Purification and characterization of a surfactin-like molecule produced by Bacillus sp. H2O-1 and its antagonistic effect against sulfate reducing bacteria

Abstract Background Bacillus sp. H2O-1, isolated from the connate water of a Brazilian reservoir, produces an antimicrobial substance (denoted as AMS H2O-1) that is active against sulfate reducing bacteria, which are the major bacterial group responsible for biogenic souring and biocorrosion in petroleum reservoirs. Thus, the use of AMS H2O-1 for sulfate reducing bacteria control in the petroleum industry is a promising alternative to chemical biocides. However, prior to the large-scale production of AMS H2O-1 for industrial applications, its chemical structure must be elucidated. This study also analyzed the changes in the wetting properties of different surfaces conditioned with AMS H2O-1 and demonstrated the effect of AMS H2O-1 on sulfate reducing bacteria cells. Results A lipopeptide mixture from AMS H2O-1 was partially purified on a silica gel column and identified via mass spectrometry (ESI-MS). It comprises four major components that range in size from 1007 to 1049 Da. The lipid moiety contains linear and branched β-hydroxy fatty acids that range in length from C13 to C16. The peptide moiety contains seven amino acids identified as Glu-Leu-Leu-Val-Asp-Leu-Leu. Transmission electron microscopy revealed cell membrane alteration of sulfate reducing bacteria after AMS H2O-1 treatment at the minimum inhibitory concentration (5 μg/ml). Cytoplasmic electron dense inclusions were observed in treated cells but not in untreated cells. AMS H2O-1 enhanced the osmosis of sulfate reducing bacteria cells and caused the leakage of the intracellular contents. In addition, contact angle measurements indicated that different surfaces conditioned by AMS H2O-1 were less hydrophobic and more electron-donor than untreated surfaces. Conclusion AMS H2O-1 is a mixture of four surfactin-like homologues, and its biocidal activity and surfactant properties suggest that this compound may be a good candidate for sulfate reducing bacteria control. Thus, it is a potential alternative to the chemical biocides or surface coating agents currently used to prevent SRB growth in petroleum industries.

Production and action of an Aspergillus phoenicis enzymatic pool using different carbon sources

Aspergillus phoenicis is an interesting heat tolerant fungus that can synthesize enzymes with several applications in the food industry due to its great hydrolytic potential. In this work, the fungus produced high enzymatic levels when cultivated on inexpensive culture media consisting of flakes from different origins such as cassava flour, wheat fibre, crushed soybean, agro-industrial wastes, starch, glucose or maltose. Several enzymatic systems were produced from these carbon sources, but amylase was the most evident, followed by pectinase and xylanase. Traces of CMCases, avicelase, lipase, β-xylosidase, β-glucosidase and α-glucosidase activities were also detected. Amylases were produced on rye flakes, starch, oat flakes, corn flakes, cassava flour and wheat fibre. Significant amylolytic levels were produced in the culture medium with glucose or when this sugar was exhausted, suggesting an enzyme in the constitutive form. Cassava flour, rye, oats, barley and corn flakes were also used as substrates in the hydrolytic reactions, aiming to verify the liberation potential of reducing sugars. Corn flakes induced greater liberation of reducing sugars as compared to the others. Thin layer chromatography of the reaction end products showed that the hydrolysis of cassava flour liberated maltooligosaccharides, but cassava flour and corn, rye, oats and barley flakes were hydrolyzed to glucose. These results suggested the presence of glucoamylase and α-amylase as part of the enzymatic pool of A. phoencis.

The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation

The down-regulation of the tumor-suppressor gene RASSF1A has been shown to increase cell proliferation in several tumors. RASSF1A expression is regulated through epigenetic events involving the polycomb repressive complex 2 (PRC2); however, the molecular mechanisms modulating the recruitment of this epigenetic modifier to the RASSF1 locus remain largely unknown. Here, we identify and characterize ANRASSF1, an endogenous unspliced long noncoding RNA (lncRNA) that is transcribed from the opposite strand on the RASSF1 gene locus in several cell lines and tissues and binds PRC2. ANRASSF1 is transcribed through RNA polymerase II and is 5'-capped and polyadenylated; it exhibits nuclear localization and has a shorter half-life compared with other lncRNAs that bind PRC2. ANRASSF1 endogenous expression is higher in breast and prostate tumor cell lines compared with non-tumor, and an opposite pattern is observed for RASSF1A. ANRASSF1 ectopic overexpression reduces RASSF1A abundance and increases the proliferation of HeLa cells, whereas ANRASSF1 silencing causes the opposite effects. These changes in ANRASSF1 levels do not affect the RASSF1C isoform abundance. ANRASSF1 overexpression causes a marked increase in both PRC2 occupancy and histone H3K27me3 repressive marks, specifically at the RASSF1A promoter region. No effect of ANRASSF1 overexpression was detected on PRC2 occupancy and histone H3K27me3 at the promoter regions of RASSF1C and the four other neighboring genes, including two well-characterized tumor suppressor genes. Additionally, we demonstrated that ANRASSF1 forms an RNA/DNA hybrid and recruits PRC2 to the RASSF1A promoter. Together, these results demonstrate a novel mechanism of epigenetic repression of the RASSF1A tumor suppressor gene involving antisense unspliced lncRNA, in which ANRASSF1 selectively represses the expression of the RASSF1 isoform overlapping the antisense transcript in a location-specific manner. In a broader perspective, our findings suggest that other non-characterized unspliced intronic lncRNAs transcribed in the human genome might contribute to a location-specific epigenetic modulation of genes.

Loss of the anorexic response to systemic 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside administration despite reducing hypothalamic AMP-activated protein kinase phosphorylation in insulin-deficient rats

This study tested whether chronic systemic administration of 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) could attenuate hyperphagia, reduce lean and fat mass losses, and improve whole-body energy homeostasis in insulin-deficient rats. Male Wistar rats were first rendered diabetic through streptozotocin (STZ) administration and then intraperitoneally injected with AICAR for 7 consecutive days. Food and water intake, ambulatory activity, and energy expenditure were assessed at the end of the AICAR-treatment period. Blood was collected for circulating leptin measurement and the hypothalami were extracted for the determination of suppressor of cytokine signaling 3 (SOCS3) content, as well as the content and phosphorylation of AMP-kinase (AMPK), acetyl-CoA carboxylase (ACC), and the signal transducer and activator of transcription 3 (STAT3). Rats were thoroughly dissected for adiposity and lean body mass (LBM) determinations. In non-diabetic rats, despite reducing adiposity, AICAR increased (∼1.7-fold) circulating leptin and reduced hypothalamic SOCS3 content and food intake by 67% and 25%, respectively. The anorexic effect of AICAR was lost in diabetic rats, even though hypothalamic AMPK and ACC phosphorylation markedly decreased in these animals. Importantly, hypothalamic SOCS3 and STAT3 levels remained elevated and reduced, respectively, after treatment of insulin-deficient rats with AICAR. Diabetic rats were lethargic and displayed marked losses of fat and LBM. AICAR treatment increased ambulatory activity and whole-body energy expenditure while also attenuating diabetes-induced fat and LBM losses. In conclusion, AICAR did not reverse hyperphagia, but it promoted anti-catabolic effects on skeletal muscle and fat, enhanced spontaneous physical activity, and improved the ability of rats to cope with the diabetes-induced dysfunctional alterations in glucose metabolism and whole-body energy homeostasis.

Traces de terre, traces d'encre... La rappresentazione dello spazio nella letteratura caraibica. (Francofona e Anglofona)

This study concerns the representation of space in Caribbean literature, both francophone and Anglophone and, in particular, but not only, in the martinican literature, in the works of the authors born in the island. The analysis focus on the second half of the last century, a period in which the martinican production of novels and romances increased considerably, and where the representation and the rule of space had a relevant place. So, the thesis explores the literary modalities of this representation. The work is constituted of 5 chapters and the critical and methodological approaches are both of an analytical and comparative type. The first chapter “The caribbean space: geography, history and society” presents the geographic context, through an analysis of the historical and political major events occurred in the Caribbean archipelago, in particular of the French Antilles, from the first colonization until the départementalisation. The first paragraph “The colonized space: historical-political excursus” the explores the history of the European colonization that marked forever the theatre of the relationship between Europe, Africa and the New World. This social situation take a long and complex process of “Re-appropriation and renegotiation of the space”, (second paragraph) always the space of the Other, that interest both the Antillean society and the writers’ universe. So, a series of questions take place in the third paragraph “Landscape and identity”: what is the function of space in the process of identity construction? What are the literary forms and representations of space in the Caribbean context? Could the writing be a tool of cultural identity definition, both individual and collective? The second chapter “The literary representation of the Antillean space” is a methodological analysis of the notions of literary space and descriptive gender. The first paragraph “The literary space of and in the novel” is an excursus of the theory of such critics like Blanchot, Bachelard, Genette and Greimas, and in particular the recent innovation of the 20th century; the second one “Space of the Antilles, space of the writing” is an attempt to apply this theory to the Antillean literary space. Finally the last paragraph “Signs on the page: the symbolic places of the antillean novel landscape” presents an inventory of the most recurrent antillean places (mornes, ravines, traces, cachots, En-ville,…), symbols of the history and the past, described in literary works, but according to new modalities of representation. The third chapter, the core of the thesis, “Re-drawing the map of the French Antilles” focused the study of space representation on francophone literature, in particular on a selected works of four martinican writers, like Roland Brival, Édouard Glissant, Patrick Chamoiseau and Raphaël Confiant. Through this section, a spatial evolution comes out step by step, from the first to the second paragraph, whose titles are linked together “The novel space evolution: from the forest of the morne… to the jungle of the ville”. The virgin and uncontaminated space of the Antilles, prior to the colonisation, where the Indios lived in harmony with the nature, find a representation in both works of Brival (Le sang du roucou, Le dernier des Aloukous) and of Glissant (Le Quatrième siècle, Ormerod). The arrival of the European colonizer brings a violent and sudden metamorphosis of the originary space and landscape, together with the traditions and culture of the Caraïbes population. These radical changes are visible in the works of Chamoiseau (Chronique des sept misères, Texaco, L’esclave vieil homme et le molosse, Livret des villes du deuxième monde, Un dimanche au cachot) and Confiant (Le Nègre et l’Amiral, Eau de Café, Ravines du devant-jour, Nègre marron) that explore the urban space of the creole En-ville. The fourth chapter represents the “2nd step: the Anglophone novel space” in the exploration of literary representation of space, through an analytical study of the works of three Anglophone writers, the 19th century Lafcadio Hearn (A Midsummer Trip To the West Indies, Two Years in the French West Indies, Youma) and the contemporary authors Derek Walcott (Omeros, Map of the New World, What the Twilight says) and Edward Kamau Brathwaite (The Arrivants: A New World Trilogy). The Anglophone voice of the Caribbean archipelago brings a very interesting contribution to the critical idea of a spatial evolution in the literary representation of space, started with francophone production: “The spatial evolution goes on: from the Martiniques Sketches of Hearn… to the modern bards of Caribbean archipelago” is the new linked title of the two paragraphs. The fifth chapter “Extended look, space shared: the Caribbean archipelago” is a comparative analysis of the results achieved in the prior sections, through a dialogue between all the texts in the first paragraph “Francophone and Anglophone representation of space compared: differences and analogies”. The last paragraph instead is an attempt of re-negotiate the conventional notions of space and place, from a geographical and physical meaning, to the new concept of “commonplace”, not synonym of prejudice, but “common place” of sharing and dialogue. The question sets in the last paragraph “The “commonplaces” of the physical and mental map of the Caribbean archipelago: toward a non-place?” contains the critical idea of the entire thesis.

Plasmonic nanorods and nanoparticle-assemblies

Die vorliegenden Dissertation beschäftigt sich mit plasmonischen Nanopartikeln, deren Wechselwirkung mit Licht in einer Plasmonenschwingung resultiert. Suspensionen dieser Partikel zeigen kräftige Farben, da sich die Resonanzfrequenz der Plasmonenschwingung im sichtbaren Bereich des elektromagnetischen Spektrum befindet. Durch die Veränderung interner (Material, Größe, Form) oder externer Parameter (Brechungsindex der Umgebung, Abstand zu anderen plasmonischen Partikeln) lässt sich die Farbe der Partikel verändern, eine Verschiebung der Resonanzfrequenz kann beobachtet werden. Ihre Sensitivität gegenüber äußeren Bedingungen ist der Grund, weshalb plasmonische Nanopartikel als Sensoren eingesetzt werden können. Wichtig ist hierbei nicht nur, dass die Partikel eine hohe Sensitivität zeigen, sondern auch die Möglichkeit, reproduzierbar Partikel zu synthetisieren, die experimentellen Anforderungen entsprechen. In der vorliegenden Arbeit wird das Wachstum von reinen Gold- und mit Silber beschichteten Goldnanostäbchen untersucht. Des Weiteren werden plasmonische Nanopartikel als Orientierungs-, Brechungsindex- und Abstandssensoren verwendet. Die Synthese von Goldnanostäbchen erfolgt auf nasschemischen Weg, ihr anisotropes Wachstum aus isotropen Keimen wird durch zahlreiche Faktoren beeinflusst. In diesem Zusammenhang wurde ein Wachstumsmodell entwickelt, das neben dem Vorhandensein eines Stabilisators auch die Rolle von Bromid- und Silberionen herausstellt, die durch selektive Adsorption das Wachstum bestimmter Kristallflächen inhibieren. Zudem konnte gezeigt werden, dass die Potentialdifferenz zwischen Reduktions- und Oxidationsmittel klein sein muss, um ein langsames selektives Wachstum zu gewährleisten. rnDurch das Aufwachsen einer dünnen Silberschicht auf Goldnanostäbchen verbessert sich deren Qualität im Bezug auf die heterogene Linienbreite. Der “Plasmonic Focusing Effect”, die Änderung der Steigung des linearen Zusammenhangs von Plasmonenresonanz und Aspektverhältnis, konnte theoretisch berechnet und experimentell verifiziert werden. Durch die Aufnahme zeitaufgelöster Spektren und die Untersuchung des Verlaufs der Reaktion wurden sowohl Reaktionsordnung, als auch Aktivierungsenergie ermittelt. Das so gefundene kinetische Model erlaubt zudem die Vorhersage des Reaktionsprodukts zu verschiedenen Zeiten. rnEinzelne Goldnanostäbchen wurden in einer Gelmatrix bei verschiedenen Temperaturen untersucht, die Aufnahme der zeitlichen Variation der polarisationsabhängigen Streuintensität konnte genutzt werden, um den Kollaps des Gels zu charakterisieren. Neben der Verwendung einzelner plasmonischer Nanopartikel wurden auch Dimere, bestehend aus zwei Goldnanokugeln, untersucht. Nach der Kalibrierung der Resonanzfrequenz gegenüber des Abstandes der beiden Partikel durch externe Methoden (Lichtstreuung, Cryo- Elektronenmikroskopie) wurde der so gefundene exponentielle Zusammenhang verwendet, um sowohl den Brechungsindex der Umgebung, als auch den Abstand der beiden Goldnanokugeln zu bestimmen. Des Weiteren wurden Goldnanopartikeldimere benutzt, um ein als Linker verwendetes thermoresponsives Elastin-Polymer bei verschiedenen Temperaturen zu charakterisieren. Neben Aggregaten aus zwei Goldnanokugeln wurden auch so genannte “core-satellite” Strukturen synthetisiert, die um einen großen Goldnanopartikelkern viele kleine Goldnanopartikel tragen. Diese Partikel haben eine theoretisch vorhergesagte höhere Sensitivität gegenüber Brechungsindexänderungen, was in ersten Experimenten gezeigt werden konnte.

[Strategies for reducing the CT radiation dose]

The rapid technical advances in computed tomography have led to an increased number of clinical indications. Unfortunately, at the same time the radiation exposure to the population has also increased due to the increased total number of CT examinations. In the last few years various publications have demonstrated the feasibility of radiation dose reduction for CT examinations with no compromise in image quality and loss in interpretation accuracy. The majority of the proposed methods for dose optimization are easy to apply and are independent of the detector array configuration. This article reviews indication-dependent principles (e.g. application of reduced tube voltage for CT angiography, selection of the collimation and the pitch, reducing the total number of imaging series, lowering the tube voltage and tube current for non-contrast CT scans), manufacturer-dependent principles (e.g. accurate application of automatic modulation of tube current, use of adaptive image noise filter and use of iterative image reconstruction) and general principles (e.g. appropriate patient-centering in the gantry, avoiding over-ranging of the CT scan, lowering the tube voltage and tube current for survey CT scans) which lead to radiation dose reduction.

