Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori

Urease plays a central role in the pathogenesis of Helicobacter pylori in humans. Maturation of this nickel metalloenzyme in bacteria requires the participation of the accessory proteins UreD (termed UreH in H. pylori), UreF, and UreG, which form sequential complexes with the urease apoprotein as well as UreE, a metallochaperone. Here, we describe the crystal structure of C‐terminal truncated UreF from H. pylori (residues 1–233), the first UreF structure to be determined, at 1.55 Å resolution using SAD methods. UreF forms a dimer in vitro and adopts an all‐helical fold congruent with secondary structure prediction. On the basis of evolutionary conservation analysis, the structure reveals a probable binding surface for interaction with other urease components as well as key conserved residues of potential functional relevance. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Intrauterine programming of ageing

Ageing is an unavoidable corollary to being alive; the most intuitive interpretation of ageing being that it is the consequence of progressive body degeneration. In agreement with this, current models propose that ageing occurs through a stepwise accumulation of DNA damage, which ultimately limits the regenerative capacity of tissues. On the other hand, there is increasing evidence that fetal distress can influence the development of disease in adult life, a phenomenon known as ‘intrauterine programming’. The extent to which an intrauterine exposure to DNA damage can compromise lifespan remains unclear. My group has recently generated a murine model of a human syndrome linked to defective DNA repair and observed that these animals age prematurely, but the accumulation of DNA damage is restricted mostly to the embryonic period. Here, I discuss the implications of this finding and propose that ageing can be influenced by fetal distress.     

Genetic association between bovine NOD2 polymorphisms and infection by Mycobacterium avium subsp. paratuberculosis in Holstein‐Friesian cattle

Nucleotide‐Binding Oligomerization Domain 2 (NOD2) has been reported to be a candidate gene for Mycobacterium avium subsp. paratuberculosis (MAP) infection in a Bos taurus × Bos indicus mixed breed based on a genetic association with the c.2197T>C single nucleotide polymorphism (SNP). Nevertheless, this SNP has also been reported to be monomorphic in the B. taurus species. In the present work, 18 SNPs spanning the bovine NOD2 gene have been analysed in a genetic association study of two independent populations of Holstein‐Friesian cattle. We found that the C allele of SNP c.*1908C>T, located in the 3′‐UTR region of the gene, is significantly more frequent in infected animals than in healthy ones, which supports the idea that the bovine NOD2 gene plays a role in susceptibility to MAP infection. However, in silico analyses of the NOD2 nucleotide sequence did not yield definitive data about a possible direct effect of SNP c.*1908C>T on susceptibility to infection and led us to consider its linkage disequilibrium with the causative variant. A more exhaustive genetic association study including all putative, functional SNPs from this gene and subsequent functional analyses needs to be conducted to achieve a more complete understanding of how different variants of NOD2 may affect susceptibility to MAP infection in cattle.     

Alavesia Waters and Arillo–a Cretaceous‐era genus discovered extant on the Brandberg Massif,Namibia (Diptera: Atelestidae)

Two new extant species of the fossil genus Alavesia Waters & Arillo (A. brandbergensis sp.n. and A. daura sp.n. ) are described from the Brandberg Massif, Namibia. The genus is reassigned to the family Atelestidae (subfamily Atelestinae) on the basis of male terminalia (elongate gonocoxal apodemes, ventral apodemes, subapical surstylus), female terminalia (absence of tergum 10) and a three‐articled stylus. This is the first record of Atelestidae from the Afrotropical Region. A genus‐level phylogeny of the Atelestidae is resolved, in which Alavesia is the sister genus to the remaining genera of the Atelestinae. The biogeographic history of the genus is briefly discussed, as is the significance of this and other relict Diptera on the Brandberg.     

Mechanisms of antimicrobial resistance and genetic relatedness among enterococci isolated from dogs and cats in the United States

Aims: In this study, mechanisms of antimicrobial resistance and genetic relatedness among resistant enterococci from dogs and cats in the United States were determined. Methods and Results: Enterococci resistant to chloramphenicol, ciprofloxacin, erythromycin, gentamicin, kanamycin, streptomycin, lincomycin, quinupristin/dalfopristin and tetracycline were screened for the presence of 15 antimicrobial resistance genes. Five tetracycline resistance genes [tet(M), tet(O), tet(L), tet(S) and tet(U)] were detected with tet(M) accounting for approx. 60% (130/216) of tetracycline resistance; erm(B) was also widely distributed among 96% (43/45) of the erythromycin‐resistant enterococci. Five aminoglycoside resistance genes were also detected among the kanamycin‐resistant isolates with the majority of isolates (25/36; 69%) containing aph(3′)‐IIIa. The bifunctional aminoglycoside resistance gene, aac(6′)‐Ie‐aph(2″)‐Ia, was detected in gentamicin‐resistant isolates and ant(6)‐Ia in streptomycin‐resistant isolates. The most common gene combination among enterococci from dogs (n = 11) was erm(B), aac(6′)‐Ie‐aph(2″)‐Ia, aph(3′)‐IIIa, tet(M), while tet(O), tet(L) were most common among cats (n = 18). Using pulsed‐field gel electrophoresis (PFGE), isolates clustered according to enterococcal species, source and antimicrobial gene content and indistinguishable patterns were observed for some isolates from dogs and cats. Conclusion: Enterococci from dogs and cats may be a source of antimicrobial resistance genes. Significance and Impact of the Study: Dogs and cats may act as reservoirs of antimicrobial resistance genes that can be transferred from pets to people. Although host‐specific ecovars of enterococcal species have been described, identical PFGE patterns suggest that enterococcal strains may be exchanged between these two animal species.     

First record of the brachiopod Lingulella waptaensis with pedicle from the Middle Cambrian Burgess Shale

Pettersson Stolk, S., Holmer, L. E. and Caron, J ‐B. 2010. First record of the brachiopod Lingulella waptaensis with pedicle from the Middle Cambrian Burgess Shale. —Acta Zoologica (Stockholm) 91 : 150–162 The organophosphatic shells of linguloid brachiopods are a common component of normal Cambrian–Ordovician shelly assemblages. Preservation of linguloid soft‐part anatomy, however, is extremely rare, and restricted to a few species in Lower Cambrian Konservat Lagerstätten. Such remarkable occurrences provide unique insights into the biology and ecology of early linguloids that are not available from the study of shells alone. Based on its shells, Lingulella waptaensis Walcott, was originally described in 1924 from the Middle Cambrian Burgess Shale but despite the widespread occurrence of soft‐part preservation associated with fossils from the same levels, no preserved soft parts have been reported. Lingulella waptaensis is restudied herein based on 396 specimens collected by Royal Ontario Museum field parties from the Greater Phyllopod Bed (Walcott Quarry Shale Member, British Columbia). The new specimens, including three with exceptional preservation of the pedicle, were collected in situ in discrete obrution beds. Census counts show that L. waptaensis is rare but recurrent in the Greater Phyllopod Bed, suggesting that this species might have been generalist. The wrinkled pedicle protruded posteriorly between the valves, was composed of a central coelomic space, and was slender and flexible enough to be tightly folded, suggesting a thin chitinous cuticle and underlying muscular layers. The nearly circular shell and the long, slender and highly flexible pedicle suggest that L. waptaensis lived epifaunally, probably attached to the substrate. Vertical cross‐sections of the shells show that L. waptaensis possessed a virgose secondary layer, which has previously only been known from Devonian to Recent members of the Family Lingulidae.     

The fitness value of information

Communication and information are central concepts in evolutionary biology. In fact, it is hard to find an area of biology where these concepts are not used. However, quantifying the information transferred in biological interactions has been difficult. How much information is transferred when the first spring rainfall hits a dormant seed, or when a chick begs for food from its parent? One measure that is commonly used in such cases is fitness value: by how much, on average, an individual's fitness would increase if it behaved optimally with the new information, compared to its average fitness without the information. Another measure, often used to describe neural responses to sensory stimuli, is the mutual information – a measure of reduction in uncertainty, as introduced by Shannon in communication theory. However, mutual information has generally not been considered to be an appropriate measure for describing developmental or behavioral responses at the organismal level, because it is blind to function; it does not distinguish between relevant and irrelevant information. In this paper we show that there is in fact a surprisingly tight connection between these two measures in the important context of evolution in an uncertain environment. In this case, a useful measure of fitness benefit is the increase in the long‐term growth rate, or the fold increase in number of surviving lineages. We show that in many cases the fitness value of a developmental cue, when measured this way, is exactly equal to the reduction in uncertainty about the environment, as described by the mutual information.