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Objectives. In parallel with the rising world population, consumption is increasing. Seafarers work intensively for the continuity of consumption. Vessel crew work under contract for specific periods. When the contract ends, new personnel join the ship while others leave. Personnel are transferred to the ship’s location by plane for the change. During this flight, seafarers are exposed to rapid time zone changes that affect their circadian rhythms. This situation causes jet lag disorder, which is a sub-factor of fatigue. It is known that ship personnel sometimes board vessels without giving them a rest period when they arrive at the destination port by plane and quickly start operations under their duties and responsibilities. Seafarers can participate in risky operations without realizing that they are under the effect of jet lag. Methods. In this study, data were obtained by applying a survey to 114 seafarers. A jet lag disorder that may occur while the seafarers’ join the ship was analyzed with an independent-sample t test using SPSS version 23. Results and Conclusion. There was a positive relationship between the seafarers’ work performance at the time they joined the ship and the duration they stayed at the hotel. [ABSTRACT FROM AUTHOR]

IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member—Tn630-NC1 and the closest homolog of IS630 from viruses—Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field. [ABSTRACT FROM AUTHOR]

Abstract IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member—Tn630-NC1 and the closest homolog of IS630 from viruses—Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field.

BackgroundThe average sleep quality of mariners during ocean voyages is notably worse than that of the general populace, and the incidence of sleep disorders among them is higher. Sleep disorders closely associate with fatigue and cognitive decline, increasing error and accident rates, and are a major safety hazard in marine navigation. At present, research on factors influencing the sleep quality of mariners during ocean voyages in China is limited and needs further investigation. ObjectiveTo investigate the sleep quality of mariners during ocean voyages and analyze its influencing factors, in order to provide reference for constructing sleep intervention plans and mitigating their sleep disorders. MethodsUsing convenience cluster sampling, a questionnaire survey was carried out in 408 crew members of a fleet who returned from a voyage on March 21, 2024. The questionnaires included a general information questionnaire, Pittsburgh Sleep Quality Index (PSQI) , and Self Rating Anxiety Scale (SAS), and the data were analyzed by SPSS 26.0 software. ResultsA total of 399 valid questionnaires were collected, with an effective recovery rate of 97.8%. The mean score of PSQI for the mariners during ocean voyages was (6.41±2.44), with 33.6% (134/399) of the mariners reporting sleep disorders. The PSQI scores varied by family structures (t=2.235, P=0.031), labor types (F=3.789, P=0.023), noise exposure (F=53.218, P＜0.001), dietary patterns (F=63.311, P＜0.001), exercise habits (F=16.416, P＜0.001), and anxiety states (t=5.963,P＜0.001). The results of linear regression showed that incomplete family structure (β=0.102, P=0.010), noise exposure (β=0.323, P

Maritime autonomous surface ships (MASS) are transforming the future of maritime transport. They are expected to shoulder important roles in seaborne trade and maritime resilience. As the primary operator of traditional ships and a significant component of maritime transport, seafarers are inevitably directly and indirectly affected by levels of automation introduced into the shipping space. Therefore, in addition to increasing attention to automated system designs, a holistic understanding of human elements in MASS operations is necessary. The current research (1) reviews human-centred MASS research, (2) categorises MASS impacts on seafarers, and (3) summarises responses to prepare seafarers for this emerging technology. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, a total of 101 articles were collected from Scopus. The systematic review reveals that MASS impacts seafarers from the following dimensions: employment, task contents, requisite skills, and human risks. Moreover, regulations and education frameworks can be adapted to respond to changes in seafarer demand and supply. Future research directions are also proposed and can serve as recommendations for future human-centred research on MASS. The research findings enhance the understanding of seafarer elements in MASS operations and provide policy implications for future seafarer management. [ABSTRACT FROM AUTHOR]

