Porin from the halophilic species Ectothiorhodospira vacuolata: cloning, structure of the gene and comparison with other porins

The gene coding for the anion-specific porin of the halophilic eubacterium Ectothiorhodospira (Ect.) vacuolata was cloned and sequenced, the first such gene so analyzed from a purple sulfur bacterium. It encodes a precursor protein consisting of 374 amino acid (aa)-residues including a signal peptide of 22-aa residues. Comparison with aa sequences of porins from several other members of the Proteobacteria revealed little homology. Only two regions showed local homology with the previously sequenced porins of Neisseria species, Comamonas acidovorans, Bordetella pertussis, Alcaligenes eutrophus, and Burkholderia cepacia. Genomic Southern blot hybridization studies were carried out with a probe derived from the 5′ end of the gene coding for the porin of Ect. vacuolata. Two related species, Ect. haloalkaliphila and Ect. shaposhnikovii, exhibited a clear signal, while the extremely halophilic bacterium Halorhodospira (Hlr.) halophila (formerly Ect. halophila) did not show any cross-hybridization even at low stringency. This result is in good accordance with a recently proposed reassignment within the family Ectothiorhodospiraceae, which included the separation of the extremely halophilic species into the new genus Halorhodospira

Biologically active peptides in cyanobacteria

Las cianobacterias se encuenlran en el medio natural tanto en aguas dulces como saladas. Ellas pueden desarrollarse en grandes masas formando "blooms" (florecimientos) en aguas dulces y saladas en diferentes partes del mundo, incluyendo América del Sur. Tales florecimientos, así como crecimientos axénicos de cianobacterias, pueden ser una rica fuente de péptidos lineales o cíclicos únicos, muchos de los cuales presentan actividad biológica. En el pasado la mayor atención ha sido puesta en las toxinas microcistinay nodularina. Estospéptidos cíclicos son hepatotoxinas que inhiben la proteína fosfatasa 1 y 2A, después de ingresar específicamente al hepatocito mediante la captación de las sales biliares. Sin embargo, en cianobacterias se están encontrando péplidos con otras actividades biológicas.No obstante, aunque no se consideren tóxicos, estos péptidos tienen actividades biológicas tales como: una fuerte y específica inhibición de las proteasas (tripsina, quimo-tripsina, elastasa, trombina, plasmina y la enzima procesadora angiotensina), anticianobacterias, antialgas, antihongos, inmunosupresores y promolores de diferenciación celar.  Ejemplos de péptidos cianobacterialesinhibidores de proteasas son las cianopeptolinas. Las inleracciones de microcistina/proteína fosfatasa y de cianopeptolina/proteasa, han sido bienestudiadas por difracción de Rayos X en cocristales y la determinación de microcistina y de otros péplidos puede ser realizada por métodos químicos y biológicos.Ambas, microcistina y cianopeptolina han sido recientemente determinadas en blooms producidos en cuerpos de agua en Chile, utilizando cromatografía líquida de alta resolución (HPLC) , espectrometría de masas (MALDI-TOF) (PSD), además de bioensayos de inhibición enzimática

The Kuramoto model in complex networks

181 pages, 48 figures. In Press, Accepted Manuscript, Physics Reports 2015 Acknowledgments We are indebted with B. Sonnenschein, E. R. dos Santos, P. Schultz, C. Grabow, M. Ha and C. Choi for insightful and helpful discussions. T.P. acknowledges FAPESP (No. 2012/22160-7 and No. 2015/02486-3) and IRTG 1740. P.J. thanks founding from the China Scholarship Council (CSC). F.A.R. acknowledges CNPq (Grant No. 305940/2010-4) and FAPESP (Grants No. 2011/50761-2 and No. 2013/26416-9) for financial support. J.K. would like to acknowledge IRTG 1740 (DFG and FAPESP).Peer reviewedPreprin

A Digital Advisor Twin for Crop Nitrogen Management

Farmers and consultants face an unmanageable amount of diverse knowledge and information for crop management decisions. To determine optimal actions, decision makers require knowledge-based support. In this way, decisions can be improved and heuristics can be replaced over time. The study presents a digital knowledge base with an integrated decision support system (DSS), using the example of nutrient supply, specifically nitrogen (N), fertilization. Therefore, the requirements of farmers and crop consultants for DSS to inform fertilization decisions for winter wheat (Triticum aestivum L.) were elaborated using surveys, expert interviews, and a prototype test. Semantic knowledge was enriched by expert knowledge and combined in a web application, the Crop Portal. To map regional and personal decision making patterns and experiences, the tacit knowledge on the complex advisory problem of N fertilization is made digitally usable. For this purpose, 16 fuzzy variables were specified and formalized. Individual decision trees and their interactions with an integrative knowledge base were used to multiply the consulting reach of experts. Using three consultants and nine model farms from different soil–climate areas in Germany, the Crop Portal was tested under practical conditions and the perceived pragmatic and hedonic quality of the system was evaluated using a standardized questionnaire. The field test showed that the variation in fertilizer recommendations from the ‘digital advisor twin’ ranged from 5 kg N ha−1 to 16 kg N ha−1 when compared with the decisions of the experts in the field. The study presents the participatory development and evaluation of a rule-based DSS prototype in agricultural practice

Channel-Forming (Porin) Activity in Herpetosiphon aurantiacus Hp a2

Detergent extracts of cell envelopes of the gliding bacterium Herpetosiphon aurantiacus formed channels in lipid bilayers. Fast protein liquid chromatography across a HiTrap-Q cation-exchange column demonstrated that a 45-kDa protein forms the channel. The observation of a channel-forming protein suggests that Herpetosiphon aurantiacus Hp a2 has a permeability barrier on its surface

Purification, characterization, crystallization, and preliminary X-ray results from Paracoccus denitrificans porin

The porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with β-d-octylglucopyra-noside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 Å, b = 193.8 Å, c = 100.5 Å and β = 129.2°. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with α = 89.7 Å, b = 98.8 Å, c = 112.5 Å, b = 112.5Å, β = 101.8°, γ = 106.7° (2 trimers per asymmetric unit). Both crystal forms diffract to 3 Å

Influence of the supramolecular structure of free lipid A on its biological activity

The three-dimensional supramolecular structures and the states of order of the acyl chains of lipid A from different Gram-negative species were investigated at 40°C, high water content (80–90%), and different [lipid A]/[Mg2+] molar ratios using synchrotron radiation X-ray diffraction and Fourier-transform infrared spectroscopy. Measurements were made on free lipid A from Salmonella minnesota R595, mono- and bi-phosphoryl, as well as those from the non-enterobacterial strains Rhodobacter capsulatus 37 b4, Rhodopseudomonas viridis F, and Rhodocyclus gelatinosus 29/1. Parallel to differences in their chemical primary structure, the structural polymorphisms and states of order at 37°C of the non-enterobacterial lipid A were found to be different from those of enterobacterial lipid A. A clear correlation between the supramolecular structure and previously determined biological activities was found. Lipid A with a strong preference for lamellar structures (Rb. capsulatus and Rp. viridis) are endotoxically inactive and lack cytokine-inducing capacity; the compounds assuming a mixed lamellar/nonlamellar structure (monophosphoryl lipid A from S. minnesota) are of lower toxicity in vivo, but may induce cytokines in vitro; those lipid A with a strong tendency to form non-lamellar inverted structures (lipid A from S. minnesota and Rc. gelatinosus) exhibit full endotoxicity in vitro and in vivo. In contrast, anti-complementary activity is most pronounced for compounds with lamellar and least expressed for those with inverted structures. The states of order at 37°C vary non-systematically, exhibiting the highest values for lipid A of S. minnesota and the lowest for that of Rc. gelatinosus.We propose to extend the term ‘endotoxic conformation’, which is used to describe the conformation of a single lipid A molecule required for optimal triggering of biological effects, to ‘endotoxic supramolecular conformation’ which denotes the particular organization of lipid A aggregates in physiological fluids causing biological activity