Bkm sequences from the human X chromosome contain large clusters of GATA/GACA repeats

In order to determine whether the regional localizations of Bkm repeats detected on the human X chromosome consisted of typical GATA/GACA repeats, clones were isolated, mapped, and sequenced. Nine Bkm-hybridizing clones from Kunkel's fluorescent-activated, cell-sorted X-chromosome library were all unique. Five were mapped in detail with restriction enzymes and the Bkm-hybridizing segments were localized. Confirmation of X chromosomal homology was obtained for 2 of the clones and Bkm segments from these 2 clones were sequenced. Seventeen contiguous GATA repeats were found in each clone and the overall repeat arrangement showed relatively few differences from previously sequenced Bkm sequences. These are the first sequences of human Bkm repeats. The results, when compared with previously published results, suggest that there may be significant differences between the organization of Bkm repeats on the human X and on the human Y chromosome.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66402/1/j.1469-1809.1988.tb01094.x.pd

Discrete Model of Ideological Struggle Accounting for Migration

A discrete in time model of ideological competition is formulated taking into account population migration. The model is based on interactions between global populations of non-believers and followers of different ideologies. The complex dynamics of the attracting manifolds is investigated. Conversion from one ideology to another by means of (i) mass media influence and (ii) interpersonal relations is considered. Moreover a different birth rate is assumed for different ideologies, the rate being assumed to be positive for the reference population, made of initially non-believers. Ideological competition can happen in one or several regions in space. In the latter case, migration of non-believers and adepts is allowed; this leads to an enrichment of the ideological dynamics. Finally, the current ideological situation in the Arab countries and China is commented upon from the point of view of the presently developed mathematical model. The massive forced conversion by Ottoman Turks in the Balkans is briefly discussed.Comment: 24 pages, with 5 figures and 52 refs.; prepared for a Special issue of Advances in Complex System

Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion

Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain – notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction

A new Late Pliocene large provannid gastropod associated with hydrothermal venting at Kane Megamullion, Mid-Atlantic Ridge

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Taylor & Francis for personal use, not for redistribution. The definitive version was published in Journal of Systematic Palaeontology 10 (2012): 423-433, doi:10.1080/14772019.2011.607193.A new gastropod, Kaneconcha knorri gen et sp. nov., was found in marlstone dredged from the surface of Adam Dome at Kane Megamullion on the flank of the Mid-Atlantic Ridge in an area of former hydrothermal activity. The snail is interpreted as a large provannid similar to the chemosymbiotic genera Ifremeria and Alviniconcha. This is the first record of presumably chemosymbiotic provannids from the Atlantic Ocean and also the first fossil record of such large provannids associated with hydrothermal venting. Extant Alviniconcha and Ifremeria are endemic to hydrothermal vents in the Pacific and Indian oceans. Kaneconcha differs from Ifremeria in having no umbilicus and a posterior notch, and it differs from Alviniconcha in having the profile of the whorl slightly flattened and having no callus on the inner lip. A dark layer covering the Kaneconcha shell is interpreted here as a fossilized periostracum. The shell/periostracum interface shows fungal traces attributed to the ichnospecies Saccomorpha clava. We hypothesize that large chemosymbiotic provannids (i.e., Kaneconcha, Ifremeria, and Alviniconcha) form a clade that possibly diverged from remaining provannids in the Late Jurassic, with the Late Jurassic/Early Cretaceous Paskentana being an early member.R/V Knorr Cruise 180- 2 to Kane Megamullion was supported by National Science Foundation grant OCE- 0118445. A. Kaim acknowledges support from the Alexander von Humboldt Foundation. B. Tucholke acknowledges support from an Andrew W. Mellon Foundation Award for Innovative Research and from the Deep Ocean Exploration Institute at Woods Hole Oceanographic Institution

Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells

A central issue in stem cell biology is to understand the mechanisms that regulate the self-renewal of haematopoietic stem cells (HSCs), which are required for haematopoiesis to persist for the lifetime of the animal(1). We found that adult and fetal mouse and adult human HSCs express the proto-oncogene Bmi-1. The number of HSCs in the fetal liver of Bmi-1(-/-) mice(2) was normal. In postnatal Bmi-1(-/-) mice, the number of HSCs was markedly reduced. Transplanted fetal liver and bone marrow cells obtained from Bmi-1(-/-) mice were able to contribute only transiently to haematopoiesis. There was no detectable self-renewal of adult HSCs, indicating a cell autonomous defect in Bmi-1(-/-) mice. A gene expression analysis revealed that the expression of stem cell associated genes(3), cell survival genes, transcription factors, and genes modulating proliferation including p16(Ink4a) and p19(Arf) was altered in bone marrow cells of the Bmi-1(-/-) mice. Expression of p16(Ink4a) and p19(Arf) in normal HSCs resulted in proliferative arrest and p53-dependent cell death, respectively. Our results indicate that Bmi-1 is essential for the generation of self-renewing adult HSCs.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62508/1/nature01587.pd

Atg21p is essential for macropexophagy and microautophagy in the yeast Hansenula polymorpha

AbstractATG genes are required for autophagy-related processes that transport proteins/organelles destined for proteolytic degradation to the vacuole. Here, we describe the identification and characterisation of the Hansenula polymorpha ATG21 gene. Its gene product Hp-Atg21p, fused to eGFP, had a dual location in the cytosol and in peri-vacuolar dots. We demonstrate that Hp-Atg21p is essential for two separate modes of peroxisome degradation, namely glucose-induced macropexophagy and nitrogen limitation-induced microautophagy. In atg21 cells subjected to macropexophagy conditions, sequestration of peroxisomes tagged for degradation is initiated but fails to complete

Association Rate Constants of Ras-Effector Interactions Are Evolutionarily Conserved

Evolutionary conservation of protein interaction properties has been shown to be a valuable indication for functional importance. Here we use homology interface modeling of 10 Ras-effector complexes by selecting ortholog proteins from 12 organisms representing the major eukaryotic branches, except plants. We find that with increasing divergence time the sequence similarity decreases with respect to the human protein, but the affinities and association rate constants are conserved as predicted by the protein design algorithm, FoldX. In parallel we have done computer simulations on a minimal network based on Ras-effector interactions, and our results indicate that in the absence of negative feedback, changes in kinetics that result in similar binding constants have strong consequences on network behavior. This, together with the previous results, suggests an important biological role, not only for equilibrium binding constants but also for kinetics in signaling processes involving Ras-effector interactions. Our findings are important to take into consideration in system biology approaches and simulations of biological networks

Membrane curvature during peroxisome fission requires Pex11

Pex11p is required for peroxisome proliferation. This study demonstrates that the N-terminus of Pex11p forms an amphipathic helix that generates membrane curvature required for peroxisome fission

Search for Pairs of Isolated Radio Pulsars - Components in Disrupted Binary Systems

We have developed a method for analyzing the kinematic association of isolated relativistic objects - possible remnants of disrupted close binary systems. We investigate pairs of fairly young radio pulsars with known proper motions and estimated distances (dispersion measures) that are spaced no more than 2-3 kpc apart. Using a specified radial velocity distribution for these objects, we have constructed 100-300 thousand trajectories of their possible motion in the Galactic gravitational field on a time scale of several million years. The probabilities of their close encounters at epochs consistent with the age of the younger pulsar in the pair are analyzed. When these probabilities exceed considerably their reference values obtained by assuming a purely random encounter between the pulsars under consideration, we conclude that the objects may have been gravitationally bound in the past. As a result, we have detected six pulsar pairs (J0543+2329/J0528+2200, J1453-6413/J1430-6623, J2354+6155/J2321+6024, J1915+1009/J1909+1102, J1832-0827/J1836-1008, and J1917+1353/J1926+1648) that are companions in disrupted binary systems with a high probability. Estimates of their kinematic ages and velocities at binary disruption and at the present epoch are provided