Competition for food in meerkats (Suricata suricatta)

In group living species animals commonly compete for limited resources such as food (Darwin 1859). Winning competition for food may be beneficial for an individuals survival or reproductive success (Williams 1966; Clutton-Brock 1988; Metcalfe et al 1995) but conflict with group members may be costly as it typically involves aggression (Huntingford&Turner 1987, Mesterton-Gibbons&Adams 1998). Asymmetries between individuals are predicted to determine the outcome of competition (Maynard-Smith&Parker 1976), and individuals are expected to steal food when the benefit to them is greatest (Barnard 1984; Trivers 1972). I therefore investigate what determines the outcome of competition for food between group members, and what factors affect whether group members try to steal food in the cooperatively breeding meerkat (Suricatta suricatta). Meerkats competed for food items infrequently and the owner of a food item typically won competition, but dominant individuals and breeding females were more likely to win competition than other group members. This provides support for models of conflict over resources in group living species which predict that ownership may determine the outcome of competition, thereby avoiding frequent costly conflict (Maynard-Smith 1982). Furthermore, where large asymmetries exist between contestants in dominance status or the value of a resource, these may determine the outcome of competition (Maynard-Smith&Parker 1976; Grafen 1987). Meerkats varied in how frequently they tried to steal food depending upon the costs and benefits of competition. Dominant individuals competed for food more frequently which is likely to reflect reduced costs of competition as subordinate individuals may avoid conflict with them (Packer&Pusey 1985). Females competed for food more frequently than males and more frequently during breeding, reflecting the higher costs of reproduction to females compared to males (Williams 1966; Trivers 1972). Meerkats compete more frequently for food when food availability is low, which indicates that food items may be more valuable when they are rare. Meerkats in smaller groups competed more frequently. In cooperatively breeding species group members undertake a large number of costly helping behaviours. Individuals in small groups each contribute more effort to helping than individuals in large groups and suffer higher costs which may increase the benefit of food to them (Clutton-Brock et al 1998a; Clutton-Brock et al 2001a). Competition for the opportunity to breed in cooperatively breeding meerkats has resulted in despotic dominance hierarchies where a dominant female monopolises breeding and reproductively suppresses subordinates (Clutton-Brock et al 2001b). Dominant females stole more food than any other group members. This is likely to be a consequence of the high costs of reproduction for the dominant breeding female in species with high reproductive skew (Creel&Creel 1991; Clutton-Brock et al 2001b). Furthermore, dominant females were more aggressive and more successful in competition for food with their reproductive competitors. Dominant females may therefore use competition for food as a means of asserting dominance over their reproductive competitors which could contribute to reproductive suppression (Creel et al 1992; Williams 2004; Kutsukake&Clutton-Brock 2006b; Young et al 2006).Dissertation (MSc)--University of Pretoria, 2011.Zoology and Entomologyunrestricte

Ten years of different crop rotations in a no-tillage system – what happened to plant diseases and nematode pests?

Aim To study the long-term effects of crop rotation and residue level on diseases and nematodes in Western Australian no-tillage systems

Molecular fluorine chemistry in the early Universe

Some models of Big Bang nucleosynthesis suggest that very high baryon density regions were formed in the early Universe, and generated the production of heavy elements other than lithium such as fluorine F. We present a comprehensive chemistry of fluorine in the post-recombination epoch. Calculation of F, F- and HF abundances, as a function of redshift z, are carried out. The main result is that the chemical conditions in the early Universe can lead to the formation of HF. The final abundance of the diatomic molecule HF is predicted to be close to 3.75 10(-17) when the initial abundance of neutral fluorine F is 10(-15). These results indicate that molecules of fluorine HF were already present during the dark age. This could have implications on the evolution of proto-objects and on the anisotropies of cosmic microwave background radiation. Hydride of fluorine HF may affect enhancement of the emission line intensity from the proto-objects and could produce spectral-spatial fluctuations.Comment: Accepted in Astronomy and Astrophysics, 7 pages, 2 figure

Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized

Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been center stage in the prediction and design of protein structure and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state -- a necessary component of these potentials -- is an unsolved problem. PMFs are loosely justified by analogy to the reversible work theorem in statistical physics, or by a statistical argument based on a likelihood function. Both justifications are insightful but leave many questions unanswered. Here, we show for the first time that PMFs can be seen as approximations to quantities that do have a rigorous probabilistic justification: they naturally arise when probability distributions over different features of proteins need to be combined. We call these quantities reference ratio distributions deriving from the application of the reference ratio method. This new view is not only of theoretical relevance, but leads to many insights that are of direct practical use: the reference state is uniquely defined and does not require external physical insights; the approach can be generalized beyond pairwise distances to arbitrary features of protein structure; and it becomes clear for which purposes the use of these quantities is justified. We illustrate these insights with two applications, involving the radius of gyration and hydrogen bonding. In the latter case, we also show how the reference ratio method can be iteratively applied to sculpt an energy funnel. Our results considerably increase the understanding and scope of energy functions derived from known biomolecular structures

FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.

