Death of Stellar Baryonic Dark Matter

The nature of the dark matter in the haloes of galaxies is one of the outstanding questions in astrophysics. All stellar candidates, until recently thought to be likely baryonic contributions to the Halo of our Galaxy, are shown to be ruled out. Faint stars and brown dwarfs are found to constitute only a few percent of the mass of the Galaxy. Stellar remnants, including white dwarfs and neutron stars, are shown to be very constrained as well. High energy gamma-rays observed in HEGRA data place the strongest constraints, $\Omega_{WD} < 3 \times 10^{-3} h^{-1}$, where $h$ is the Hubble constant in units of 100 km s$^{-1}$ Mpc$^{-1}$. Hence one is left with several unanswered questions: 1) What are MACHOs seen in microlensing surveys? 2) What is the dark matter in our Galaxy? Indeed a nonbaryonic component in the Halo seems to be required.Comment: 6 pages ps fil

Intensive Mutagenesis of the Nisin Hinge Leads to the Rational Design of Enhanced Derivatives

peer-reviewedNisin A is the most extensively studied lantibiotic and has been used as a preservative by the food industry since 1953. This 34 amino acid peptide contains three dehydrated amino acids and five thioether rings. These rings, resulting from one lanthionine and four methyllanthionine bridges, confer the peptide with its unique structure. Nisin A has two mechanisms of action, with the N-terminal domain of the peptide inhibiting cell wall synthesis through lipid II binding and the C-terminal domain responsible for pore-formation. The focus of this study is the three amino acid ‘hinge’ region (N 20, M 21 and K 22) which separates these two domains and allows for conformational flexibility. As all lantibiotics are gene encoded, novel variants can be generated through manipulation of the corresponding gene. A number of derivatives in which the hinge region was altered have previously been shown to possess enhanced antimicrobial activity. Here we take this approach further by employing simultaneous, indiscriminate site-saturation mutagenesis of all three hinge residues to create a novel bank of nisin derivative producers. Screening of this bank revealed that producers of peptides with hinge regions consisting of AAK, NAI and SLS displayed enhanced bioactivity against a variety of targets. These and other results suggested a preference for small, chiral amino acids within the hinge region, leading to the design and creation of producers of peptides with hinges consisting of AAA and SAA. These producers, and the corresponding peptides, exhibited enhanced bioactivity against Lactococcus lactis HP, Streptococcus agalactiae ATCC 13813, Mycobacterium smegmatis MC2155 and Staphylococcus aureus RF122 and thus represent the first example of nisin derivatives that possess enhanced activity as a consequence of rational design.This work was financed by a grant from the Irish Department of Agriculture, Food and the Marine through the Food Institutional Research Measure (08/RD/C/691) and with Science Foundation Investigator award (10/IN.1/B3027)

Gas phase characterization of the noncovalent quaternary structure of Cholera toxin and the Cholera toxin B subunit pentamer

Cholera toxin (CTx) is an AB5 cytotonic protein that has medical relevance in cholera and as a novel mucosal adjuvant. Here, we report an analysis of the noncovalent homopentameric complex of CTx B chain (CTx B5) using electrospray ionization triple quadrupole mass spectrometry and tandem mass spectrometry and the analysis of the noncovalent hexameric holotoxin usingelectrospray ionization time-of-flight mass spectrometry over a range of pH values that correlate with those encountered by this toxin after cellular uptake. We show that noncovalent interactions within the toxin assemblies were maintained under both acidic and neutral conditions in the gas phase. However, unlike the related Escherichia coli Shiga-like toxin B5 pentamer (SLTx B), the CTx B5 pentamer was stable at low pH, indicating that additional interactions must be present within the latter. Structural comparison of the CTx B monomer interface reveals an additional α-helix that is absent in the SLTx B monomer. In silico energy calculations support interactions between this helix and the adjacent monomer. These data provide insight into the apparent stabilization of CTx B relative to SLTx B

Senior men's pacing profiles at the IAAF World Cross Country Championships.

The aim of this study was to describe pacing profiles used by senior men competing in the World Cross Country Championships. Lap times were collated for 1273 competitors across 10 races. Each individual's lap times were expressed as a percentage of the eventual winner's lap times, and athletes were grouped according to finishing position. Most athletes started the race by following the pace set by the leaders but slowed relative to the winner with each successive lap. The gold medallists were faster than the other medallists only after the final lap (P < 0.001). Most athletes who dropped out (61%) had completed the first lap within 105% of the winner's lap time. The medallists used a strategy of running close to the front from an early stage, but did not separate themselves from other top 15 finishers until halfway, with the eventual medal positions decided even closer to the finish. Athletes finishing further down had positive pacing profiles relative to the winner, possibly because of early fatigue caused by a relatively quick first lap. Athletes should note that a patient approach during the early stages can benefit not only the mass field but also those who aim to win a medal

Pacing, packing and sex-based differences in Olympic and IAAF World Championship marathons

The aim of this study was to describe pacing profiles and packing behaviours of athletes in Olympic and World Championship marathons. Finishing and split times were collated for 673 men and 549 women across nine competitions. Mean speeds for each intermediate 5 km and end 2.2 km segments were calculated. Medallists of both sexes maintained even-paced running from 10 km onwards whereas slower finishers dropped off the lead pack at approximately half-distance. Athletes who ran with the same opponents throughout slowed the least in the second half (P < .001, men: ES ≥ 1.19; women: ES ≥ 1.06), whereas other strategies such as moving between packs or running alone were less successful. Overall, women slowed less (P < .001, ES = 0.44) and were more likely to run a negative split (P < .001), and their more conservative start meant fewer women dropped out (P < .001). This also meant that women medallists sped up in the final 2.2 km, which might have decided the medal positions. Marathon runners are advised to identify rivals with similar abilities and ambitions to run alongside provided they start conservatively. Coaches should note important sex-based differences in tactics adopted and design training programmes accordingly

Ground reaction forces of Olympic and World Championship race walkers.

Abstract Race walking is an Olympic event where no visible loss of contact should occur and the knee must be straightened until midstance. The purpose of this study was to analyse ground reaction forces of world-class race walkers and associate them with key spatiotemporal variables. Nineteen athletes race walked along an indoor track and made contact with two force plates (1000 Hz) while being filmed using high-speed videography (100 Hz). Race walking speed was correlated with flight time (r = .46, p = .049) and flight distance (r = .69, p = .001). The knee's movement from hyperextension to flexion during late stance meant the vertical push-off force that followed midstance was smaller than the earlier loading peak (p < .001), resulting in a flattened profile. Athletes with narrower stride widths experienced reduced peak braking forces (r = .49, p = .046), peak propulsive forces (r = .54, p = .027), peak medial forces (r = .63, p = .007) and peak vertical push-off forces (r = .60, p = .011). Lower fluctuations in speed during stance were associated with higher stride frequencies (r = .69, p = .001), and highlighted the importance of avoiding too much braking in early stance. The flattened trajectory and consequential decrease in vertical propulsion might help the race walker avoid visible loss of contact (although non-visible flight times were useful in increasing stride length), while a narrow stride width was important in reducing peak forces in all three directions and could improve movement efficiency

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression

The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate

BIRCH: A user-oriented, locally-customizable, bioinformatics system

BACKGROUND: Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. RESULTS: BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. CONCLUSION: BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere

Nipah Virus Infection in Dogs, Malaysia, 1999

The 1999 outbreak of Nipah virus encephalitis in humans and pigs in Peninsular Malaysia ended with the evacuation of humans and culling of pigs in the epidemic area. Serologic screening showed that, in the absence of infected pigs, dogs were not a secondary reservoir for Nipah virus