On the traces of XPD: cell cycle matters - untangling the genotype-phenotype relationship of XPD mutations

Abstract Mutations in the human gene coding for XPD lead to segmental progeria - the premature appearance of some of the phenotypes normally associated with aging - which may or may not be accompanied by increased cancer incidence. XPD is required for at least three different critical cellular functions: in addition to participating in the process of nucleotide excision repair (NER), which removes bulky DNA lesions, XPD also regulates transcription as part of the general transcription factor IIH (TFIIH) and controls cell cycle progression through its interaction with CAK, a pivotal activator of cyclin dependent kinases (CDKs). The study of inherited XPD disorders offers the opportunity to gain insights into the coordination of important cellular events and may shed light on the mechanisms that regulate the delicate equilibrium between cell proliferation and functional senescence, which is notably altered during physiological aging and in cancer. The phenotypic manifestations in the different XPD disorders are the sum of disturbances in the vital processes carried out by TFIIH and CAK. In addition, further TFIIH- and CAK-independent cellular activities of XPD may also play a role. This, added to the complex feedback networks that are in place to guarantee the coordination between cell cycle, DNA repair and transcription, complicates the interpretation of clinical observations. While results obtained from patient cell isolates as well as from murine models have been elementary in revealing such complexity, the Drosophila embryo has proven useful to analyze the role of XPD as a cell cycle regulator independently from its other cellular functions. Together with data from the biochemical and structural analysis of XPD and of the TFIIH complex these results combine into a new picture of the XPD activities that provides ground for a better understanding of the patophysiology of XPD diseases and for future development of diagnostic and therapeutic tools.

Reducing vulnerability to climate change in the Swiss Alps: a study of adaptive planning

The Swiss Alps will experience pronounced effects of climate change due to the combination of their latitudinal positioning, altitude and unique ecosystems, placing socio-economic stresses on alpine communities, many of which rely on seasonal tourism. Studies into tourism adaptation within the Swiss Alps have so far focused on the technical adaptation options of alpine stakeholders, rather than perceptions of adaptation to climate change at the operational and community level. This article investigates attitudes to adaptation in two alpine regions within Switzerland's well-established decentralized political framework, through semi-structured qualitative interviews. Stakeholders focused almost entirely on maintaining the status quo of winter tourism, through technical or marketing measures, with mixed attitudes towards climatic impacts. A matrix based on the relative internal strengths and weaknesses, external opportunities and threats of adaptation measures (a SWOT framework) was used to assess the measures and suggest how stakeholders could capitalize on the new opportunities thrown up by climate change to create a competitive advantage. A comprehensive and collaborative planning approach is vital to enable policy makers and stakeholders to maximize opportunities, minimize the adverse effects of climate change on the local economy, and develop inclusive adaptation measures that benefit the entire region in order to create more sustainable social, economic and environmental structures.

Land use policies and practices for reducing vulnerability in rural Tajikistan

Tajikistan, with 93% of its surface area taken up by mountains and 65% of its labor force employed in agriculture, is judged to be highly vulnerable to risks, including climate change risks and food insecurity risks. The article examines a set of land use policies and practices that can be used to mitigate the vulnerability of Tajikistan’s large rural population, primarily by increasing family incomes. Empirical evidence from Tajikistan and other CIS countries suggests that families with more land and higher commercialization earn higher incomes and achieve higher well-being. The recommended policy measures that are likely to increase rural family incomes accordingly advocate expansion of smallholder farms, improvement of livestock productivity, increase of farm commercialization through improvement of farm services, and greater diversification of both income sources and the product mix. The analysis relies for supporting evidence on official statistics and recent farm surveys. Examples from local initiatives promoting sustainable land management practices and demonstrating the implementation of the proposed policy measures are presented.

Maximum flight velocity of blood drops in analysing blood traces

When analysing blood spatters, traces often occur which regarding the collision angle, cannot be allocated to any supposed centre of origin. Drops following highly curved (ballistic) trajectories usually form these types of traces. The reconstruction of such trajectories requires knowledge of the mass, the diameter (of which approximations are known) and the velocity of the blood drops. This article provides an upper range of the velocity in relation to the diameter of the blood drops based on physical laws. This is very helpful in analysing ballistic trajectories.

Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals

Desulfovibrio sp. A2 is an anaerobic gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms.