Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Silencing of Mu Transposable Elements in Maize

Transposable genetic elements interact with specific DNA-binding proteins to facilitate their excision from the chromosome and their integration elsewhere. Autonomous transposons carry genes that encode some of these proteins, and so provide the trans -acting functions, such as transposase, required for their own transposition and that of related non-autonomous elements. Transposons are frequently subject to epigenetic regulation and share many of the properties associated with chromosomal genes that are epigenetically regulated: They are found in multiple copies; they are integrated at diverse sites and are often subject to position effects; they sometimes encode multivalent DNA-binding proteins that can alter chromatin structure; and they are often subject to DNA methylation. It is possible that some epigenetic mechanisms of gene regulation evolved as a means of controlling transposons and viruses that were otherwise capable of widespread integration throughout the genome (for review, see Martienssen and Richards 1995). Epigenetic regulation of transposons can be monitored in vivo because the expression of chromosomal genes disrupted by transposon insertion is influenced by transposase in two different ways. (1) Transposon excision depends on transposase and often restores wild-type chromosomal gene expression. (2) Transposons inserted in regulatory regions of some genes interact with transposase, resulting in alterations in chromosomal gene expression without transposon excision (McClintock 1965b; Peterson 1966; Rutledge et al. 1988; Boeke 1989; Robertson and Engels 1989; Gierl 1990; Corces and Geyer 1991). These regulatory interactions are particularly convenient assays for transposon activity, because they affect gene expression in a uniform fashion without relying on occasional transposon.
PLANT BASED QUORUM SENSING INHIBITORS OF PSEUDOMONAS AERUGINOSA

Phytochemical research has gained a lot of momentum in the medical field for the discovery of new, safe, and effective remedies. In the context of antimicrobial research, various plant sources have been discovered with the potential to disrupt bacterial quorum sensing (QS), which plays a key role in the regulation of virulence in many Gram positive and Gram negative bacteria. Pseudomonas aeruginosa , a Gram negative bacterium, is known to produce multiple QS systems that control the expression of virulence determinants and biofilm development in this pathogen. Hence, the inhibition of QS has been pursued as a promising therapy for treatment of drug resistant Pseudomonas infections. A comprehensive review of the research data available for plant products as QS inhibitors of the organism has been presented here, while further suggesting the future prospects for these inhibitors.
Integrating pelagic and coastal MPAs into large‐scale ecosystem‐wide management

Marine Protected Areas (MPAs) have gained increasing popularity worldwide as tools for biodiversity conservation and management of human uses. This rise in popularity has been accompanied by an increasing body of scientific papers and books on MPA design and management, the vast majority of which are almost completely focused on coastal or insular MPAs. A small number of MPAs have also been established in the pelagic domain, however, these pelagic sites have been considered in isolation from coastal/insular MPAs, even when the sites are adjacent or nearby. Pelagic and coastal ecosystems are not at all isolated from each other, but interconnected both physically via the flow of water, and biologically, via the movement of organisms. In order to maximize the effectiveness of MPAs, it is suggested that spatial management planning encompass large areas that span both coastal and pelagic domains. This requires integrated, large-scale spatial management, which may extend across borders and thus require international cooperation. Copyright © 2012 John Wiley & Sons, Ltd.
Snakes of Sulawesi: checklist, key and additional Biogeographical remarks

A checklist with concise synonymy and a key to the snakes of Sulawesi is presented, comprising 63 species in 38 genera; 3 subspecies and 15 species, of which one constitutes a monotypic genus, are considered endemic. There is a strong Indo-Malayan relationship. Sea-snakes and Candoia carinata excluded, no Philippine, Papuan or Australian affinities were found. Geological and ecological barriers, together with a low immigration pressure from the south and east, are considered causal factors. Although Sulawesi has been an instable island region at least since the Late Cretaceous as compared with most surrounding islands, which were parts of Sundaland or Sahulland and as such were formed relatively recently, the species richness in Wallacea is of the same order as in the neighbouring islands and more dependent of the Asian relationships of the snakes and the present day distance from landmasses.
Screening of protease and cellulase producing Bacillus subtilis Natto strain and its growth characteristics.

According to the biological qualification of hydrolysised casein and CMC of Bacillus subtilis Natto,10 strains were screened by pour plate method from their parent strains of Bacillus subtilis natto NB-1 and NR-1.The strain named NY-3 was selected with higher protease activity and cellulase activity through the test of protease activity and cellulase activity in 48 h fermenting medium among 10 strains.Further research of its growth characteristics showed that the best time of inoculation and fermentation were 14 and 48 h,respectively.
3 Assembly of Pre-replication Complexes

DNA replication is tightly regulated such that each daughter cell receives exactly one copy of the parental cell’s DNA content upon cell division. Disturbing this controlled series of events can lead to genomic instability—a hallmark of cancer—and understanding the mechanism and regulation of DNA replication therefore becomes essential. Not surprisingly, the cell has developed intricate mechanisms and regulatory networks to guarantee the complete and accurate duplication of the genome. These mechanisms ensure that the DNA is replicated exactly once per cell cycle and that DNA replication is arrested in response to DNA damage and other replication stresses (e.g., low nucleotide levels). In many instances, the target of these regulatory mechanisms is a key intermediate in the initiation of DNA replication called the pre-replication complex (pre-RC). The pre-RC is a multiprotein assembly that forms at all potential origins of replication. Originally identified on the basis of in vivo DNase I protection assays (Diffley et al. 1994), pre-RC formation requires at least four different proteins: the origin recognition complex (ORC), Cdc6, Cdt1, and the Mcm2-7 complex. Consistent with the central role of the pre-RC, the steps involved in its formation and the proteins involved are conserved across eukaryotic organisms (see Appendix, Table III). Formation of the pre-RC is initiated by the recognition of the origin DNA by ORC. ORC then recruits Cdc6, Cdt1, and the Mcm2-7 complex to the origin. After all of these proteins are present at the origin, a series of ATP-dependent events results in the loading of.
DIAGNOSING PARELAPHOSTRONGYLOSIS IN MOOSE (ALCES ALCES)

Thirty-six moose (Alces alces) reported as acting abnormally were examined in north- western Ontario and adjacent northeastern Minnesota in 1986 - 2000. Thirty-four typically had little fear of humans, remained in an area for some time, and showed clinical signs of neuromotor inco- RUGLQDWLRQLQFOXGLQJZDONLQJLQFLUFOHV��VKRZLQJZHDNQHVVDQGG
Horizontal gene transfer in the evolution of pathogenesis

Part I. Theoretical Considerations on the Evolution of Bacterial Pathogens: 1. Genomes in motion - gene transfer as a catalyst for genome change Jeffrey G. Lawrence and Heather Hendrickson 2. Bacterial recombination in vivo Xavier Didelot and Daniel Falush Part II. Mobile Genetic Elements in Bacterial Evolution: 3. Phage-bacterium co-evolution and its implication for bacterial pathogenesis Harald Brussow 4. Phage conversion - driving forces in the development and spread of bacterial pathogens Roger W. Hendrix and Sherwood R. Casjens 5. Genomic islands in the bacterial chromosome - paradigms of microevolution in quantum leaps Tobias Olschlager and Jorg Hacker Part III. Paradigms of Bacterial Evolution: 6. Genomic islands in plant-pathogenic bacteria Dawn L. Arnold and Robert W. Jackson 7. Prophage contribution to salmonella virulence and diversity Sebastien Lemire, Nara Figueroa-Bossi and Lionello Bossi 8. Pathogenic yersiniae: stepwise gain of virulence due to sequential acquisition of mobile genetic elements Elisabeth Carniel 9. Genomic or pathogenicity islands in streptococcus pneumoniae Barbara Albiger, Christel Blomberg, Jessica Dagerhamm, Staffan Normark and Brigitta Henriques-Normark 10. The mobile genetic elements of staphylococcus aureus Richard P. Novick 11. Influence of human lifestyle on dissemination of transferable elements Wolfgang Witte Part IV. Interkingdom Transfer and Endosymbiosis: 12. Eukaryotic gene transfer: adaptation and replacements Jan O. Andersson 13. Lessons in evolution from genome reduction in bacterial endosymbionts Andres Moya and Amparo Latorre.
The Passions and the Interests: Unpacking the 'Sharing Economy'

The phenomenal growth of "sharing economy" platforms, the increasing number of economic sectors affected and the conflicting interests among involved stakeholders explain the huge controversies around the "Sharing economy". This report aims to provide a better understanding of this phenomenon and the issues at stake. The platforms reviewed cover both factor (capital, labour) and product markets (goods and services), i.e. the entire economy (and potentially society at large), taking account of both empirical evidence and rhetorical discourses in order to remove confusion and identify both available and lacking empirical evidence. There is controversy on what the "sharing economy" is or is not. Because of its positive connotation, more companies started to claim belonging to the "sharing economy" although they actually pursue economic self-interest. The conditions of "on-demand workers" raise conflicting views, as earnings for providers are not as high as claimed and practices add to the erosion of the labour contract and to the increase of "contingent" labour. Another controversial issue is whether or not the "sharing economyâ€™ has positive redistributive effects, for which evidence is lacking or not conclusive. Last but not least conflicts, legal disputes, and consumer protection concerns are on the rise. In this respect, the size and scope of a platform may pose very different regulatory and policy challenges which is why a conceptual clarification is needed.
Use of metabolomics to study water deficit stress on the medicinal plant thyme

Thyme is one of the best known genera because of its diverse medicinal and culinary uses. To understand plant response to drought, a range of genotypes of thyme was examined including Thymus vulgaris, T. serpyllum, T. daenensis, T. kotchyanous, T. capitata and T. zygis. Drought stress was imposed on 30 day old plants and some morpho-physiological traits were measured. Together these traits indicated that T. serpyllum was the most tolerant and T. vulgaris the most susceptible populations. Metabolite profiling using direct-infusion FT-ICR mass spectrometry identified differences in both polar and non-polar fractions. These results suggested that mechanisms adapting thyme to drought may include osmotic adjustment, ROS scavenging, cellular components protection, membrane lipid changes and hormone activity in which the key metabolites were proline, betaine, mannitol, sorbitol, ascorbate, JA, SA, ABA precursor, unsaturated fatty acids and tocopherol. Profiling of volatiles using GC/MS, showed an increasing-decreasing trend at major terpenes apart from thymol, alpha-cubebene and germacrene in sensitive plants. These results suggests that tolerant and susceptible populations of thyme employing different strategies in response to drought. In conclusion, the combination of metabolite profiling and physiological parameters contributed to a greater understanding of the mechanisms of thyme plant response at metabolomics level.
Survival of Listeria monocytogenes in Three Zimbabwean Fermented Milk Products.

The growth and survival of Listeria monocytogenes was studied in traditionally fermented unpasteurized and pasteurized milk and in an industrially fermented milk marketed in Zimbabwe. Inoculated milk samples were incubated at 20°C for 24 h, and then one set of samples of each type of milk was stored at ambient (20°C) and a duplicate set at refrigeration (5°C) temperatures for a further 96 h. The industrially fermented milk was least favorable to the survival of L. monocytogenes , followed by traditionally fermented unpasteurized milk and traditionally fermented pasteurized milk when these milks were stored at ambient temperature. A different trend was observed when the milks were stored at refrigeration temperature with traditionally fermented unpasteurized milk allowing the least survival of L. monocytogenes followed by industrially fermented milk and traditionally fermented pasteurized milk. More L. monocytogenes survived in all the three fermented milks when they were stored at refrigeration temperature than at ambient temperature.
Plasminogen activator inhibitor 1: mechanisms of its synergistic regulation by growth factors

My research is on the synergistic regulation of PAI-1 by EGF and TGF-β. The mechanism of synergistic regulation of PAI-1 by EGF and TGF-β are addressed. Methods are described for effective identification of RNA accessible sites for antisense oligodexoxynucleotides (ODNs) and siRNA. In this study effective AS-ODN sequences for both Lcn2 and Bcl2 were identified by in vitro tiled microarray studies. Our results suggest that hybridization of ODN arrays to a target mRNA under physiological conditions might be used as a rapid and reliable in vitro method to accurately identify targets on mRNA molecules for effective antisense and potential siRNA activity in vivo.
Conservation of Endangered Wild Harvested Medicinal Plants: Use of DNA Barcoding

The field of molecular biology has brought many innovations to biodiversity research, with the emerging field of DNA barcoding, which is having a growing impact on plant identification. In DNA barcoding, standard molecular markers are used for species identification of material that has hitherto been hard or impossible to identify, such as sterile plant vouchers, plant parts and even processed herbal products. Widespread use of DNA barcoding for plant identification faces challenges such as the selection of suitable markers that are both variable and easy to amplify, and the exhaustive presence of these markers for species in public nucleotide repositories. In recent years, researchers have successfully shown the power and accuracy of plant barcoding by creating molecular identification systems for various purposes, such as the identification of specific medicinal plant species susceptible to adulteration, overharvested and endangered taxa, and monitoring of cross-border trade in CITES-listed species. As markers, nucleotide repositories and sequencing technology improve, these methods will become ubiquitous and will facilitate the identification of products derived from wild-harvested medicinal plants and the enforcement of the Convention on Biological Diversity Nagoya protocol on Access and Benefit Sharing.
Worldwide phylogeography of the globally invasive plant: Jatropha gossypiifolia

Dhileepan, Raghu and colleagues recently published their paper 'Worldwide phylogeography of the globally invasive plant: Jatropha gossypiifolia' in Proceedings of the 16th Australian Weeds Conference. They used chloroplast microsatellites to establish patterns of phylogeographic structure in the native and introduced range of Jatropha gossypiifolia, and to determine the origin(s) of introductions and the level of genetic diversity present in native and introduced populations. J. gossypiifolia exhibited limited phylogeographic structure in its native range which was best explained by contemporary movement associated with the ornamental plant trade. Multiple introductions from diverse source locations and no reduction in genetic diversity was found in the introduced range which includes Australia, Africa and Asia. These results have implications for our current biocontrol project.
Shoot elongation patterns for loblolly pine families selected for contrasting growth potential.

In all but two families, the different patterns of annual shoot elongation were consistent in irrigated and nonirrigated treatments. Two families that ranked high for growth rate in the 8-year-old field trials also had greater annual shoot growth in the seedling trial without irrigation, but performed poorer than expected when well watered. The different patterns in annual height increment arose as a consequence of changes in the relative contributions of numbers of stem units, the average shoot length per stem unit, and the percentage of trees elongating (.)
The regulation of p53 transcriptional activity by hnRNPUL-1 and the DNA damage response induced by a novel chemotherapeutic agent, ALX

The tumour suppressor, p53, is a vital DNA damage response protein and its means of transcriptional regulation are vast. hnRNPUL-1 is a multifunctional protein and previous studies have implicated it in the modulation of p53 transcriptional activity, although this has been rather poorly understood. Results presented here demonstrate that hnRNPUL-1 represses p53 transcriptional activity and negatively regulates p21 levels. This is consistent with the depletion of hnRNPUL-1 leading to an increase in cells arrested in G1/S. Together these results confirm that hnRNPUL-1 acts as a p53 co-repressor with specific cellular targets. Mutations in p53 and other DNA damage response proteins not only often contribute to the onset of tumourigenesis but can also be the cause of drug resistance during treatment. The development of a novel chemotherapeutic agent, Alchemix (ALX), was based on the requirement for effective treatment in the face of resistance mechanisms. Little has been known about the mechanism of action of ALX up to now. Findings here demonstrate that ALX treatment primarily induces an ATR-dependent DNA damage response that occurs specifically in cycling cells and culminates in cell death via mitotic catastrophe. Results also show that the response elicited by ALX requires TOP2α and TOP2β, as well as its alkylating ability, but does not involve ATM, p53, or components of the MMR and FA pathway. Therefore, ALX has the potential to treat tumours that have developed resistance to conventional chemotherapeutic drugs.
Using the tools of genetic epidemiology to understand sex differences in neuropsychiatric disorders

Many neuropsychiatric disorders exhibit differences in prevalence, age of onset, symptoms or course of illness between males and females. For the most part, the origins of these differences are not well understood. In this article, we provide an overview of sex differences in psychiatric disorders including autism spectrum disorder (ASD), attention deficit/hyperactivity disorder (ADHD), anxiety, depression, alcohol and substance abuse, schizophrenia, eating disorders and risk of suicide. We discuss both genetic and nongenetic mechanisms that have been hypothesized to underlie these differences, including ascertainment bias, environmental stressors, X‐ or Y‐linked risk loci, and differential liability thresholds in males and females. We then review the use of twin, family and genome‐wide association approaches to study potential genetic mechanisms of sex differences and the extent to which these designs have been employed in studies of psychiatric disorders. We describe the utility of genetic epidemiologic study designs, including classical twin and family studies, large‐scale studies of population registries, derived recurrence risks, and molecular genetic analyses of genome‐wide variation that may enhance our understanding sex differences in neuropsychiatric disorders.
Identifying alien macroalgae through DNA barcoding: the case of Hypnea cornuta (Cystocloniaceae, Rhodophyta)

1 - Introduction of non-indigenous macroalgae has become a major topic in the last decades. Potential vectors are aquaculture, fouling on hulls, ballast water, aquarium trading, fishing nets. 2 - Within a program of census of macroalgal alien species through DNA barcoding we found a population of previously unreported rhodophyte in Cape Peloro Lagoon and nearby marine coasts (north-eastern Sicily, Italy). 3 - All collected individuals were identified as the alien species Hypnea cornuta based on morphological characters confirmed by the analysis of COI-5’ sequences.
The production of management knowledge : on the relationship between research and practice

Since the early days of management research, its relevance to practice has been the subject of vigorous debate. Understanding the relationship between research and practice implies studying how management knowledge is produced. We first aim at understanding the controversy surrounding the relevance of management research. We develop four complementary approaches on how academics apprehend the relationship between research and practice. Then, we develop a framework that allows the identification of four modes of interactions between scholars and practitioners and discover a developmental process that is specific to the management innovations that are developed between research and practice. Then, we study how the strategic concept of “Blue Ocean Strategy” is performed. We show how its innovators have performed the concept by applying its own principles. Finally, we are interested in scholar-practitioners given they straddle the worlds of research and practice to produce management knowledge. We seek to understand how they overcome role conflicts related to their activities in both research and practice. These four studies shed light on how management knowledge is produced.
The effects of low-calorie diet with canola oil on blood lipids in hyperlipidemic patients

Summary Hyperlipidemia is known as a risk factor for cardiovascular disease. The purpose of this study was to investigate the effect of canola oil with low-calorie diet on blood lipids in hyperlipidemic patients. The study was carried out on sixty hyperlipidemic patients of both sexes and age range of 25–65 years. The patients received low-calorie diet based on 5 857 KJ energy per day for 4 weeks, containing 29% fats, 17% proteins and 54% carbohydrates. In addition to the low-calorie diet, the intervention group received canola oil (30 g·d-1). Weight, body mass index, waist and hip circumferences were significantly reduced (P < 0.05) after 4 weeks in both groups. Treatment with canola oil was associated with a significant reduction (P < 0.05) in serum triacylglycerols.