuries. Brief-flood frequency increases recorded during the early and middle Holocene can be attributed to climatic oscillations. On a centennial time scale, major changes in flood frequency, such as those observed after ca. 4500/4000 and 500 cal BP, can be attributed to large-scale climatic changes such as the Neo-glacial and Little Ice Age, which are under orbital and possibly solar control. However, in the Bronze Age and during the Middle Ages and modern times, forest clearing and land use probably partially control the flood activity

First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes.

Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research

Ultrahigh ionic exclusion through carbon nanomembranes

The collective “single‐file” motion of water molecules through natural and artificial nanoconduits inspires the development of high‐performance membranes for water separation. However, a material that contains a large number of pores combining rapid water flow with superior ion rejection is still highly desirable. Here, a 1.2 nm thick carbon nanomembrane (CNM) made from cross‐linking of terphenylthiol (TPT) self‐assembled monolayers is reported to possess these properties. Utilizing their extremely high pore density of 1 sub‐nm channel nm−2, TPT CNMs let water molecules rapidly pass, while the translocation of ions, including protons, is efficiently hindered. Their membrane resistance reaches ≈104 Ω cm2 in 1 m Cl− solutions, comparable to lipid bilayers of a cell membrane. Consequently, a single CNM channel yields an ≈108 higher resistance than pores in lipid membrane channels and carbon nanotubes. The ultrahigh ionic exclusion by CNMs is likely dominated by a steric hindrance mechanism, coupled with electrostatic repulsion and entrance effects. The operation of TPT CNM membrane composites in forward osmosis is also demonstrated. These observations highlight the potential of utilizing CNMs for water purification and opens up a simple avenue to creating 2D membranes through molecular self‐assembly for highly selective and fast separations

500,000 Years of Environmental History in Eastern Anatolia: The PALEOVAN Drilling Project

International Continental Scientific Drilling Program (ICDP) drilled a complete succession of the lacustrine sediment sequence deposited during the last ~500,000 years in Lake Van, Eastern Anatolia (Turkey). Based on a detailed seismic site survey, two sites at a water depth of up to 360 m were drilled in summer 2010, and cores were retrieved from sub-lake-floor depths of 140 m (Northern Basin) and 220 m (Ahlat Ridge). To obtain a complete sedimentary section, the two sites were multiple-cored in order to investigate the paleoclimate history of a sensitive semi-arid region between the Black, Caspian, and Mediterranean seas. Further scientific goals of the PALEOVAN project are the reconstruction of earthquake activity, as well as the temporal, spatial, and compositional evolution of volcanism as reflected in the deposition of tephra layers. The sediments host organic matter from different sources and hence composition, which will be unravelled using biomarkers. Pathways for migration of continental and mantle-derived noble gases will be analyzed in pore waters. Preliminary 40Ar/39Ar single crystal dating of tephra layers and pollen analyses suggest that the Ahlat Ridge record encompasses more than half a million years of paleoclimate and volcanic/geodynamic history, providing the longest continental record in the entire Near East to date

Evolution through segmental duplications and losses : A Super-Reconciliation approach

The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes

A dimensioning and tolerancing methodology for concurrent engineering applications II: comprehensive solution strategy

Dimensioning and tolerancing (D&T) is a multidisciplinary problem which requires the fulfillment of a large number of dimensional requirements. However, almost all of the currently available D&T tools are only intended for use by the designer. In addition, they typically provide solutions for the requirements one at time. This paper presents a methodology for determining the dimensional specifications of the component parts and sub-assemblies of a product by satisfying all of its requirements. The comprehensive solution strategy presented here includes: a strategy for separating D&T problems into groups, the determination of an optimum solution order for coupled functional equations, a generic tolerance allocation strategy, and strategies for solving different types of D&T problems. A number of commonly used cost minimization strategies, such as the use of standard parts, preferred sizes, preferred fits, and preferred tolerances, have also been incorporated into the proposed methodology. The methodology is interactive and intended for use in a concurrent engineering environment by members of a product development team

Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms

The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular