Control of the master virulence regulatory gene atxA in Bacillus anthracis

Transcription of the Bacillus anthracis structural genes for the anthrax toxin proteins and biosynthetic operon for capsule are positively regulated by AtxA, a transcription regulator with unique properties. Consistent with the role of atxA in virulence factor expression, a B. anthracis atxA-null mutant is avirulent in a murine model for anthrax. In batch culture, multiple signals impact atxA transcript levels, and the timing and steady state level of atxA expression is critical for optimal toxin and capsule synthesis. Despite the apparent complex control of atxA transcription, only one trans-acting protein, the transition state regulator AbrB, has been demonstrated to directly interact with the atxA promoter. The AbrB-binding site has been described, but additional cis-acting control sequences have not been defined. Using transcriptional lacZ fusions, electrophoretic mobility shift assays, and Western blot analysis, the cis-acting elements and trans-acting factors involved in regulation of atxA in B. anthracis strains containing either both virulence plasmids, pXO1 and pXO2, or only one plasmid, pXO1, were studied. This work demonstrates that atxA transcription from the major start site P1 is dependent upon a consensus sequence for the housekeeping sigma factor SigA, and an A+T-rich upstream element (UP-element) for RNA polymerase (RNAP). In addition, the data show that a trans-acting protein(s) other than AbrB negatively impacts atxA transcription when it binds specifically to a 9-bp palindrome within atxA promoter sequences located downstream of P1. Mutation of the palindrome prevents binding of the trans-acting protein(s) and results in a corresponding increase in AtxA and anthrax toxin production in a strain- and culture-dependent manner. The identity of the trans-acting repressor protein(s) remains elusive; however, phenotypes associated with mutation of the repressor binding site have revealed that the trans-acting repressor protein(s) indirectly controls B. anthracis development. Mutation of the repressor binding site results in misregulation and overexpression of AtxA in conditions conducive for development, leading to a marked sporulation defect that is both atxA- and pXO2-61-dependent. pXO2-61 is homologous to the sensor domain of sporulation sensor histidine kinases and is proposed to titrate an activating signal away from the sporulation phosphorelay when overexpressed by AtxA. These results indicate that AtxA is not only a master virulence regulator, but also a modulator of proper B. anthracis development. Also demonstrated in this work is the impact of the developmental regulators AbrB, Spo0A, and SigH on atxA expression and anthrax toxin production in a genetically incomplete (pXO1+, pXO2-) and genetically complete (pXO1+, pXO2+) strain background. AtxA and anthrax toxin production resulting from deletion of the developmental regulators are strain-dependent suggesting that factors on pXO2 are involved in control of atxA. The only developmental deletion mutant that resulted in a prominent and consistent strain-independent increase in AtxA protein levels was an abrB-null mutant. As a result of increased AtxA levels, there is early and increased production of anthrax toxins in an abrB-null mutant. In addition, the abrB-null mutant exhibited an increase in virulence in a murine model for anthrax. In contrast, virulence of the atxA promoter mutant was unaffected in a murine model for anthrax despite the production of 5-fold more AtxA than the abrB-null mutant. These results imply that AtxA is not the only factor impacting pathogenesis in an abrB-null mutant. Overall, this work highlights the complex regulatory network that governs expression of atxA and provides an additional role for AtxA in B. anthracis development.

{\it cis\/} -acting elements and {\it trans\/} -acting factors that control serum amyloid A gene expression during inflammation

To understand how the serum amyloid A (SAA) genes are regulated, the cis-acting elements and trans-acting factors involved in the regulation of mouse SAA3 and rat SAA1 genes expression during inflammation were analyzed.^ To identify DNA sequences involved in the liver-specific expression of the mouse SAA3 gene, the 5$\sp\prime$ flanking region of this gene was analyzed by transient transfection studies. Results suggest that C/EBP, a liver-enriched transcription factor, plays an important role for the enhanced expression of the mouse SAA3 gene in hepatocytes.^ Transfection studies of the regulation of the expression of rat SAA1 gene indicated that a 322 bp fragment ($-$304 to +18) of the gene contains sufficient information for cytokine-induced expression of the reporter gene in a liver cell-specific manner. Further functional analysis of the 5$\sp\prime$ flanking region of the rat SAA1 gene demonstrated that a 65 bp DNA fragment ($-$138/$-$73) can confer cytokine-inducibility onto a heterologous promoter both in liver and nonliver cells. DNase I footprint and gel retardation assays identified five putative cis-regulatory elements within the 5$\sp\prime$ flanking region of the gene: one inducible element, a NF$\kappa$B binding site and four constitutive elements. Two constitutive elements, footprint regions I and III, were identified as C/EBP binding sites with region III having over a 10-fold higher affinity for C/EBP binding than region I. Functional analysis of the cis-elements indicated that C/EBP(I) and C/EBP(III) confer liver cell-specific activation onto a heterologous promoter, while sequences corresponding to the NF$\kappa$B element and C/EBP(I) impart cytokine responsiveness onto the heterologous promoter. These results suggest that C/EBP(I) possesses two functions: liver-specific activation and cytokine responsiveness. The identification of two cytokine responsive elements (NF$\kappa$B and C/EBP(I)), and two liver-specific elements (C/EBP(I) and C/EBP(III)) implies that multiple cis-acting elements are involved in the regulation of the expression of the rat SAA1 gene. The tissue-specific and cytokine-induced expression of rat SAA1 gene is likely the result of the interactions of these cis-acting elements with their cognate trans-acting factors as well as the interplay between the different cis-acting elements and their binding factors. (Abstract shortened with permission of author.) ^

Mechanisms of HER2/{\it neu\/} proto-oncogene overexpression in breast cancer cells

Overexpression and amplification of HER2/neu have been documented in many primary tumors, most notably in breast. Not only do approximately 30% of breast cancer patients carry tumors that overexpress the gene, but those that do generally have shorter overall and disease-free survival times than patients with tumors expressing low levels of HER2/neu. Thus, overexpression of HER2/neu plays an important role in the pathogenesis of breast cancer. We have examined the mechanisms that result in HER2/neu overexpression in breast cancer by using, as a model system, established breast cancer cell lines that express much higher levels of HER2/neu mRNA than normal breast tissue while maintaining a near normal HER2/neu gene copy number. Nuclear run-on experiments indicate that the breast cancer cell lines MDA-MB453, BT483, and BT474 have an increased HER2/neu gene transcription rate. By using HER2/neu promoter-CAT constructs, we have found that the enhanced HER2/neu transcription rate in MDA-MB453 cells is due to activation of the gene in trans, while the enhanced transcription rate in BT483 cells is due to activation of the gene in either trans or cis. In BT474 cells, transcriptional upregulation is primarily due to gene amplification. Since the levels of increased transcription are not as high as the levels of HER2/neu mRNA in any of these three lines, post-transcriptional deregulation that increases HER2/neu expression must also be functioning in these cells. The half-life of HER2/neu mRNA was measured and found to be equivalent in these lines as in a control. Thus, the post-transcriptional deregulation is not increased stability of the HER2/neu transcript.^ Much work has been performed in characterizing the altered trans-acting factor involved in increased HER2/neu transcription in MDA-MB453 cells. Using promoter deletion constructs linked to a reporter gene, the region responsive to this factor was localized in the rat neu promoter. When human HER2/neu promoter constructs were used, the homologous sequence in the human promoter was identified. Furthermore, a number of protein/DNA complexes are detected when these promoter regions are used in gel mobility shift assays. UV-crosslinking experiments indicate DNA-binding proteins of roughly 110 kDa, 70 kDa, and 35 kDa are capable of interacting with the human promoter element. ^

Diversity and faunal composition of benthic foraminifera in Hole 44-390A on the Blake Nose Plateau

Benthic foraminiferal assemblages are a widespread tool to understand changes in organic matter flux and bottom-water oxygenation and their relation to paleoceanographic changes in the Upper Cretaceous oceans. In this study, assemblage data (diversity, total number, and number per species and gram) from Deep Sea Drilling Project (DSDP) Site 390 (Blake Nose, western North Atlantic) were processed for the lower Maastrichtian (Globotruncana falsostuarti - Gansserina gansseri Planktic Foraminiferal Zone). These data document significant changes in nutrient flux to the sea floor as well as bottom-water oxygenation during this time interval. Parallel to the observed changes in the benthic foraminiferal assemblages the number of inoceramid shells decreases, reflecting also a significant increase in bottom-water oxygenation. We speculate, that these data could reflect the onset of a shift from warmer low-latitude to cooler high-latitude deep-water sources. This speculation will predate the major reorganization of the oceanic circulation resulting in a circulation mode similar to today at the Early/Late Maastrichtian boundary by ~1 Ma and therefore improves our understanding of Late Cretaceous paleoceanography.

Geochemical parameters of sediments and water of the Black Sea, data of Cruise 8 of R/V Vityaz-2

The book presents results of comprehensive geological investigations carried out during Cruise 8 of R/V "Vityaz-2" to the western part of the Black Sea in 1984. Systematic studies in the Black Sea during about hundred years have not weakened interest in the sea. Lithological and geochemical studies of sediments in estuarine areas of the Danube and the Kyzyl-Irmak rivers, as well as in adjacent parts of the deep sea and some other areas were the main aims of the cruise. Data on morphological structures of river fans, lithologic and chemical compositions of sediments in the fans and their areal distribution, forms of occurrence of chemical elements, role of organic matter and gases in sedimentation and diagenesis are given and discussed in the book.

(Table 2) Chemistry of the organic matter at DSDP Leg 62 Holes

The wide distribution of sapropelic deposits in the sedimentary cover of the oceans, their Cretaceous age, and their possible oil- and gas-generating characteristics allow us to regard these deposits as a regular global stage in the history of oceanic sedimentation. So, Cretaceous sapropelic deposits are a unique object for study. Cretaceous sapropelic deposits of DSDP Sites 463, 465, and 466, as well as similar sediments of the Atlantic and Indian Oceans, are characterized by enrichment in organic matter, which sometimes reaches 33% (Cape Verde Basin, DSDP Sites 367 and 368). The objective of this study is the elucidation of genesis, paleogeographic environment of sedimentation, and oil-generating potential of Cretaceous sapropelic deposits at these sites. Attention is given to petrographic composition and distribution of the organic matter.

Los promotores en la metodología de intervención del programa Pro-Huerta Córdoba, Argentina

El Pro-Huerta (PPH) es un programa estatal nacional que aborda la seguridad alimentaria, dirigido a la población pobre. La zona Gran Córdoba comprende la ciudad de Córdoba y un amplio territorio que involucra los pueblos cercanos en un radio aproximado de unos 50 km de la capital, donde se trabaja con más de 120 promotores y 14.500 huerteros. Debido a que los promotores son los actores que los técnicos destacan como fundamentales en el funcionamiento del programa, las principales preguntas que este estudio se formula son: ¿quiénes son los actores que participan como promotores en el PPH de la provincia de Córdoba? y ¿cómo perciben los promotores los beneficios y limitaciones del componente de capacitación? La metodología utilizada combina procedimientos cuanti y cualitativos en el tratamiento de los datos. El universo de promotores fue clasificado contemplando las funciones que desempeñan en el programa y sus demandas de capacitación. Se observó una relación significativa entre el subtipo que cumple una función de promoción más integral y el subtipo que demanda capacitación en aspectos sociales. Asimismo es importante la relación entre el subtipo que limita su función sólo a convocar reuniones para repartir semillas con el que manifiesta una menor demanda de capacitación en general.

Iron and manganese in bottom sediments and interstitial waters sampled in the White Sea on August 21-30, 2003

Iron and manganese in bottom sediments studied along the sublatitudinal transect from Kandalaksha to Arkhangelsk are characterized by various contents and speciations depending on sedimentation environment, grain size of sediments, and diagenetic processes. The latter include redistribution of reactive forms leading to enrichment in Fe and Mn of surface sediments, formation of films, incrustations, and ferromanganese nodules. Variations in total Fe content (2-8%) are accompanied by changes in concentration of its reactive forms (acid extraction) and concentration of dissolved Fe in interstitial waters (1-14 µM). Variations in Mn content in bottom sediments (0.03-3.7%) and interstitial waters (up to 500 µM) correspond to high diagenetic mobility of this element. Changes in oxidation degree of chemical elements result in redox stratification of sediment strata with maximum concentrations of Fe, Mn, and sulfides. Organic matter of bottom sediments with considerable terrestrial constituent is oxidized by bottom water oxygen mainly at the sediment surface or in anaerobic conditions within the sediment strata. The role of inorganic components in organic matter oxidation changes from surface layer bottom sediments (where manganese oxyhydroxide dominates among oxidants) to deeper layers (where sulfate of interstitial water serves as the main oxidant). Differences in river runoff and hydrodynamics are responsible for geochemical asymmetry of the transect. The deep Kandalaksha Bay serves as a sediment trap for manganese (Mn content in sediments varies within 0.5-0.7%), whereas the sedimentary environment in the Dvina Bay promotes its removal from bottom sediments (Mn 0.05%).

Los desafíos de publicar en web en Ciencias Sociales y Humanas

En este ensayo reflexionamos sobre los desafíos tecnológicos, económicos, académicos y políticos que implica la edición científica en formato digital para los investigadores argentinos en Ciencias Sociales y Humanas. Basándonos en la trayectoria de la Facultad de Humanidades y Ciencias de la Educación de la Universidad Nacional de La Plata en la materia, proponemos que el trabajo interdisciplinario, el acceso abierto y la revisión por pares son los pilares fundamentales para llevar adelante una revista científica publicada en la web desde una unidad académica, es decir, desarrollada por el trabajo ad honorem de docentes-investigadores y sostenida económicamente con el presupuesto universitario

Los desafíos de publicar en web en Ciencias Sociales y Humanas

En este ensayo reflexionamos sobre los desafíos tecnológicos, económicos, académicos y políticos que implica la edición científica en formato digital para los investigadores argentinos en Ciencias Sociales y Humanas. Basándonos en la trayectoria de la Facultad de Humanidades y Ciencias de la Educación de la Universidad Nacional de La Plata en la materia, proponemos que el trabajo interdisciplinario, el acceso abierto y la revisión por pares son los pilares fundamentales para llevar adelante una revista científica publicada en la web desde una unidad académica, es decir, desarrollada por el trabajo ad honorem de docentes-investigadores y sostenida económicamente con el presupuesto universitario

Los desafíos de publicar en web en Ciencias Sociales y Humanas

En este ensayo reflexionamos sobre los desafíos tecnológicos, económicos, académicos y políticos que implica la edición científica en formato digital para los investigadores argentinos en Ciencias Sociales y Humanas. Basándonos en la trayectoria de la Facultad de Humanidades y Ciencias de la Educación de la Universidad Nacional de La Plata en la materia, proponemos que el trabajo interdisciplinario, el acceso abierto y la revisión por pares son los pilares fundamentales para llevar adelante una revista científica publicada en la web desde una unidad académica, es decir, desarrollada por el trabajo ad honorem de docentes-investigadores y sostenida económicamente con el presupuesto universitario

Organic compounds in snow, ice, and sub-ice waters from the mouth of the Severnaya Dvina River and the Kandalaksha Gulf (White Sea)

The paper reports data on concentrations of organic compounds (organic carbon, lipids; aliphatic hydrocarbons, and polycyclic aromatic hydrocarbons) in snow, ice, and sub-ice waters from the mouth of the Severnaya Dvina River in March 2005-2007 and the Kandalaksha Gulf (Chupa Bay) in March 2004. It was established that organic compounds are accumulated in snow and the upper ice layer near Archangelsk city. Distribution of molecular markers indicates that pollutions were mainly caused by local fallouts. In the Chupa Bay organic compounds are concentrated in the lower ice layer; it is typical for Arctic snow-ice cover. High contents of organic compounds in the snow-ice cover of the White Sea are caused by pollution of air and water during the winter season.

Composition of organic matter from water, suspended matter, and bottom sediments of Nha Trang Bay, South China Sea

This research has been carried out in the Nha Trang Bay (Southern Vietnam, South China Sea) at a section from the estuary of the Cai River to the marine part of the bay, as well as in the area of coral reefs. River- and sea waters, suspended matter, and bottom sediments are studies. Data on dissolved organic carbon and total nitrogen in water are obtained. Organic carbon concentration is estimated in suspended matter; organic carbon and molecular and group compositions of n-alkanes are determined in bottom sediments. Molecular and group compositions of n-alkanes in bottom sediments of the landfill made it possible to identify three types of organic matter (OM): marine, mixed, and mainly of terrigenous origin. All these types of OM are closely related to specificity of sedimentation and hydrodynamics of waters in this area.

Analysis of organic matter from DSDP Leg 81 Holes

Organic geochemical and visual kerogen analyses were carried out on approximately 50 samples from Leg 81 (Rockall Plateau, North Atlantic). The sediments are from four sites (Sites 552-555), Pleistocene to Paleocene in age, and represent significantly different depositional environments and sources of organic matter. The Pleistocene glacial-interglacial cycles show differences in sedimentary organic matter based on Rock-Eval pyrolysis, organic phosphorus, and pyrolysis/mass-spectrometry analyses. Glacial samples contain more organic carbon, with a larger proportion of reworked organic matter. This probably reflects increased erosion of continental and shelf areas as a result of low sea level stands. Inter glacial samples contain a larger proportion of marine organic matter as determined by organic phosphorus and pyrolysis analyses. This immature, highly oxidized marine organic matter may be associated with the skeletal organic matrix of calcareous organisms. In addition, Rock-Eval data indicate no significant inorganic-carbonate contribution to the S3 pyrolysis peak. The Pliocene-Miocene sediments consist of pelagic, biogenic carbonates. The organic matter is similar to that of the Pleistocene interglacial periods; a mixture of oxidized marine organic matter and reworked, terrestrial detritus. The Paleocene-Oligocene organic matter reflects variations in source and depositional factors associated with the isolation of Rockall from Greenland. Paleocene sediments contain primarily terrestrial organic matter with evidence of in situ thermal stress resulting from interbedded lava flows. Late Paleocene and early Eocene organic matter suggests a highly oxidized marine environment, with major periods of deposition of terrestrially derived organic matter. These fluctuations in organic-matter type are probably the result of episodic shallowing and deepening of Rockall Basins. The final stage of Eocene/Oligocene sedimentation records the accelerating subsidence of Rockall and its isolation from terrestrial sources (Rockall and Greenland). This is shown by the increasingly marine character of the organic matter. The petroleum potential of sediments containing more than 0.5% organic carbon is poor because of their thermal immaturity and their highly oxidized and terrestrial organic-matter composition.

Zoobenthos and oceanographical parameters in the Kemskaya Guba (Bay) - estuary of the Kem' River entering the Onega Bay, White Sea

Data on distribution of zoobenthos in the Kemskaya Guba (or Kemskaya Bay - the estuary of the Kem' River entering the Onega Bay of the White Sea), which is strongly influenced by river runoff, are presented. The number of species at sampling stations varied from 4 to 65. Density of communities and zoobenthos biomass varied from 342±68 to 4293±96 #/m**2 and from 0.418±0.081 to 1975.22±494.36 g/m**2, respectively. Shannon index values varied between 1.19 to 4.7 bit/ind. At the upper part of the estuary, detritivores dominated, while in the central part and at outlets sestonophages prevailed. Changes in quantitative parameters of the zoobenthos along gradient of water salinity were traced, and relations of these parameters with seven other environmental factors were revealed. It was found that species composition, biodiversity, and trophic structure of the zoobenthos significantly correlated with some of parameters mentioned above. Multiple regression analysis was used to assess combined effect of factors, and it revealed which of them played a determining role in Kemskaya Guba: for species composition - depth, water color, and total concentration of suspended matter; for number of species - contents of <0.01 mm grain size (pelite) fraction and organic carbon in bottom sediments. Biomass depended on water salinity, water chromaticity, and organic carbon contents in bottom sediments and suspended matter. Values of the Shannon index of diversity are determined by water color, and contents of organic carbon and pelite fraction in bottom sediments. Calculations of ecological stress values revealed two zones with unstable state of the zoobenthos.