CAG repeat expansion in the HTT gene drives Huntington's disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch repair pathway (MMR), is not defined. Here, we identify a highly conserved SPYF motif at the N terminus of FAN1 that binds to MLH1. Our data support a model where FAN1 has two distinct functions to stabilize CAG repeats. On one hand, it binds MLH1 to restrict its recruitment by MSH3, thus inhibiting the assembly of a functional MMR complex that would otherwise promote CAG repeat expansion. On the other hand, it promotes accurate repair via its nuclease activity. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion

Fe XIII emission lines in active region spectra obtained with the Solar Extreme-Ultraviolet Research Telescope and Spectrograph

Recent fully relativistic calculations of radiative rates and electron impact excitation cross sections for Fe {\sc xiii} are used to generate emission-line ratios involving 3s$^{2}$3p$^{2}$--3s3p$^{3}$ and 3s$^{2}$3p$^{2}$--3s$^{2}$3p3d transitions in the 170--225 \AA and 235--450 \AA wavelength ranges covered by the Solar Extreme-Ultraviolet Research Telescope and Spectrograph (SERTS). A comparison of these line ratios with SERTS active region observations from rocket flights in 1989 and 1995 reveals generally very good agreement between theory and experiment. Several new Fe {\sc xiii} emission features are identified, at wavelengths of 203.79, 259.94, 288.56 and 290.81 \AA. However, major discrepancies between theory and observation remain for several Fe {\sc xiii} transitions, as previously found by Landi (2002) and others, which cannot be explained by blending. Errors in the adopted atomic data appear to be the most likely explanation, in particular for transitions which have 3s$^{2}$3p3d $^{1}$D$_{2}$ as their upper level. The most useful Fe {\sc xiii} electron density diagnostics in the SERTS spectral regions are assessed, in terms of the line pairs involved being (i) apparently free of atomic physics problems and blends, (ii) close in wavelength to reduce the effects of possible errors in the instrumental intensity calibration, and (iii) very sensitive to changes in N$_{e}$ over the range 10$^{8}$--10$^{11}$ cm$^{-3}$. It is concluded that the ratios which best satisfy these conditions are 200.03/202.04 and 203.17/202.04 for the 170--225 \AA wavelength region, and 348.18/320.80, 348.18/368.16, 359.64/348.18 and 359.83/368.16 for 235--450 \AA.Comment: 11 pages, 8 figures, 10 tables, MNRAS, in pres

Accurate fundamental parameters for 23 bright solar-type stars

We combine results from interferometry, asteroseismology and spectroscopy to determine accurate fundamental parameters of 23 bright solar-type stars, from spectral type F5 to K2 and luminosity classes III to V. For some stars we can use direct techniques to determine the mass, radius, luminosity and effective temperature, and we compare with indirect methods that rely on photometric calibrations or spectroscopic analyses. We use the asteroseismic information available in the literature to infer an indirect mass with an accuracy of 4-15 percent. From indirect methods we determine luminosity and radius to 3 percent. For Teff we find a slight offset of -40+-20 K between the spectroscopic method and the direct method, meaning the spectroscopic temperatures are too high. From the spectroscopic analysis we determine the detailed chemical composition for 13 elements, including Li, C and O. We find no significant offset between the spectroscopic surface gravity and the value from combining asteroseismology with radius estimates. From the spectroscopy we also determine vsini and we present a new calibration of macro- and microturbulence. From the comparison between the results from the direct and spectroscopic methods we claim that we can determine Teff, log g, and [Fe/H] with absolute accuracies of 80 K, 0.08 dex, and 0.07 dex. The indirect methods are important to obtain reliable estimates of the fundamental parameters of relatively faint stars when interferometry cannot be used. Our study is the first to compare direct and indirect methods for a large sample of stars, and we conclude that indirect methods are valid, although slight corrections may be needed.Comment: Accepted by MNRAS. Abstract abridge

New Noncovalent Inhibitors of Penicillin-Binding Proteins from Penicillin-Resistant Bacteria

BACKGROUND: Penicillin-binding proteins (PBPs) are well known and validated targets for antibacterial therapy. The most important clinically used inhibitors of PBPs beta-lactams inhibit transpeptidase activity of PBPs by forming a covalent penicilloyl-enzyme complex that blocks the normal transpeptidation reaction; this finally results in bacterial death. In some resistant bacteria the resistance is acquired by active-site distortion of PBPs, which lowers their acylation efficiency for beta-lactams. To address this problem we focused our attention to discovery of novel noncovalent inhibitors of PBPs. METHODOLOGY/PRINCIPAL FINDINGS: Our in-house bank of compounds was screened for inhibition of three PBPs from resistant bacteria: PBP2a from Methicillin-resistant Staphylococcus aureus (MRSA), PBP2x from Streptococcus pneumoniae strain 5204, and PBP5fm from Enterococcus faecium strain D63r. Initial hit inhibitor obtained by screening was then used as a starting point for computational similarity searching for structurally related compounds and several new noncovalent inhibitors were discovered. Two compounds had promising inhibitory activities of both PBP2a and PBP2x 5204, and good in-vitro antibacterial activities against a panel of Gram-positive bacterial strains. CONCLUSIONS: We found new noncovalent inhibitors of PBPs which represent important starting points for development of more potent inhibitors of PBPs that can target penicillin-resistant bacteria.Eur-Intafa

Dust Devil Tracks

Dust devils that leave dark- or light-toned tracks are common on Mars and they can also be found on the Earth’s surface. Dust devil tracks (hereinafter DDTs) are ephemeral surface features with mostly sub-annual lifetimes. Regarding their size, DDT widths can range between ∼1 m and ∼1 km, depending on the diameter of dust devil that created the track, and DDT lengths range from a few tens of meters to several kilometers, limited by the duration and horizontal ground speed of dust devils. DDTs can be classified into three main types based on their morphology and albedo in contrast to their surroundings; all are found on both planets: (a) dark continuous DDTs, (b) dark cycloidal DDTs, and (c) bright DDTs. Dark continuous DDTs are the most common type on Mars. They are characterized by their relatively homogenous and continuous low albedo surface tracks. Based on terrestrial and martian in situ studies, these DDTs most likely form when surficial dust layers are removed to expose larger-grained substrate material (coarse sands of ≥500 μm in diameter). The exposure of larger-grained materials changes the photometric properties of the surface; hence leading to lower albedo tracks because grain size is photometrically inversely proportional to the surface reflectance. However, although not observed so far, compositional differences (i.e., color differences) might also lead to albedo contrasts when dust is removed to expose substrate materials with mineralogical differences. For dark continuous DDTs, albedo drop measurements are around 2.5 % in the wavelength range of 550–850 nm on Mars and around 0.5 % in the wavelength range from 300–1100 nm on Earth. The removal of an equivalent layer thickness around 1 μm is sufficient for the formation of visible dark continuous DDTs on Mars and Earth. The next type of DDTs, dark cycloidal DDTs, are characterized by their low albedo pattern of overlapping scallops. Terrestrial in situ studies imply that they are formed when sand-sized material that is eroded from the outer vortex area of a dust devil is redeposited in annular patterns in the central vortex region. This type of DDT can also be found in on Mars in orbital image data, and although in situ studies are lacking, terrestrial analog studies, laboratory work, and numerical modeling suggest they have the same formation mechanism as those on Earth. Finally, bright DDTs are characterized by their continuous track pattern and high albedo compared to their undisturbed surroundings. They are found on both planets, but to date they have only been analyzed in situ on Earth. Here, the destruction of aggregates of dust, silt and sand by dust devils leads to smooth surfaces in contrast to the undisturbed rough surfaces surrounding the track. The resulting change in photometric properties occurs because the smoother surfaces have a higher reflectance compared to the surrounding rough surface, leading to bright DDTs. On Mars, the destruction of surficial dust-aggregates may also lead to bright DDTs. However, higher reflective surfaces may be produced by other formation mechanisms, such as dust compaction by passing dust devils, as this may also cause changes in photometric properties. On Mars, DDTs in general are found at all elevations and on a global scale, except on the permanent polar caps. DDT maximum areal densities occur during spring and summer in both hemispheres produced by an increase in dust devil activity caused by maximum insolation. Regionally, dust devil densities vary spatially likely controlled by changes in dust cover thicknesses and substrate materials. This variability makes it difficult to infer dust devil activity from DDT frequencies. Furthermore, only a fraction of dust devils leave tracks. However, DDTs can be used as proxies for dust devil lifetimes and wind directions and speeds, and they can also be used to predict lander or rover solar panel clearing events. Overall, the high DDT frequency in many areas on Mars leads to drastic albedo changes that affect large-scale weather patterns

NMR Structure of Lipoprotein YxeF from Bacillus subtilis Reveals a Calycin Fold and Distant Homology with the Lipocalin Blc from Escherichia coli

The soluble monomeric domain of lipoprotein YxeF from the Gram positive bacterium B. subtilis was selected by the Northeast Structural Genomics Consortium (NESG) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins. The solution NMR structure of YxeF reveals a calycin fold and distant homology with the lipocalin Blc from the Gram-negative bacterium E.coli. In particular, the characteristic β-barrel, which is open to the solvent at one end, is extremely well conserved in YxeF with respect to Blc. The identification of YxeF as the first lipocalin homologue occurring in a Gram-positive bacterium suggests that lipocalins emerged before the evolutionary divergence of Gram positive and Gram negative bacteria. Since YxeF is devoid of the α-helix that packs in all lipocalins with known structure against the β-barrel to form a second hydrophobic core, we propose to introduce a new lipocalin sub-family named ‘slim lipocalins’, with YxeF and the other members of Pfam family PF11631 to which YxeF belongs constituting the first representatives. The results presented here exemplify the impact of structural genomics to enhance our understanding of biology and to generate new biological hypotheses