A Romano-British settlement with ovens and field system at Theobalds Road, Wivelsfield, East Sussex

Excavation west of Wivelsfield, East Sussex, revealed part of an early Romano-British settlement. One of the round-houses may have had a non-domestic, possibly ritual, function. The settlement appears to have been subsequently incorporated within a rectilinear arrangement of field/enclosure ditches. Along the edge of one of these ditches were built a series of features interpreted as ovens, of varying form and likely use, from which charred waste from cereal processing and charcoal from coppiced woodland were recovered.

In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

Effects of isoflavones on the coagulation and fibrinolytic system of postmenopausal women

Objective: We evaluated the effects of soy isoflavone supplementation on hemostasis in healthy postmenopausal women. Methods: In this double-blinded, placebo-controlled study, 47 postmenopausal women 47-66 y of age received 40 mg of soy isoflavone (n = 25) or 40 mg of casein placebo (n = 22) once a day for 6 mo. Levels of factors VII and X. fibrinogen, thrombin-antithrombin complex, prothrombin fragments I plus 2, antithrombin, protein C, total and free protein S, plasminogen, plasminogen activator inhibitor-1, and D-dimers were measured at baseline and 6 mo. Urinary isoflavone concentrations (genistein and daidzein) were measured as a marker of compliance and absorption using high-performance liquid chromatography. Baseline characteristics were compared by unpaired Student`s t test. Within-group changes and comparison between the isoflavone and casein placebo groups were determined by a mixed effects model. Results: The levels of hemostatic variables did not change significantly throughout the study in the isoflavone group; however, the isoflavone group showed a statistically significant reduction in plasma concentration of prothrombin fragments I plus 2; both groups showed a statistically significant reduction in antithrombin, protein C, and free protein S levels. A significant increase in D-dimers was observed only in the isoflavone group. Plasminogen activator inhibitor-l levels increased significantly in the placebo group. However, these changes were not statistically different between groups. Conclusion: The results of the present study do not support a biologically significant estrogenic effect of soy isoflavone on coagulation and fibrinolysis in postmenopausal women. However, further research will be necessary to definitively assess the safety and efficacy of isoflavone. (D 2008 Elsevier Inc. All rights reserved.

Identification and characterization of antigenic proteins potentially expressed during the infectious process of Paracoccidioides brasiliensis

Paracoccidioides brasiliensis causes paracoccidioidomycosis (PCM), a systemic mycosis presenting clinical manifestations ranging from mild to severe forms. A P. brasiliensis cDNA expression library was produced and screened with pooled sera from PCM patients adsorbed against antigens derived from in vitro-grown P. brasiliensis yeast cells. Sequencing DNA inserts from clones reactive with PCM patients sera indicated 35 open reading frames presenting homology to genes involved in metabolic pathways, transport, among other predicted functions. The complete cDNAs encoding aromatic-L-amino-acid decarboxylase (Pbddc), lumazine synthase (Pbls) and a homologue of the high affinity copper transporter (Pbctr3) were obtained. Recombinant proteins PbDDC and PbLS were obtained; a peptide was synthesized for PbCTR3. The proteins and the synthetic peptide were recognized by sera of patients with confirmed PCM and not by sera of healthy patients. Using the in vivo-induced antigen technology (IVIAT), we identified immunogenic proteins expressed at high levels during infection. Quantitative real time RTPCR demonstrated high transcript levels of Pbddc, Pbls and Pbctr3 in yeast cells infecting macrophages. Transcripts in yeast cells derived from spleen and liver of infected mice were also measured by qRT-PCR. Our results suggest a putative role for the immunogenic proteins in the infectious process of P. brasiliensis. (C) 2009 Elsevier Masson SAS. All rights reserved.

Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding

Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi. T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes. (C) 2010 Elsevier B.V. All rights reserved.

A real-time polymerase chain reaction assay for the identification and quantification of American Leishmania species on the basis of glucose-6-phosphate dehydrogenase

A real-time polymerase chain reaction (PCR) test was developed on the basis of the Leishmania glucose-6-phosphate dehydrogenase locus that enables identification and quantification of parasites. Using two independent pairs of primers in SYBR-Green assays, the test identified etiologic agents of cutaneous leishmaniasis belonging to both subgenera, Leishmania (Viannia) and Leishmania (Leishmania) in the Americas. Furthermore, use of TaqMan probes enables distinction between L. (V.) braziliensis or L. (V.) peruviania from the other L. (Viannia) species. All assays were negative with DNA of related trypanosomatids, humans, and mice. The parasite burden was estimated by normalizing the number of organisms per total amount of DNA in the sample or per host glyceraldehyde-3-phosphate dehydrogenase copies. The real-time PCR assay for L. (Leishmania) subgenus showed a good linear correlation with quantification on the basis of a limiting dilution assay in experimentally infected mice. The test successfully identifies and quantifies Leishmania in human biopsy specimens and represents a new tool to study leishmaniasis.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

Demonstration of Solar Heating and Cooling System using Sorption Integrated Solar Thermal Collectors

Producing cost-competitive small and medium-sized solar cooling systems is currently a significant challenge. Due to system complexity, extensive engineering, design and equipment costs; the installation costs of solar thermal cooling systems are prohibitively high. In efforts to overcome these limitations, a novel sorption heat pump module has been developed and directly integrated into a solar thermal collector. The module comprises a fully encapsulated sorption tube containing hygroscopic salt sorbent and water as a refrigerant, sealed under vacuum with no moving parts. A 5.6m2 aperture area outdoor laboratory-scale system of sorption module integrated solar collectors was installed in Stockholm, Sweden and evaluated under constant re-cooling and chilled fluid return temperatures in order to assess collector performance. Measured average solar cooling COP was 0.19 with average cooling powers between 120 and 200 Wm-2 collector aperture area. It was observed that average collector cooling power is constant at daily insolation levels above 3.6 kWhm-2 with the cooling energy produced being proportional to solar insolation. For full evaluation of an integrated sorption collector solar heating and cooling system, under the umbrella of a European Union project for technological innovation, a 180 m2 large-scale demonstration system has been installed in Karlstad, Sweden. Results from the installation commissioned in summer 2014 with non-optimised control strategies showed average electrical COP of 10.6 and average cooling powers between 140 and 250 Wm-2 collector aperture area. Optimisation of control strategies, heat transfer fluid flows through the collectors and electrical COP will be carried out in autumn 2014.

Identification and characterization of a lymphocytic Rho-GTPase effector: rhotekin-2

Rhotekin belongs to the group of proteins containing a Rho-binding domain that are target peptides (effectors) for the Rho-GTPases. We previously identified a novel cDNA with homology to human rhotekin and in this study we cloned and characterized the coding region of this novel 12-exon gene. The ORF encodes a 609 amino-acid protein comprising a Class I Rho-binding domain and pleckstrin homology (PH) domain. Cellular cDNA expression of this new protein, designated Rhotekin-2 (RTKN2), was shown in the cytosol and nucleus of CHO cells. Using bioinformatics and RTPCR we identified three major splice variants, which vary in both the Rho-binding and PH domains. Real-time PCR studies showed exclusive RTKN2 expression in pooled lymphocytes and further purification indicated sole expression in CD4^_pos T-cells and bone marrow-derived B-cells. Gene expression was increased in quiescent T-cells but negligible in activated proliferating cells. In malignant samples expression was absent in myeloid leukaemias, low in most B-cell malignancies and CD8^pos T-cell malignancies, but very high in CD4^pos/CD8^pos T-lymphoblastic lymphoma. As the Rho family is critical in lymphocyte development and function, RTKN2 may play an important role in lymphopoiesis.

The indigenous art market: a roadmap to a more equitable and efficient system

The Indigenous art market plays a significant role both in promoting appreciation for the accomplishments of Aboriginal culture and within broader concepts of the export of a national culture.[1] Despite the growth in status and impact of Indigenous art over the past decade, very little scholarship or resources exist to assist their development and analyse their impact on economic or social wellbeing. This paper canvasses new ways of operating the Indigenous art market to better support emerging and established artists in a globalised economy and suggests that there is a pressing need for future research to develop a new framework for its operation.

Freshwater reserves in Australia : directions and challenges for the development of a comprehensive, adequate and representative system of protected areas

The establishment of a system of protected areas that samples all ecosystems, including freshwater environments, in a comprehensive, adequate and representative (CAR) manner is regarded as a cornerstone for the conservation of biodiversity. There have been few quantitative assessments of the comprehensiveness, adequacy and representativeness of freshwater reserves in Australia. This paper reviews and quantifies the effect of classification of freshwater ecosystems for conservation planning, the importance of reservation status and protection measures for developing a CAR reserve system, and aspects of reserve design for freshwater ecosystems. We propose a strategic and iterative process that incorporates these measures to assist in the efficient and effective development of freshwater reserve systems worldwide. However, the provision of suitable water regimes for freshwater reserves presents further ecological and political challenges, and even adequate reservation of freshwater ecosystems may not conserve constituent biodiversity without effective management.

The long and winding road : the development of a comprehensive, adequate and representative system of highly protected marine protected areas in Victoria, Australia

In 2002, the state of Victoria, Australia increased its “no-take” marine protected areas (MPAs) 100 fold to cover over 5% of its coastal waters in a comprehensive, adequate and representative system of marine national parks and sanctuaries. Given the ambitious targets set for MPA establishment globally in 2003 at the World Summit for Sustainable Development this apparently remarkable achievement could be an example to other nations and states attempting to establish substantial MPA systems.

This paper describes and discusses the factors that contributed to the establishment of the Victorian system and the relevance of these factors to other jurisdictions.

Child protection and public health: nurses' responsibilities

Background. Health care workers have been recognized as having a key role in the protection and care of Scotland's children, particularly in respect of identification and detection of child abuse. Nurses, especially health visitors, are often the first professionals to suspect that child abuse has taken place. While previous research has found that health visitors have primarily perceived their role as that of providing support and advice to vulnerable families, there are pressures on them to fulfil a more narrow surveillance role. Concurrent with a lack of clarity about the role of health visitors in child protection, there has been increasing recognition that other nurses can also make an important contribution, including those who do not work directly with children.

Aims. The aim of the study was to explore nurses' understanding of their professional responsibilities in relation to child protection, and the potential for nurses to be involved in the protection of children from abuse.

Methods. A qualitative interview-based design was used, and 99 nurses working in an National Health Service trust in a Scottish city were interviewed, either individually or in groups, about their professional involvements in child protection issues. Interview data were subjected to thematic analysis.

Findings. There was lack of consensus among interviewees about the nursing remit in child protection issues, particularly with respect to the extent to which nurses should actively seek to detect cases of child abuse. An emphasis on identification and detection was not easily accepted by many nurses, and was perceived by some to be a change from their more traditional role of supporting families, as well as being potentially in conflict with some public health responsibilities.

Conclusion. In spite of the perception of some nurses that there is a sharp divide between child protection work and public health interventions, many of the child protection roles identified by nurses, such as supporting families, parenting education and service development, are clearly within the ambit of contemporary notions of public health. Furthermore, it is clear that there is a role in child protection for a much wider group of nurses than health visitors.