In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family

The Synechocystis sp. PCC6803 insertion sequence ISY100 (ISTcSa) belongs to the Tc1/mariner/IS630 family of transposable elements. ISY100 transposase was purified and shown to promote transposition in vitro. Transposase binds specifically to ISY100 terminal inverted repeat sequences via an N-terminal DNA-binding domain containing two helix–turn–helix motifs. Transposase is the only protein required for excision and integration of ISY100. Transposase made double-strand breaks on a supercoiled DNA molecule containing a mini-ISY100 transposon, cleaving exactly at the transposon 3′ ends and two nucleotides inside the 5′ ends. Cleavage of short linear substrates containing a single transposon end was less precise. Transposase also catalysed strand transfer, covalently joining the transposon 3′ end to the target DNA. When a donor plasmid carrying a mini-ISY100 was incubated with a target plasmid and transposase, the most common products were insertions of one transposon end into the target DNA, but insertions of both ends at a single target site could be recovered after transformation into Escherichia coli. Insertions were almost exclusively into TA dinucleotides, and the target TA was duplicated on insertion. Our results demonstrate that there are no fundamental differences between the transposition mechanisms of IS630 family elements in bacteria and Tc1/mariner elements in higher eukaryotes

Description of the inelastic collision of two solitary waves for the BBM equation

We prove that the collision of two solitary waves of the BBM equation is inelastic but almost elastic in the case where one solitary wave is small in the energy space. We show precise estimates of the nonzero residue due to the collision. Moreover, we give a precise description of the collision phenomenon (change of size of the solitary waves).Comment: submitted for publication. Corrected typo in Theorem 1.

Adapting the Marine Stewardship Council risk-based framework to estimate impacts on seabirds, marine mammals, marine turtles and sea snakes

Information available on impacts of fisheries on target or bycatch species varies greatly, requiring development of risk assessment tools to determine potentially unacceptable levels. Seabirds, marine mammals, marine turtles and sea snakes are particularly vulnerable given their extreme life histories, and data are often lacking on their populations or bycatch rates with which to quantify fisheries impacts. The Marine Stewardship Council (MSC) use a semi-quantitative Productivity Susceptibility Analysis (PSA) that is applicable to all species, target and non-target, to calculate risk of impact and to provide a score for relevant Performance Indicators for fisheries undertaking certification. The most recent MSC Fisheries Standard Review provided an opportunity to test the appropriateness of using this tool and whether it was sufficiently precautionary for seabirds, marine mammals and reptiles . The existing PSA was tested on a range of species and fisheries and reviewed in relation to literature on these species groups. New taxa-specific PSAs were produced and then reviewed by taxa-specific experts and other relevant stakeholders (e.g., assessors, fisheries managers, non-governmental conservation organizations). The conclusions of the Fishery Standard Review process were that the new taxa-specific PSAs were more appropriate than the existing PSA for assessing fisheries risk for seabirds, marine mammals and reptiles, and that, as intended, they resulted in precautionary outcomes. The taxa-specific PSAs provide useful tools for true data-deficient fisheries to assess relative risk of impact. Where some data are available, the MSC could consider developing or adapting other approaches to support robust and relevant risk assessments

Updating requirements for Endangered, Threatened and Protected species MSC Fisheries Standard v3.0 to operationalise best practices

Bycatch in fisheries is a key threat to non-target marine species, particularly for those species that have life histories with low productivity or poor conservation status. In this paper, the requirements of the new Marine Stewardship Council (MSC) Fisheries Standard (hereafter “the Standard”) are summarised relevant to Endangered, Threatened and Protected (ETP) species. This covers both how species are designated as ETP, and how performance of management is assessed with respect to ETP species, when scoring fisheries against the Standard. The process used to select these requirements is described, including a review of the requirements for earlier versions of the Standard and the scoring of these requirements in assessment reports for a selection of fisheries that have achieved MSC certification. The review identified a lack of consistency in the implementation of scoring guidelines, which was in part due to a lack of clarity in the requirements of the Standard. The revised Standard has been designed to achieve more consistent implementation of the requirements with respect to management of impacts on ETP species, and to align the requirements more closely with global best practice. The requirements may be used as a template for fisheries managers seeking to prioritise bycatch species for improved management and setting more specific and measurable objectives in relation to population status and minimising mortalities

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

Open string amplitudes and large order behavior in topological string theory

We propose a formalism inspired by matrix models to compute open and closed topological string amplitudes in the B-model on toric Calabi-Yau manifolds. We find closed expressions for various open string amplitudes beyond the disk, and in particular we write down the annulus amplitude in terms of theta functions on a Riemann surface. We test these ideas on local curves and local surfaces, providing in this way generating functionals for open Gromov-Witten invariants in the spirit of mirror symmetry. In the case of local curves, we study the open string sector near the critical point which leads to 2d gravity, and we show that toric D-branes become FZZT branes in a double-scaling limit. We use this connection to compute non-perturbative instanton effects due to D-branes that control the large order behavior of topological string theory on these backgroundsComment: 40 pages, 5 figures, v3: further clarifications and references adde

A New Definition of Learning Disabilities

Learning disabilities is a generic term that refers to a heterogeneous group of disorders manifested by significant difficulties in the acquisition and use of listening, speaking, reading, writing, reasoning or mathematical abilities. These disorders are intrinsic to the individual and presumed to be due to central nervous system dysfunction. Even though a learning disability may occur concomitantly with other handicapping conditions (e.g., sensory impairment, mental retardation, social and emotional disturbance) or environmental influences (e.g., cultural differences, insufficient/inappropriate instruction, psychogenic factors), it is not the direct result of those conditions or influences.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10-11 to 5.0 × 10-21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10-6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation