Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Seawater carbonate chemistry and trace element accumulation during experiments with common cuttlefish, Sepia officinalis, 2009

Cephalopods play a key role in many marine trophic networks and constitute alternative fisheries resources, especially given the ongoing decline in finfish stocks. Along the European coast, the eggs of the cuttlefish Sepia officinalis are characterized by an increasing permeability of the eggshell during development, which leads to selective accumulation of essential and non-essential elements in the embryo. Temperature and pH are two critical factors that affect the metabolism of marine organisms in the coastal shallow waters. In this study, we investigated the effects of pH and temperature through a crossed (3?2; pH 8.1 (pCO2, 400 ppm), 7.85 (900 ppm) and 7.6 (1400 ppm) at 16 and 19°C, respectively) laboratory experiment. Seawater pH showed a strong effect on the egg weight and non-significant impact on the weight of hatchlings at the end of development implying an egg swelling process and embryo growth disturbances. The lower the seawater pH, the more 110 mAg was accumulated in the tissues of hatchlings. The 109Cd concentration factor (CF) decreased with decreasing pH and 65Zn CF reached maximal values pH 7.85, independently of temperature. Our results suggest that pH and temperature affected both the permeability properties of the eggshell and embryonic metabolism. To the best of our knowledge, this is one of the first studies on the consequences of ocean acidification and ocean warming on metal uptake in marine organisms, and our results indicate the need to further evaluate the likely ecotoxicological impact of the global change on the early-life stages of the cuttlefish.

English for tourism : contribution to language use through mobile learning

Tourism is growing and is becoming more competitive. Destinations need to find elements which demonstrate their uniqueness, the singularity which allows them to differentiate themselves from others. This struggle for uniqueness makes economies become more competitive and competition is a central element in the dynamics of Tourism. Technology is also an added value for tourism competitiveness, as it allows destinations to become internationalised and known worldwide. In this scenario, research has increased as a means to study Tourism trends in fields such as sociology and marketing. Nevertheless, there are areas in which there is not much research done and which are fundamental: these are the areas concerned with identities, communication and interpersonal relations. In this regard, Linguistics has a major role for different reasons: firstly, it studies language itself and through it, communication, secondly, language conveys culture and, thirdly, it is by enriching language users that innovation in Tourism and in knowledge, as a whole, is made possible. This innovation, on the other hand, has repercussions in areas such as management, internationalisation and marketing as well. It is, therefore, the objective of this thesis to report on how learning experiences take place in Tourism undergraduate English language classes as well as to give an account of enhanced results in classes where mobile learning was adopted. In this way, an alliance between practice and research was established. This is beneficial for the teaching and learning process because by establishing links between research based insight and practice, the outcome is grounded knowledge which helps make solid educational decisions. This research, therefore, allows to better understand if learners accept working with mobile technologies in their learning process. Before introducing any teaching and learning approach, it was necessary to be informed, as well, of how English for tourism programmes are organised. This thesis also illustrates through the premises of Systemic Functional Linguistics that language use can be enhanced by using mobile technology in Tourism undergraduate language classes.

A New Genetic Algorithm for Set Covering Problems

An indirect genetic algorithm for the non-unicost set covering problem is presented. The algorithm is a two-stage meta-heuristic, which in the past was successfully applied to similar multiple-choice optimisation problems. The two stages of the algorithm are an ‘indirect’ genetic algorithm and a decoder routine. First, the solutions to the problem are encoded as permutations of the rows to be covered, which are subsequently ordered by the genetic algorithm. Fitness assignment is handled by the decoder, which transforms the permutations into actual solutions to the set covering problem. This is done by exploiting both problem structure and problem specific information. However, flexibility is retained by a self-adjusting element within the decoder, which allows adjustments to both the data and to stages within the search process. Computational results are presented.

Nurse Rostering with Genetic Algorithms

In recent years genetic algorithms have emerged as a useful tool for the heuristic solution of complex discrete optimisation problems. In particular there has been considerable interest in their use in tackling problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle constraints and successful implementations usually require some sort of modification to enable the search to exploit problem specific knowledge in order to overcome this shortcoming. This paper is concerned with the development of a family of genetic algorithms for the solution of a nurse rostering problem at a major UK hospital. The hospital is made up of wards of up to 30 nurses. Each ward has its own group of nurses whose shifts have to be scheduled on a weekly basis. In addition to fulfilling the minimum demand for staff over three daily shifts, nurses’ wishes and qualifications have to be taken into account. The schedules must also be seen to be fair, in that unpopular shifts have to be spread evenly amongst all nurses, and other restrictions, such as team nursing and special conditions for senior staff, have to be satisfied. The basis of the family of genetic algorithms is a classical genetic algorithm consisting of n-point crossover, single-bit mutation and a rank-based selection. The solution space consists of all schedules in which each nurse works the required number of shifts, but the remaining constraints, both hard and soft, are relaxed and penalised in the fitness function. The talk will start with a detailed description of the problem and the initial implementation and will go on to highlight the shortcomings of such an approach, in terms of the key element of balancing feasibility, i.e. covering the demand and work regulations, and quality, as measured by the nurses’ preferences. A series of experiments involving parameter adaptation, niching, intelligent weights, delta coding, local hill climbing, migration and special selection rules will then be outlined and it will be shown how a series of these enhancements were able to eradicate these difficulties. Results based on several months’ real data will be used to measure the impact of each modification, and to show that the final algorithm is able to compete with a tabu search approach currently employed at the hospital. The talk will conclude with some observations as to the overall quality of this approach to this and similar problems.

The RGBarrier assay: the parallel study of gene regulatory element performance at defined chromosomal locations

Vertebrate genomes are organised into a variety of nuclear environments and chromatin states that have profound effects on the regulation of gene transcription. This variation presents a major challenge to the expression of transgenes for experimental research, genetic therapies and the production of biopharmaceuticals. The majority of transgenes succumb to transcriptional silencing by their chromosomal environment when they are randomly integrated into the genome, a phenomenon known as chromosomal position effect (CPE). It is not always feasible to target transgene integration to transcriptionally permissive “safe harbour” loci that favour transgene expression, so there remains an unmet need to identify gene regulatory elements that can be added to transgenes which protect them against CPE. Dominant regulatory elements (DREs) with chromatin barrier (or boundary) activity have been shown to protect transgenes from CPE. The HS4 element from the chicken beta-globin locus and the A2UCOE element from a human housekeeping gene locus have been shown to function as DRE barriers in a wide variety of cell types and species. Despite rapid advances in the profiling of transcription factor binding, chromatin states and chromosomal looping interactions, progress towards functionally validating the many candidate barrier elements in vertebrates has been very slow. This is largely due to the lack of a tractable and efficient assay for chromatin barrier activity. In this study, I have developed the RGBarrier assay system to test the chromatin barrier activity of candidate DREs at pre-defined isogenic loci in human cells. The RGBarrier assay consists in a Flp-based RMCE reaction for the integration of an expression construct, carrying candidate DREs, in a pre-characterised chromosomal location. The RGBarrier system involves the tracking of red, green and blue fluorescent proteins by flow cytometry to monitor on-target versus off-target integration and transgene expression. The analysis of the reporter (GFP) expression for several weeks gives a measure of the protective ability of each candidate elements from chromosomal silencing. This assay can be scaled up to test tens of new putative barrier elements in the same chromosomal context in parallel. The defined chromosomal contexts of the RGBarrier assays will allow for detailed mechanistic studies of chromosomal silencing and DRE barrier element action. Understanding these mechanisms will be of paramount importance for the design of specific solutions for overcoming chromosomal silencing in specific transgenic applications.

An idiotypic immune network as a short-term learning architecture for mobile robots

A combined Short-Term Learning (STL) and Long-Term Learning (LTL) approach to solving mobile robot navigation problems is presented and tested in both real and simulated environments. The LTL consists of rapid simulations that use a Genetic Algorithm to derive diverse sets of behaviours. These sets are then transferred to an idiotypic Artificial Immune System (AIS), which forms the STL phase, and the system is said to be seeded. The combined LTL-STL approach is compared with using STL only, and with using a handdesigned controller. In addition, the STL phase is tested when the idiotypic mechanism is turned off. The results provide substantial evidence that the best option is the seeded idiotypic system, i.e. the architecture that merges LTL with an idiotypic AIS for the STL. They also show that structurally different environments can be used for the two phases without compromising transferability.

Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

BACKGROUND Integrons are found in hundreds of environmental bacterial species, but are mainly known as the agents responsible for the capture and spread of antibiotic-resistance determinants between Gram-negative pathogens. The SOS response is a regulatory network under control of the repressor protein LexA targeted at addressing DNA damage, thus promoting genetic variation in times of stress. We recently reported a direct link between the SOS response and the expression of integron integrases in Vibrio cholerae and a plasmid-borne class 1 mobile integron. SOS regulation enhances cassette swapping and capture in stressful conditions, while freezing the integron in steady environments. We conducted a systematic study of available integron integrase promoter sequences to analyze the extent of this relationship across the Bacteria domain. RESULTS Our results showed that LexA controls the expression of a large fraction of integron integrases by binding to Escherichia coli-like LexA binding sites. In addition, the results provide experimental validation of LexA control of the integrase gene for another Vibrio chromosomal integron and for a multiresistance plasmid harboring two integrons. There was a significant correlation between lack of LexA control and predicted inactivation of integrase genes, even though experimental evidence also indicates that LexA regulation may be lost to enhance expression of integron cassettes. CONCLUSIONS Ancestral-state reconstruction on an integron integrase phylogeny led us to conclude that the ancestral integron was already regulated by LexA. The data also indicated that SOS regulation has been actively preserved in mobile integrons and large chromosomal integrons, suggesting that unregulated integrase activity is selected against. Nonetheless, additional adaptations have probably arisen to cope with unregulated integrase activity. Identifying them may be fundamental in deciphering the uneven distribution of integrons in the Bacteria domain.

Genetic diversity of Mycobacterium avium isolates recovered from clinical samples and from the environment: molecular characterization for diagnostic purposes

Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR for detection of IS1245 and IS901, sequencing of the hsp65 gene, and pulsed-field gel electrophoresis) were evaluated. The same strain was found in all the environmental isolates, 21 out of 23 (91.3%) of the isolates cultured from urine samples, and 5 out of 19 (26.3%) isolates from respiratory specimens. This strain did not cause disease in the patients. Testing best characterized the strain as M. avium subsp. hominissuis, with the unusual feature that 81.4% of these isolates lacked the IS1245 element. Contamination of certain clinical samples with an environmental strain was the most likely event; therefore, characterization of the environmental mycobacteria present in health care facilities should be performed to discard false-positive isolations in nonsterile samples, mainly urine samples. Molecular techniques applied in this study demonstrated their usefulness for this purpose.

WIPO and the Reinforcement of the Nagoya Protocol: Towards Effective Implementation of an Access and Benefit Sharing Regime for the Protection of Traditional Knowledge Associated with Genetic Resources

Traditional knowledge associated with genetic resources (TKaGRs) is acknowledged as a valuable resource. Its value draws from economic, social, cultural, and innovative uses. This value places TK at the heart of competing interests as between indigenous peoples who hold it and depend on it for their survival, and profitable industries which seek to exploit it in the global market space. The latter group seek, inter alia, to advance and maintain their global competitiveness by exploiting TKaGRs leads in their research and development activities connected with modern innovation. Biopiracy remains an issue of central concern to the developing world and has emerged in this context as a label for the inequity arising from the misappropriation of TKaGRs located in the South by commercial interests usually located in the North. Significant attention and resources are being channeled at global efforts to design and implement effective protection mechanisms for TKaGRs against the incidence of biopiracy. The emergence and recent entry into force of the Nagoya Protocol offers the latest example of a concluded multilateral effort in this regard. The Nagoya Protocol, adopted on the platform of the Convention on Biological Diversity (CBD), establishes an open-ended international access and benefit sharing (ABS) regime which is comprised of the Protocol as well as several complementary instruments. By focusing on the trans-regime nature of biopiracy, this thesis argues that the intellectual property (IP) system forms a central part of the problem of biopiracy, and so too to the very efforts to implement solutions, including through the Nagoya Protocol. The ongoing related work within the World Intellectual Property Organization (WIPO), aimed at developing an international instrument (or a series of instruments) to address the effective protection of TK, constitutes an essential complementary process to the Nagoya Protocol, and, as such, forms a fundamental element within the Nagoya Protocol’s evolving ABS regime-complex. By adopting a third world approach to international law, this thesis draws central significance from its reconceptualization of biopiracy as a trans-regime concept. By construing the instrument(s) being negotiated within WIPO as forming a central component part of the Nagoya Protocol, this dissertation’s analysis highlights the importance of third world efforts to secure an IP-based reinforcement to the Protocol for the effective eradication of biopiracy.

Effect Of Platform Connection And Abutment Material On Stress Distribution In Single Anterior Implant-supported Restorations: A Nonlinear 3-dimensional Finite Element Analysis.

Although various abutment connections and materials have recently been introduced, insufficient data exist regarding the effect of stress distribution on their mechanical performance. The purpose of this study was to investigate the effect of different abutment materials and platform connections on stress distribution in single anterior implant-supported restorations with the finite element method. Nine experimental groups were modeled from the combination of 3 platform connections (external hexagon, internal hexagon, and Morse tapered) and 3 abutment materials (titanium, zirconia, and hybrid) as follows: external hexagon-titanium, external hexagon-zirconia, external hexagon-hybrid, internal hexagon-titanium, internal hexagon-zirconia, internal hexagon-hybrid, Morse tapered-titanium, Morse tapered-zirconia, and Morse tapered-hybrid. Finite element models consisted of a 4×13-mm implant, anatomic abutment, and lithium disilicate central incisor crown cemented over the abutment. The 49 N occlusal loading was applied in 6 steps to simulate the incisal guidance. Equivalent von Mises stress (σvM) was used for both the qualitative and quantitative evaluation of the implant and abutment in all the groups and the maximum (σmax) and minimum (σmin) principal stresses for the numerical comparison of the zirconia parts. The highest abutment σvM occurred in the Morse-tapered groups and the lowest in the external hexagon-hybrid, internal hexagon-titanium, and internal hexagon-hybrid groups. The σmax and σmin values were lower in the hybrid groups than in the zirconia groups. The stress distribution concentrated in the abutment-implant interface in all the groups, regardless of the platform connection or abutment material. The platform connection influenced the stress on abutments more than the abutment material. The stress values for implants were similar among different platform connections, but greater stress concentrations were observed in internal connections.

Genetic Aspects Of Athletic Performance: The African Runners Phenomenon.

The current dominance of African runners in long-distance running is an intriguing phenomenon that highlights the close relationship between genetics and physical performance. Many factors in the interesting interaction between genotype and phenotype (eg, high cardiorespiratory fitness, higher hemoglobin concentration, good metabolic efficiency, muscle fiber composition, enzyme profile, diet, altitude training, and psychological aspects) have been proposed in the attempt to explain the extraordinary success of these runners. Increasing evidence shows that genetics may be a determining factor in physical and athletic performance. But, could this also be true for African long-distance runners? Based on this question, this brief review proposed the role of genetic factors (mitochondrial deoxyribonucleic acid, the Y chromosome, and the angiotensin-converting enzyme and the alpha-actinin-3 genes) in the amazing athletic performance observed in African runners, especially the Kenyans and Ethiopians, despite their environmental constraints.

Genetic Predictors Of Long-term Response To Growth Hormone (gh) Therapy In Children With Gh Deficiency And Turner Syndrome: The Influence Of A Socs2 Polymorphism.

There is great interindividual variability in the response to GH therapy. Ascertaining genetic factors can improve the accuracy of growth response predictions. Suppressor of cytokine signaling (SOCS)-2 is an intracellular negative regulator of GH receptor (GHR) signaling. The objective of the study was to assess the influence of a SOCS2 polymorphism (rs3782415) and its interactive effect with GHR exon 3 and -202 A/C IGFBP3 (rs2854744) polymorphisms on adult height of patients treated with recombinant human GH (rhGH). Genotypes were correlated with adult height data of 65 Turner syndrome (TS) and 47 GH deficiency (GHD) patients treated with rhGH, by multiple linear regressions. Generalized multifactor dimensionality reduction was used to evaluate gene-gene interactions. Baseline clinical data were indistinguishable among patients with different genotypes. Adult height SD scores of patients with at least one SOCS2 single-nucleotide polymorphism rs3782415-C were 0.7 higher than those homozygous for the T allele (P < .001). SOCS2 (P = .003), GHR-exon 3 (P= .016) and -202 A/C IGFBP3 (P = .013) polymorphisms, together with clinical factors accounted for 58% of the variability in adult height and 82% of the total height SD score gain. Patients harboring any two negative genotypes in these three different loci (homozygosity for SOCS2 T allele; the GHR exon 3 full-length allele and/or the -202C-IGFBP3 allele) were more likely to achieve an adult height at the lower quartile (odds ratio of 13.3; 95% confidence interval of 3.2-54.2, P = .0001). The SOCS2 polymorphism (rs3782415) has an influence on the adult height of children with TS and GHD after long-term rhGH therapy. Polymorphisms located in GHR, IGFBP3, and SOCS2 loci have an influence on the growth outcomes of TS and GHD patients treated with rhGH. The use of these genetic markers could identify among rhGH-treated patients those who are genetically predisposed to have less favorable outcomes.

Transmission Of Intra-cellular Genetic Information: A System Proposal.

One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to DNA sequences. In this paper we propose a model of an intra-cellular transmission system of genetic information similar to a model of a power and bandwidth efficient digital communication system in order to identify a mathematical structure in DNA sequences where such sequences are biologically relevant. The model of a transmission system of genetic information is concerned with the identification, reproduction and mathematical classification of the nucleotide sequence of single stranded DNA by the genetic encoder. Hence, a genetic encoder is devised where labelings and cyclic codes are established. The establishment of the algebraic structure of the corresponding codes alphabets, mappings, labelings, primitive polynomials (p(x)) and code generator polynomials (g(x)) are quite important in characterizing error-correcting codes subclasses of G-linear codes. These latter codes are useful for the identification, reproduction and mathematical classification of DNA sequences. The characterization of this model may contribute to the development of a methodology that can be applied in mutational analysis and polymorphisms, production of new drugs and genetic improvement, among other things, resulting in the reduction of time and laboratory costs.