Mechanical control of the directional stepping dynamics of the kinesin motor

Among the multiple steps constituting the kinesin's mechanochemical cycle, one of the most interesting events is observed when kinesins move an 8-nm step from one microtubule (MT)-binding site to another. The stepping motion that occurs within a relatively short time scale (~100 microsec) is, however, beyond the resolution of current experiments, therefore a basic understanding to the real-time dynamics within the 8-nm step is still lacking. For instance, the rate of power stroke (or conformational change), that leads to the undocked-to-docked transition of neck-linker, is not known, and the existence of a substep during the 8-nm step still remains a controversial issue in the kinesin community. By using explicit structures of the kinesin dimer and the MT consisting of 13 protofilaments (PFs), we study the stepping dynamics with varying rates of power stroke (kp). We estimate that 1/kp <~ 20 microsec to avoid a substep in an averaged time trace. For a slow power stroke with 1/kp>20 microsec, the averaged time trace shows a substep that implies the existence of a transient intermediate, which is reminiscent of a recent single molecule experiment at high resolution. We identify the intermediate as a conformation in which the tethered head is trapped in the sideway binding site of the neighboring PF. We also find a partial unfolding (cracking) of the binding motifs occurring at the transition state ensemble along the pathways prior to binding between the kinesin and MT.Comment: 26 pages, 10 figure

Observations and properties of candidate high frequency GPS radio sources in the AT20G survey

We used the Australia Telescope Compact Array (ATCA) to obtain 40 GHz and 95 GHz observations of a number of sources that were selected from the Australia Telescope Compact Array 20 GHz (AT20G) survey . The aim of the observations was to improve the spectral coverage for sources with spectral peaks near 20 GHz or inverted (rising) radio spectra between 8.6 GHz and 20 GHz. We present the radio observations of a sample of 21 such sources along with optical spectra taken from the ANU Siding Spring Observatory 2.3m telescope and the ESO-New Technology Telescope (NTT). We find that as a group the sources show the same level of variability as typical GPS sources, and that of the 21 candidate GPS sources roughly 60% appear to be genuinely young radio galaxies. Three of the 21 sources studied show evidence of being restarted radio galaxies. If these numbers are indicative of the larger population of AT20G radio sources then as many as 400 genuine GPS sources could be contained within the AT20G with up to 25% of them being restarted radio galaxies.Comment: 21 pages, 24 figures, Table 1 truncated at 11 column

ATPMN: accurate positions and flux densities at 5 and 8 GHz for 8,385 sources from the PMN survey

We present a source catalogue of 9,040 radio sources resulting from high-resolution observations of 8,385 PMN sources with the Australia Telescope Compact Array. The catalogue lists flux density and structural measurements at 4.8 and 8.6 GHz, derived from observations of all PMN sources in the declination range -87 deg < delta < -38.5 deg (exclusive of galactic latitudes |b| 70 mJy (50 mJy south of delta = -73 deg). We assess the quality of the data, which was gathered in 1992-1994, describe the population of catalogued sources, and compare it to samples from complementary catalogues. In particular we find 127 radio sources with probable association with gamma-ray sources observed by the orbiting Fermi Large Area Telescope.Comment: 20 pages, 21 figure

Mixed Models with n>1 and Large Scale Structure constraints

Recent data on CBR anisotropies show a Doppler peak higher than expected in CDM cosmological models, if the spectral index $n=1$. However, CDM and LCDM models with n>1 can hardly be consistent with LSS data. Mixed models, instead, whose transfer function is naturally steeper because of free--streaming in the hot component, may become consistent with data if n>1, when Omega_h is large. This is confirmed by our detailed analysis, extended both to models with a hot component whose momentum space distribution had a thermal origin (like massive neutrinos), and to models with a non--cold component arising from heavier particle decay. In this work we systematically search models which fulfill all constraints which can be implemented at the linear level. We find that a stringent linear constraint arises from fitting the extra-power parameter Gamma. Other significant constraints arise comparing the expected abundances of galaxy clusters and high-z systems with observational data. Keeping to models with Gamma \geq 0.13, a suitable part of the space parameter still allows up to \sim 30% of hot component (it is worth outlining that our stringent criteria allow only models with 0.10 \mincir Omega_h \mincir 0.16, if n \leq 1). We also outline that models with such large non--cold component would ease the solution of the so--called baryon catastrophe in galaxy clusters.Comment: 28 pages + 9 figures, uses elsart.sty, to be published in New Astronom

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals

Molecular characterization of a multidrug resistance IncF plasmid from the globally disseminated Escherichia coli ST131 clone.

Escherichia coli sequence type 131 (E. coli ST131) is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections. Plasmids represent a major vehicle for the carriage of antibiotic resistance genes in E. coli ST131. In this study, we determined the complete sequence and performed a comprehensive annotation of pEC958, an IncF plasmid from the E. coli ST131 reference strain EC958. Plasmid pEC958 is 135.6 kb in size, harbours two replicons (RepFIA and RepFII) and contains 12 antibiotic resistance genes (including the blaCTX-M-15 gene). We also carried out hyper-saturated transposon mutagenesis and multiplexed transposon directed insertion-site sequencing (TraDIS) to investigate the biology of pEC958. TraDIS data showed that while only the RepFII replicon was required for pEC958 replication, the RepFIA replicon contains genes essential for its partitioning. Thus, our data provides direct evidence that the RepFIA and RepFII replicons in pEC958 cooperate to ensure their stable inheritance. The gene encoding the antitoxin component (ccdA) of the post-segregational killing system CcdAB was also protected from mutagenesis, demonstrating this system is active. Sequence comparison with a global collection of ST131 strains suggest that IncF represents the most common type of plasmid in this clone, and underscores the need to understand its evolution and contribution to the spread of antibiotic resistance genes in E. coli ST131

Unexpected host dependency of Antarctic Nanohaloarchaeota

In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships