Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences.

Halobacterium-halobium NRC-1 harbors a 200-kb plasmid, pNRC100, which contains a cluster of genes for synthesis of buoyant gas-filled vesicles. Physical mapping of pNRC100 by using pulsed-field gel electrophoresis showed the presence of a large (35 to 38-kb) inverted repeat (IR) sequence. Inversion isomers of pNRC100 were demonstrated by Southern hybridization analysis using two restriction enzymes, AflII and SfiI, that cut asymmetrically within the intervening small single-copy region and the large single-copy region, respectively, but not within the large IRs. No inversion isomers were observed for a deletion derivative of pNRC100 lacking one IR, which suggests that both copies are required for inversion to occur. Additionally, the identities and approximate positions of 17 insertion sequences (IS) in pNRC100 were determined by Southern hybridization and limited nucleotide sequence analysis across the IS element-target site junctions: ISH2, a 0.5-kb element, was found in four copies; ISH3, a 1.4-kb heterogeneous family of elements, was present in seven copies; ISH8, a 1.4-kb element, was found in five copies; and ISH50, a 1.0-kb element, was present in a single copy. The large IRs terminated at an ISH2 element at one end and an ISH3 element at the other end. pNRC100 is similar in structure to chloroplast and mitochondrial genomes, which contain large IRs and other large halobacterial and prokaryotic plasmids that are reservoirs of IS elements but lack the large IRs.     

Pulsatile contractions and pattern formation in excitable actomyosin cortex

The actin cortex is an active adaptive material, embedded with complex regulatory networks that can sense, generate, and transmit mechanical forces. The cortex exhibits a wide range of dynamic behaviours, from generating pulsatory contractions and travelling waves to forming organised structures. Despite the progress in characterising the biochemical and mechanical components of the actin cortex, the emergent dynamics of this mechanochemical system is poorly understood. Here we develop a reaction-diffusion model for the RhoA signalling network, the upstream regulator for actomyosin assembly and contractility, coupled to an active actomyosin gel, to investigate how the interplay between chemical signalling and mechanical forces regulates stresses and patterns in the cortex. We demonstrate that mechanochemical feedback in the cortex acts to destabilise homogeneous states and robustly generate pulsatile contractions. By tuning active stress in the system, we show that the cortex can generate propagating contraction pulses, form network structures, or exhibit topological turbulence.     

The C-terminal Domain (CTD) of Human DNA Glycosylase NEIL1 Is Required for Forming BERosome Repair Complex with DNA Replication Proteins at the Replicating Genome: DOMINANT NEGATIVE FUNCTION OF THE CTD*

The human DNA glycosylase NEIL1 was recently demonstrated to initiate prereplicative base excision repair (BER) of oxidized bases in the replicating genome, thus preventing mutagenic replication. A significant fraction of NEIL1 in cells is present in large cellular complexes containing DNA replication and other repair proteins, as shown by gel filtration. However, how the interaction of NEIL1 affects its recruitment to the replication site for prereplicative repair was not investigated. Here, we show that NEIL1 binarily interacts with the proliferating cell nuclear antigen clamp loader replication factor C, DNA polymerase δ, and DNA ligase I in the absence of DNA via its non-conserved C-terminal domain (CTD); replication factor C interaction results in ∼8-fold stimulation of NEIL1 activity. Disruption of NEIL1 interactions within the BERosome complex, as observed for a NEIL1 deletion mutant (N311) lacking the CTD, not only inhibits complete BER in vitro but also prevents its chromatin association and reduced recruitment at replication foci in S phase cells. This suggests that the interaction of NEIL1 with replication and other BER proteins is required for efficient repair of the replicating genome. Consistently, the CTD polypeptide acts as a dominant negative inhibitor during in vitro repair, and its ectopic expression sensitizes human cells to reactive oxygen species. We conclude that multiple interactions among BER proteins lead to large complexes, which are critical for efficient BER in mammalian cells, and the CTD interaction could be targeted for enhancing drug/radiation sensitivity of tumor cells.     

Translation of Henrich Klebahn's 'Damaging agents of the klippfish - a contribution to the knowledge of the salt-loving organisms'

Background

Henrich Klebahn was a German linguist, mycologist and phytopathologist, who was known as Dr. Dr. h. c. Henrich Klebahn, Hauptcustos a. D., Honorarprofessor an der Hanischen Universität. He was born February 20, 1859 in Bremen, and died October 5, 1942 in Hamburg. He taught linguistics from 1885-1899, studied Natural Science at the Universities of Jena and Berlin (1881) and received his PhD from the University of Jena. In 1899, he was appointed scientific assistant at the Hamburg botanical garden, where he worked until 1905. From 1905 to 1930, he was at the agricultural institute of Bromberg. In 1921, he was named honorary professor and lecturer in cryptogams and soil biology at the Institut für Allgemeine Botanik where he taught until 1934. He is well known for his work on gas vesicles and halophiles, among other topics. This re-print of 'Die Schädlinge des Klippfisches. Ein Beitrag zur Kenntnis der salzliebenden Organismen. Von H. Klebahn. Mit zwei Tafeln und vier Abbildungen im Text.' was originally published in 1919 in the Jahrbuch der Hamb. Wissensch. Anstaltes. XXXVI. Beiheft pages 11-69, by Latcke & Waltt, E. H. Buchdrucker. The translators have tried to remain faithful to the contents and to the original sense of the article by minimizing modifications.

Results

The original paper reported the conclusions of a 3 year long study of the microbes causing damage to the fish industry as well as a summation of work on the subject up until 1919. The findings were that the causative agents were fungi and other microbes, the chief of which was a red, Gram-negative rod-shaped bacillus, Bacillus halobius ruber, that formed pale reddish colonies and was found to oscillate, but after extensive testing, was found not possess flagella. The initial appearance of "a shiny corpuscle" at the ends of cells was determined not to be spores; rather that it was the "result of the coherence of the light beams due to a total reflection of the light in the optically denser little rods". The cells were osmotically sensitive to the addition of water. In addition, a Gram-negative, red Sarcina morrhuae that appeared pinker in color, was less salt-sensitive than the red bacillus, in fact surviving the transfer to water. These were "round individual cells or groups of only two or four cells, usually; however, there are eight or more round cells that are arranged like cube corners to great cube-like or irregular packages lying together, just in the same manner as with the familiar Sarcina ventriculi." This organism was also identified from the walls of a fish storage room. Finally, a third, red microorganism was isolated: a Gram-negative micrococcus, Micrococcus (Diplococcus) morrhuae, which was "spherically rounded" and barely sensitive to water: "If one distributes a sample of a colony in water, the cells partly separate, to a great degree; however, they stay together in groups of two or four cells."

Conclusions

This article provides evidence for identification of halophilic microbes as the major cause of fish spoilage, and is one of the earliest publications in the field of halophile microbiology.