Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Norms of Presentational Force

This is the author's accepted manuscript, made available with permission of the American Forensic Association.Can style or presentational devices reasonably compel us to believe, agree, act? I submit that they can, and that the normative pragmatic project explains how. After describing a normative pragmatic approach to presentational force, I analyze and evaluate presentational force in Susan B. Anthony's "Is it a Crime for a U. S. Citizen to Vote" as it apparently proceeds from logic, emotion, and style. I conclude with reflections on the compatibility of the normative pragmatic approach with the recently-developed pragma-dialectical treatment of presentational devices

Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production

Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils

The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00792-016-0874-2) contains supplementary material, which is available to authorized users

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions

Pollution de l'étang de l'Olivier (Bouches-du-Rhône) par du lindane en septembre 1967 ; mortalité de la faune

La mortalité de la faune de l'étang de l'Olivier, constatée au cours d'une crise de dystrophie estivale, a été aggravée par un épandage de lindane exécuté en vue de la démoustication. Les observations ont été effectuées dès l'apparition du phénomène. L'étang de l'Olivier (225 ha) est situé au Nord d'Istres à 55 km de Marseille. On sait que les eaux des fonds de cet étang (hypolimnion) présentent au cours de la période estivale un déficit presque permanent en oxygène avec dégagement de H2S, contribuant ainsi à l'installation d'une stratification des couches d'eau de densités différentes. Plusieurs travaux ont déjà signalé les crises dystrophiques de cet étang, suivies d'une mortalité de sa faune (SCHACHTER, SENEZ, GILLERON, 1954. SCHACHTER 1958). La mortalité de la faune constatée le 20 septembre à la suite d'une nouvelle phase de dystrophie a été malencontreusement amplifiée le 21 septembre par un épandage de lindane exécuté sur le pourtour de l'étang, en vue de la démoustication. Nous avons pu assister, dès le début, au déclanchement de ce phénomène à allure catastrophique. Le 20 septembre, un grand nombre de poissons fut rejeté sur les rives ; la surface de l'étang était parsemée de nombreux cadavres et d'individus agités de soubresauts. La surface des eaux de l'étang était couverte par endroits par un grand nombre de poissons comportant des athérines (Atherina boyeri R) des nuages (Mugil cephalus L, Liza aurata (RISSO), Liza ramada (RISSO) des chevennes, des carpes, des sandres. Sur les bords de l'étang les petites anguilles se regroupaient au milieu de la végétation flottante (Enteromorpha intestinalis, Ruppia maritima, Chaetomorpha sp., Zostera nana) en sortant la tête de l'eau, les branchies congestionnées ; les grosses anguilles, localisées au milieu des rochers, venaient également respirer en surface. Elles présentaient des plaques rouges sanguinolentes, souvent constatées sur des sujets stockés en été dans un volume insuffisant (LAGARDE, E. et CHAKROUN, F. 1965). Les Gobius microps KR se hissaient également hors de l'eau sur les parties humides des rochers. Les invertébrés tels Sphaeroma hookeri LESCH, des chironomes, des mollusques se rassemblaient sur la végétation flottante. Il nous a semblé intéressant de signaler à nouveau ce phénomène saisi cette fois-ci sur le vif, pour essayer d'analyser les principaux facteurs pouvant être à l'origine de cette nouvelle hécatombe

Gene transfer into Xenopus hepatocytes: transcriptional regulation by members of the nuclear receptor superfamily.

A procedure to culture Xenopus laevis hepatocytes that allows the cells in primary culture to be subjected to gene transfer experiments has been developed. The cultured cells continue to present tissue-specific markers such as expression of the albumin gene or estrogen-controlled vitellogenin gene expression, which are both restricted to liver. Two efficient and reproducible gene transfer procedures have been adapted to the Xenopus hepatocytes, namely lipofection and calcium phosphate-mediated precipitation. The transcription of transfected reporter genes controlled by estrogen-, glucocorticoid- or peroxisome proliferator-response elements was stimulated by endogenous or co-transfected receptor in a ligand-dependent manner. Furthermore, the expression of a reporter gene under the control of the entire promoter of the vitellogenin B1 gene mimicked the expression of the chromosomal vitellogenin gene with respect to basal and estrogen-induced activity. Thus, this culture-transfection system will prove very useful to study the regulation of genes expressed in the liver under the control of various hormones or xenobiotics