This paper scrutinizes the cultural strangeness of Coleridge's line "Instead of the cross, the Albatross about my neck was hung", arguing that the image of the bird hung around the Mariner's neck is borrowed from Holy Quran. The paper provides a close reading of the line under discussion while associating it with the Quranic verse 13 of Chapter 17 (al-isrāʼ; meaning: The Night Journey), which declares that a bird is bound to the neck of every single human. The paper concludes that the image of the Albatross hung around the Mariner's neck testifies to the heavy influence of Holy Quran on Coleridge's poetry, which complies with Coleridge's statement that he will never forget Mohammad the Prophet. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are abundant in genomes. Their mobilization can lead to genetic variability that is useful for evolution, but can also have deleterious biological effects. Somatic mobilization (SM) has been linked to degenerative diseases, such as Alzheimer's disease and cancer. We used a Drosophila simulans strain, in which SM can be measured by counting red spots in the eyes, to investigate how chemotherapeutic agents affect expression and SM of the mariner TE. Flies were treated with Cisplatin, Dacarbazine, and Daunorubicin. After acute exposure, relative expression of mariner was quantified by RT-qPCR and oxidative stress was measured by biochemical assays. Exposure to 50 and 100 µg/mL Cisplatin increased mariner expression and ROS levels; catalase activity increased at 100 µg/mL. With chronic exposure, the number of spots also increased, indicating higher mariner SM. Dacarbazine (50 and 100 µg/mL) did not significantly alter mariner expression or mobilization or ROS levels, but decreased catalase activity (100 µg/mL). Daunorubicin (25 and 50 µM) increased mariner expression, but decreased mariner SM. ROS and catalase activity were also reduced. Our data suggest that stress factors may differentially affect the expression and SM of TEs. The increase in mariner transposase gene expression is necessary, but not sufficient for mariner SM. [ABSTRACT FROM AUTHOR]

Abstract Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

The maritime industry is vital to international trade, however, it also poses inimitable challenges to the health and well-being of mariners. Long voyages at sea might make it grim to receive high-quality healthcare. This is a descriptive study that highlights the use of ChatGPT in providing healthcare amenities to mariners. AI technologies can revolutionize maritime healthcare to tackle this issue. ChatGPT, a state-of-the-art AI system developed by OpenAI can provide valuable support for the health and welfare of seafarers'. By harnessing the extensive expertise and conversational capacities of ChatGPT, maritime industries can provide personalized and prompt healthcare services to their stakeholders. This research work will highlight how ChatGPT-powered healthcare services can boost the health and well-being of seafarers. ChatGPT has the potential to revolutionize the marine sector by enabling virtual consultations with healthcare professionals for the analysis of health data. The assimilation of ChatGPT technology into maritime healthcare has the potential to revolutionize the way seafarers receive care and support. Certainly, some challenges need to be taken into consideration. [ABSTRACT FROM AUTHOR]

Simple Summary: Transposable elements are capable of promoting somatic mobilization, and this may potentially have biological consequences. However, the rate of somatic mobilization is poorly known. The mariner element causes somatic mobilization in Drosophila simulans. We used an assay based on sequencing of the flanking mariner region and developed a pipeline to identify new mariner insertions in D. simulans. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had approximately 300 new somatic insertions during fly development (eggs to adult). We show that the rate of somatic insertion of the mariner element in D. simulans is high. Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequencing of the mariner flanking region and developed a pipeline to identify novel mariner insertions in Drosophila simulans at 20 and 28 °C. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had an average of 236.4 (±99.3) to 279 (±107.7) new somatic insertions at 20 °C and an average of 172.7 (±95.3) to 252.6 (±67.3) at 28 °C. In addition, we detected fragments containing mariner and others without mariner in the same regions with low-coverage long-read sequencing, indicating the process of excision and insertion. In conclusion, a low number of autonomous copies of the mariner transposon can promote a high rate of new somatic insertions during the developmental stages of Drosophila. Additionally, the developed method seems to be sensitive and adequate for the verification and estimation of somatic insertion. [ABSTRACT FROM AUTHOR]

OBJECTIVES: Maritime workers may be exposed to several occupational hazards at sea. The aim of this study was to assess cancer incidence among seafarers and fishermen in the Nordic countries and identify patterns in morbidity in the context of existing studies in this field. METHODS: A cohort of 81 740 male seafarers and 66 926 male fishermen was established from census data on 15 million citizens in the five Nordic countries. Using personal identity codes, information on vital status and cancer was linked to members of the cohort from the national population and cancer registries for the follow-up period 1961–2005. Standardized incidence ratios (SIR) were calculated applying national cancer incidence rates for each country and pooling results. RESULTS: The overall incidence of cancer was increased among the male seafarers [SIR 1.22, 95% confidence interval (CI) 1.19–1.23]. Significant excesses were observed for multiple cancer sites among the seafarers, while results for the fishermen were mixed. Lip cancer incidence was increased among both maritime populations. For mesothelioma (SIR 2.17, 95% CI 1.83–2.56 seafarers) and non-melanoma skin cancer (SIR 1.23, 95% CI 1.14–1.32 seafarers), incidence was increased among the seafarers. CONCLUSION: In our cohort, seafaring was associated with a higher overall incidence of cancer compared to the general population. While the majority of cancers could not be linked to specific occupational factors, increases in mesothelioma, lip and non-melanoma-skin cancer indicate previous exposure to asbestos, ultraviolet radiation and potentially also chemicals with dermal carcinogenic properties at sea.

Abstract Background Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed. Results Fourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5′ and 3′ untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b. Conclusion Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequencing of the mariner flanking region and developed a pipeline to identify novel mariner insertions in Drosophila simulans at 20 and 28 °C. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had an average of 236.4 (±99.3) to 279 (±107.7) new somatic insertions at 20 °C and an average of 172.7 (±95.3) to 252.6 (±67.3) at 28 °C. In addition, we detected fragments containing mariner and others without mariner in the same regions with low-coverage long-read sequencing, indicating the process of excision and insertion. In conclusion, a low number of autonomous copies of the mariner transposon can promote a high rate of new somatic insertions during the developmental stages of Drosophila. Additionally, the developed method seems to be sensitive and adequate for the verification and estimation of somatic insertion.

Purpose: The aim of this study was to investigate whether Swedish seafarers have increased mortality from cardiovascular disease compared with the general population. Methods: Register-based longitudinal cohort study of 85,169 Swedish seafarers where all subjects with a minimum of 30 days service registered in the Seafarers' Register 1985–2013 were included. Mortality from coronary heart disease, cerebrovascular disease and total mortality for comparison were analysed by calculating standardised mortality ratios (SMRs), with 95% confidence intervals (CIs). Mortality was further analysed by gender, duty on board, type of vessel, and over time. Results: There was no increase in either mortality from cardiovascular disease or total mortality for seafarers, who had worked solely on passenger ferries. Mortality from coronary heart disease and cerebrovascular disease was increased for male seafarers < 46 years old who had worked on different types of vessels, SMR 1.48 (95% CI 1.06–2.01) and SMR 1.93 (95% CI 1.16–3.02), respectively. Analysing the seafarers by duty showed significantly increased SMRs from coronary heart disease in males aged < 46 of the categories "deck crew" and "engine officer/crew (ever)". The total mortality for seafarers who had worked on different types of vessels was increased; males SMR 1.05 (95% CI 1.02–1.09) and females SMR 1.17 (95% CI 1.04–1.30), but decreased over time. Conclusions: No increased mortality on passenger ferries but younger male seafarers on different types of vessels had increased mortality from cardiovascular disease. Reduction of hazardous occupational exposures onboard is important, such as shift work, stress and noise. [ABSTRACT FROM AUTHOR]

Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed ‘cross-hybridization’, as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries.

Abstract Background Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses. Results galluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros). The copy number ranged from 5 to 10,158, in the genomes of C. japonica and G. gallus respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the G. gallus and M. gallopavo genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that galluhop homolog sequences form a new mariner subfamily, which we termed Gallus. Inter-species and intragenomic galluhop distance analyses indicated a high identity between the consensus of B. rhinoceros and the other 5 related species, and different emergence ages of the element between the Galliformes species and B. rhinocerus, suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species. Conclusions Overall, our results showed that mariner elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of G. gallus and M. gallopavo. In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new mariner family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a galluhop element occurred between Galliformes and Buceritiformes.

Objective: Describe health conditions and injury and illness rates in a population of United States mariners, an understudied workforce vital to economic security. Methods: In this survey study, mariner health data was collected and analyzed to provide injury and illness rates (including mental health conditions) and associated risk factors. Results: In this mariner population of highly tenured vessel masters and pilots, hypertension, obesity, sleep disorders, smoking, alcohol consumption, and symptoms of depression and anxiety were common. BMI ≥35 was associated with increased likelihood of work injury (OR 5.7; 95%CI 1.01, 32.59). Conclusions: The mariners were in poor overall health, raising public health and safety concerns in this population of essential transportation workers. Follow-up studies including a wider distribution of domestic mariners (deck hands, engineers) would further characterize occupational risks. [ABSTRACT FROM AUTHOR]

Standard econometric filters fail to extract explicit trend component from macroeconomic data series. Isolated cycles provide no economic interpretation of the extracted component. Adding new data to the sample (filtering) period results in instability of extracted components. This study proposes a new econometric filtering technique (MARINER) able to overcome known shortcomings in standard econometrics filters such as Hodrick and Prescott (1997), Baxter and King (1999), Christiano and Fitzgerald (2003). MARINER provides a practical tool for policy makers dealing with business cycles. It also provides economic interpretation (new theory) on causes and sources of business cycles elaborating on theories developed by Phillips (1962) and Škare (2010). MARINER decomposes GDP macroeconomic data series in trend (long term) and cycles (medium term) components using three year moving average recursive filtering method. Extracted cycles are defined as deviations from equilibrium GDP path (minimized output gap) caused by poor synchronization between monetary and fiscal policy. MARINER bridge the gap in the literature on measuring and causes of business cycles. MARINER can purpose as foundation for building a new, primer econometric filtering methods.

Background: Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses. Results: galluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros). The copy number ranged from 5 to 10,158, in the genomes of C. japonica and G. gallus respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the G. gallus and M. gallopavo genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that galluhop homolog sequences form a new mariner subfamily, which we termed Gallus. Inter-species and intragenomic galluhop distance analyses indicated a high identity between the consensus of B. rhinoceros and the other 5 related species, and different emergence ages of the element between the Galliformes species and B. rhinocerus, suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species. Conclusions: Overall, our results showed that mariner elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of G. gallus and M. gallopavo. In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new mariner family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a galluhop element occurred between Galliformes and Buceritiformes. [ABSTRACT FROM AUTHOR]

During colonization of new areas, natural populations have to deal with changing environments, and transposable elements ( TEs) can be useful 'tools' in the adaptation process as they are major contributor to the structural and functional evolution of genomes. In this general context, the activity (copy number, transcriptional and excision rate) of the mariner mos1 element was estimated in 19 natural populations of D. simulans. It is shown (i) that mos1 expression is always higher and more variable in testes than in ovaries; (ii) that mos1 activity is higher in colonizing populations compared to the sub-Saharan African ones (ancestral populations); (iii) that mos1 variations in transcript levels and copy number are negatively correlated with transcriptional variations of pi RNA genes, aubergine and argonaute3. Furthermore, mos1 levels of expression in testes highly contrast with the low expression patterns of ago3. These results strongly suggest that the expression polymorphism of pi RNA genes could be responsible for the mos1 variations, first between male and female germlines and second, according to the status of natural populations (colonizing or not). These results provide new perspectives about TEs and pi RNA genes co-evolution in Drosophila germlines. [ABSTRACT FROM AUTHOR]

Standard econometric filters fail to extract explicit trend component from macroeconomic data series. Isolated cycles provide no economic interpretation of the extracted component. Adding new data to the sample (filtering) period results in instability of extracted components. This study proposes a new econometric filtering technique (MARINER) able to overcome known shortcomings in standard econometrics filters such as Hodrick and Prescott (1997), Baxter and King (1999), Christiano and Fitzgerald (2003). MARINER provides a practical tool for policy makers dealing with business cycles. It also provides economic interpretation (new theory) on causes and sources of business cycles elaborating on theories developed by Phillips (1962) and Škare (2010). MARINER decomposes GDP macroeconomic data series in trend (long term) and cycles (medium term) components using three year moving average recursive filtering method. Extracted cycles are defined as deviations from equilibrium GDP path (minimized output gap) caused by poor synchronization between monetary and fiscal policy. MARINER bridge the gap in the literature on measuring and causes of business cycles. MARINER can purpose as foundation for building a new, primer econometric filtering methods. [ABSTRACT FROM AUTHOR]

Transposable elements are DNA sequences present in all the large phylogenetic groups, both capable of changing position within the genome and constituting a significant part of eukaryotic genomes. The mariner family of transposons is one of the few which occurs in a wide variety of taxonomic groups, including freshwater planarians. Nevertheless, so far only five planarian species have been reported to carry mariner-like elements (MLEs), although several different species have been investigated. Regarding the number of copies of MLEs, Girardia tigrina is the only planarian species in which this has been evaluated, with an estimation of 8,000 copies of the element per haploid genome. Preliminary results obtained in our laboratory demonstrated that MLE is found in a large number of different species of planarians, including terrestrial. With this in mind, the aim was to evaluate the occurrence and estimate the number of MLE copies in different planarian species collected in south Brazil. Twenty-eight individuals from 15 planarian species were analyzed. By using PCR and the hybridization of nucleic acids, it was found that MLE was present in all the analyzed species, the number of copies being high, probably over 10³ per haploid genome.

Background: The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species. Results: Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome. Conclusion: These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome. [ABSTRACT FROM AUTHOR]

The Ancient Mariner is unlike other conventional ballads because its focus is not an event but rather the symbolism that derives from an event. It describes a voyage into the interior spaces of the poetic self, whose potentialities are limitless. The poetic self emerges after the Mariner undergoes a process of transformation. The tension in the poem exists between the familiar self and the imaginative, creative self. Coleridge uses various images that correspond to the purpose of the voyage. The poet suffers from a deep spiritual crisis that demands the use of a symbolic language. The use of such language, in turn, requires a symbolic reading of the poem to capture the significance of its events. Otherwise, important events simply appear to be strange, inconsistent, or incoherent. The symbols that are used in the poem are both traditional and personal, in the sense of being unique to Coleridge. Despite the range of images and symbols that are used in the poem, they are merged into a consistent whole. [ABSTRACT FROM AUTHOR]

In their metaphoric implication, the Mariner and Wedding-Guest represent binary opposition shedding light on all human relatedness. They represent the two aspects constituents of the very paradox of cosmic realities. Sharing within the ambit of two different spheres of life, the Wedding-Guest's world is of formal duties and stereotyped values, while the Mariner is though in this world but somehow not of this world. But they are mutually indispensable for each other. From the beginning the movement of both is towards a convergent point of resolution of some deep crisis. The fear of, protest against, and disagreement with the "other" are shown vehemently in the initial course of discourse or dialogue, but both need a settlement for a mutual benefit. The Wedding-Guest's protestations are all humanly understandable. No one willingly wants to face the shadowy side of life as it would be too horrible to face. But the "other" cannot sustain his/her intransigence for long as the Wedding-Guest has to listen passively to the Mariner like "a three years' child," "sat on a stone," and finally "cannot choose but hear." [ABSTRACT FROM AUTHOR]

Bacteroides is one of the most predominant groups of human gut microbiota. Recent metagenomic analyses and studies on gnotobiotic mice demonstrated the tight association of Bacteroides with epithelial function, the gut immune system and systemic metabolism in the host. The mariner family transposon shows relatively low target site specificity and has hosts ranging from prokaryotes to eukaryotes. Thereby, random mutagenesis using the mariner family transposon is expected to identify key molecules for human- Bacteroides symbiosis. In this study, we constructed the plasmid pMI07 to deliver the gene cassette ( ermF/ITR), which harbors the erythromycin resistant marker ( ermF) and the inverted repeat sequences (ITRs) recognized by Himar1 transposase, to Bacteroides via electrotransformation. pMI07 successfully delivered ermF/ITR to the Bacteroides genomes and generated thousands of insertion mutants/μg of pMI07 in B. thetaiotaomicron, B. fragilis, B. ovatus, and also, although to a lesser extent, B. vulgatus. Analyses of the ermF/ITR insertion sites in B. thetaiotaomicron and B. vulgatus revealed that the cassette targeted the dinucleotide TA and integrated into the genomes in an unbiased manner. The data reported here will provide useful information for transposon mutagenesis in Bacteroides species, which will enable identification of the genes responsible for their unique phenotypes. [ABSTRACT FROM AUTHOR]

Background: Transposon-mediated transgenesis is an excellent method for creating stable transgenic lines and insertional mutants. In the chordate Ciona intestinalis, Minos is the only transposon that has been used as the tool for germline transformation. Adding another transposon system in this organism enables us to conduct genetic techniques which can only be realized with the use of two transposons. Results: In the present study, we found that another Tc1/ mariner superfamily transposon, sleeping beauty (SB), retains sufficient activity for germline transformation of C. intestinalis. SB shows efficiencies of germline transformation, insertion into gene coding regions, and enhancer detection comparable to those of Minos. We have developed a system for the remobilization of SB copies in the C. intestinalis genome by using transgenic lines expressing SB transposase in the germ cells. With this system, we examined the manner of SB mobilization in the C. intestinalis genome. SB shows intrachromosomal transposition more frequently than Minos. Conclusions: SB-based germline transformation and the establishment of a new method that uses its frequent intrachromosomal transposition will result in breakthroughs in genetic approaches that use C. intestinalis together with Minos. Developmental Dynamics 242:30-43, 2013. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We analyze here the presence and abundance of three types of transposable elements (TEs), i.e. Gypsy, RTE and Mariner, in the genome of the grasshopper Eyprepocnemis plorans. PCR experiments allowed amplification, cloning and sequencing of these elements ( EploGypI, EploRTE5, EploMar20) from the E. plorans genome. Fluorescent in situ hybridization (FISH) showed that all three elements are restricted to euchromatic regions, thus being absent from the pericentromeric region of all A chromosomes, which contain a satellite DNA (satDNA) and ribosomal DNA (rDNA), and being very scarce in B chromosomes mostly made up of these two types of repetitive DNA. FISH suggested that EploGypI is the most abundant and EploMar20 is the least abundant, with EploRTE5 showing intermediate abundance. An estimation of copy number, by means of quantitative PCR, showed that EploGypI is, by far, the most abundant element, followed by EploRTE5 and EploMar20, in consistency with FISH results. RNA isolation and PCR experiments on complementary DNA (cDNA) showed the presence of transcripts for the three TE elements. The implications of the preferential location of these TE elements into euchromatin, the significance of TE abundance in the giant genome of this species, and a possible relationship between TEs and B chromosome mutability, are discussed. [ABSTRACT FROM AUTHOR]

Background: Active transposable elements (TEs) can be passed between genomes of different species by horizontal transfer (HT). This may help them to avoid vertical extinction due to elimination by natural selection or silencing. HT is relatively frequent within eukaryotic taxa, but rare between distant species. Findings: Closely related Mariner-type DNA transposon families, collectively named as Mariner-1_Tbel families, are present in the genomes of two ants and two mammalian genomes. Consensus sequences of the four families show pairwise identities greater than 95%. In addition, mammalian Mariner1_BT family shows a close evolutionary relationship with some insect Mariner families. Mammalian Mariner1_BT type sequences are present only in species from three groups including ruminants, tooth whales (Odontoceti), and New World leaf-nosed bats (Phyllostomidae). Conclusions: Horizontal transfer accounts for the presence of Mariner_Tbel and Mariner1_BT families in mammals. Mariner_Tbel family was introduced into hedgehog and tree shrew genomes approximately 100 to 69 million years ago (MYA). Most likely, these TE families were transferred from insects to mammals, but details of the transfer remain unknown. [ABSTRACT FROM AUTHOR]

Almost half the human genome consists of mobile DNA elements, and their analysis is a vital part of understanding the human genome as a whole. Many of these elements are ancient and have persisted in the genome for tens or hundreds of millions of years, providing a window into the evolution of modern mammals. The Golem family have been used as model transposons to highlight computational analyses which can be used to investigate these elements, particularly the use of molecular dating with large transposon families. Whole-genome searches found Golem sequences in 20 mammalian species. Golem A and B subsequences were only found in primates and squirrel. Interestingly, the full-length Golem, found as a few copies in many mammalian genomes, was found abundantly in horse. A phylogenetic profile suggested that Golem originated after the eutherian-metatherian divergence and that the A and B subfamilies originated at a much later date. Molecular dating based on sequence diversity suggests an early age, of 175 Mya, for the origin of the family and that the A and B lineages originated much earlier than expected from their current taxonomic distribution and have subsequently been lost in some lineages. Using publically available data, it is possible to investigate the evolutionary history of transposon families. Determining in which organisms a transposon can be found is often used to date the origin and expansion of the families. However, in this analysis, molecular dating, commonly used for determining the age of gene sequences, has been used, reducing the likelihood of errors from deleted lineages. [ABSTRACT FROM AUTHOR]

Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism (ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets of TE insertions specific to Beta and Patellifolia. [ABSTRACT FROM AUTHOR]

The Hessian fly ( Mayetiola destructor) is an agriculturally important pest of wheat. A mariner element ( Desmar1) has been previously identified in the Hessian fly genome. Using Desmar1 as a probe, we isolated individual copies of Desmar-like elements from the Hessian fly genome cloned in bacterial artificial chromosomes (BACs) and studied their structural variability and flanking DNA sequences. The partial Desmar-like copies are relatively more abundant (∼64%) than full length copies (∼36%) in the Hessian fly genome. Most of the full length copies are consistently flanked by an EcoRI restriction site that occurs 32 bp from one end and 66 bp from the other end of the mariner. Using an amplified fragment length polymorphism-PCR (AFLP-PCR) based method, we identified segregating polymorphisms associated with Desmar elements in a F mapping population. We were able to use the segregation data to localize the chromosomal position of three Desmar elements by linkage analysis. As paternal chromosomes are eliminated in the Hessian fly during early embryogenesis, two-thirds of the AFLPs were expected to be polymorphic in the mapping population and this was observed for AFLPs anchored to full length Desmar copies but not to the partial copies. Thus, our data indicate that dead and partial Desmar-like copies are probably associated with less polymorphic regions and may represent mariner graveyards in the Hessian fly genome. [ABSTRACT FROM AUTHOR]

Abstract: Subtelomeric secondary metabolite (SM) gene clusters are frequently surrounded by DNA repeats and transposon-like elements. The Aspergillus nidulans penicillin cluster, 30kb from the telomere of chromosome VI, is bordered by such elements. Deletions of penicillin telomere proximal and distal border regions resulted in decreased penicillin production. A 3.7kb distal region called PbIa, consisting of the putative transposable element DNA-2, was examined further where its replacement by a pyrG marker presented a similar phenotype as loss of the global SM regulator LaeA, resulting in a decrease in penicillin gene expression and product formation. In contrast, placement of the pyrG marker on either side of PbIa had no effect on penicillin synthesis. A requirement for PbIa in penicillin production was also apparent in a histone deacetylase mutant, ΔhdaA, enhanced for penicillin production. Trans-complementation of the PbIa element near and within the terrequinone A cluster on chromosome V did not restore penicillin biosynthesis or increase production of terrequinone A. Taken together, this data provides evidence for transposon involvement in SM cluster regulation. [Copyright &y& Elsevier]

Mariners are small DNA mediated transposons of eukaryotes that fortuitously function in bacteria. Using bacterial genetics, it is possible to study a variety of properties of mariners, including transpositional ability, dominant-negative regulation, overexpresson inhibition, and the function of cis-acting sequences like the inverted terminal repeats. In conjunction with biochemical techniques, the structure of the transposase can be elucidated and the activity of the elements can be improved for genetic tool use. Finally, it is possible to uncover functional transposase genes directly from genomes given a suitable bacterial genetic screen. [ABSTRACT FROM AUTHOR]

The mariner-like transposon Mos1 is used for insertional mutagenesis and transgenesis in different animals (insects, nematodes), but has never been used in plants. In this paper, the transposition activity of Mos1 was tested in Nicotiana tabacum, but no transposition event was detected. In an attempt to understand the absence of in planta transposition, Mos1 transposase (MOS1) was produced and purified from transgenic tobacco (HM NtMOS1). HM NtMOS1 was able to perform all transposition reaction steps in vitro: binding to ITR, excision and integration of the same pseudo-transposon used in in planta transposition assays. The in vitro transposition reaction was not inhibited by tobacco nuclear proteins, and did not depend on the temperature used for plant growth. Several hypotheses are proposed that could explain the inhibition of HM NtMOS1 activity in planta. [ABSTRACT FROM AUTHOR]

Protozoan parasites affect millions of people around the world. Treatment and control of these diseases are complicated partly due to the intricate biology of these organisms. The interactions of species of Plasmodium, Leishmania and trypanosomes with their hosts are mediated by an unusual control of gene expression that is not fully understood. The availability of the genome sequence of these protozoa sets the stage for using more comprehensive, genome-wide strategies to study gene function. Transposons are effective tools for the systematic introduction of genetic alterations and different transposition systems have been adapted to study gene function in these human pathogens. A mariner transposon toolkit for use in vivo or in vitro in Leishmania parasites has been developed and can be used in a variety of applications. These modified mariner elements not only permit the inactivation of genes, but also mediate the rescue of translational gene fusions, bringing a major contribution to the investigation of Leishmania gene function. The piggyBac and Tn5 transposons have also been shown to mobilize across Plasmodium spp. genomes circumventing the current limitations in the genetic manipulation of these organisms. [ABSTRACT FROM AUTHOR]