Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces

S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K(D) value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K(D)=160(+/-40)microM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme.     

Occurrence of antibiotic resistance in Escherichia coli from surface waters and fecal pollution sources near Hamilton, Ontario

Antibiotic resistance was examined in 462 Escherichia coli isolates from surface waters and fecal pollution sources around Hamilton, Ontario. Escherichia coli were resistant to the highest concentrations of each of the 14 antibiotics studied, although the prevalence of high resistance was mostly low. Two of 12 E. coli isolates from sewage in a CSO tank had multiple resistance to ampicillin, ciprofloxacin, gentamicin, and tetracycline above their clinical breakpoints. Antibiotic resistance was less prevalent in E. coli from bird feces than from municipal wastewater sources. A discriminant function calculated from antibiotic resistance data provided an average rate of correct classification of 68% for discriminating E. coli from bird and wastewater fecal pollution sources. The preliminary microbial source tracking results suggest that, at times, bird feces might be a more prominent contributor of E. coli to Bayfront Park beach waters than municipal wastewater sources.     

Blockade of CD14 increases Shigella-mediated invasion and tissue destruction

Shigella is a diarrheal pathogen that causes disease through invasion of the large intestinal mucosa. The endotoxin of the invading bacterium may play a key role in the disease process by causing inflammation and tissue injury during infection. Earlier studies have shown that various animal species lacking functional CD14 were protected against endotoxin-mediated shock. Rabbits experimentally infected with Shigella were used to test the hypothesis that blockade of endotoxin-induced cell activation with anti-CD14 mAb would diminish inflammation and thus disease severity. Unexpectedly, we observed that the intestinal mucosa of anti-CD14-treated animals exhibited a 50-fold increase in bacterial invasion and more severe tissue injury compared with controls. Despite higher bacterial loads in treated animals, the numbers of polymorphonuclear leukocytes that were recruited to the infection site were similar to those in controls. Furthermore, the phagocytic cells of CD14-blocked animals produced IL-1 and TNF-alpha. Moreover, in vitro blockade of CD14 did not impede bactericidal activity. Thus, anti-CD14 treatment interfered with host defense mechanisms involved with removal/eradication of Shigella.     

The reduction potential of the beta-carotene.+ /beta-carotene couple in an aqueous micro-heterogeneous environment

There is a resurgence of interest in the role of electron transfer reactions involving beta-carotene in photosynthesis. There is also current debate on the health benefits of dietary carotenoids and the possible deleterious effects on certain sub-populations such as smokers. The impact of dietary carotenoids on health may well be also related to radical reactions. A key parameter in biological systems is therefore the one-electron reduction potential of the carotenoid radical cation, now reported for the first time in a model biological aqueous environment. The value obtained is 1.06+/-0. 01 V and is sufficiently high to oxidise cell membrane proteins, but is low enough to repair P(680).+ in the photosynthetic reaction centre.     

Using genetic techniques to quantify reinvasion,survival and in situ breeding rates during control operations

Determining the origin of individuals caught during a control/eradication programme enables conservation managers to assess the reinvasion rates of their target species and evaluate the level of success of their control methods. We examine how genetic techniques can focus management by distinguishing between hypotheses of ‘reinvasion’ and ‘survivor’, and defining kin groups for invasive stoats (Mustela erminea) on Secretary Island, New Zealand. 205 stoats caught on the island were genotyped at 16 microsatellite loci, along with 40 stoats from the opposing mainland coast, and the age and sex were determined for each individual. Using these data, we compare and combine a variety of genetic techniques including genetic clustering, population assignment and kinship‐based techniques to assess the origin of each stoat. The population history and individual movement could be described in fine detail, with results indicating that both in‐situ survival and breeding, and reinvasion are occurring. Immigration to the island was found to be generally low, apart from in 1 year where around 8 stoats emigrated from the mainland. This increased immigration was probably linked to a stoat population spike on the mainland in that year, caused by a masting event of southern beech forest (Nothofagus sp.) and the subsequent rodent irruption. Our study provides an example of some of the ways genetic analyses can feed directly into informing management practices for invasive species.     

Structural elucidation of glycosaminoglycans through characterization of disaccharides obtained after fragmentation by hydrazine-nitrous acid treatment

Hydrazinolysis of glycosaminoglycans to bring about N-deacetylation followed by nitrous acid treatment to effect deaminative cleavage at alternating hexosamine residues has been used to make possible identification and quantitation of disaccharide sequences and position of O-sulfate substitution in nanogram amounts of these polymers. After radiolabeling by NaB3H4 reduction the hydrazine-nitrous acid products were fractionated on Dowex 1 and further resolved by thin-layer chromatography into disaccharides terminating in either sulfated or unsulfated anhydromannitol or anhydrotalitol. Fragmentation of hyaluronic acid, keratan sulfate, chondroitin 4-sulfate, chondroitin 6-sulfate, dermatan sulfate, and heparin yielded a total of 14 disaccharides comprising the major sequences (greater than 1 mol%) occurring in mammalian glycosaminoglycans. Disaccharides representing the predominant variants of the chondroitin sulfates [GlcUA beta 1----3anhydrotalitol(4-SO4) and GlcUA beta 1----3anhydrotalitol(6-SO4)] as well as of dermatan sulfate chains [IdUA alpha 1----3anhydrotalitol(4-SO4) and GlcUA beta 1----3anhydrotalitol(4-SO4)] chains could readily be quantitated by this approach. In the case of heparin a comparison of the disaccharides produced by direct nitrous acid and hydrazine-nitrous acid treatments moreover provided an assessment of the distribution of N-sulfate groups. The characterization of the various disaccharides by Smith periodic acid degradation and glycosidase digestions was facilitated by the preparation and thin-layer chromatographic resolution of the complete series of monosulfated derivatives of anhydromannitol and anhydrotalitol; the sulfate esters were shown to be stable to both the hydrazine and nitrous acid treatments. The high sensitivity of the hydrazine-nitrous acid fragmentation procedure should prove useful in the structural elucidation of cell surface and basement membrane proteoglycans as well as other sulfated glycoconjugates which are present in small amounts.     

Effect of Incubation Temperature on the Detection of Thermophilic Campylobacter Species from Freshwater Beaches,Nearby Wastewater Effluents,and Bird Fecal Droppings

This large-scale study compared incubation temperatures (37°C versus 42°C) to study the detection of thermophilic Campylobacter species, including Campylobacter jejuni, C. coli, and C. lari, in various surface water samples and bird fecal droppings around Hamilton Harbor, Lake Ontario. The putative culture isolates obtained from incubation temperatures of 37 and 42°C were confirmed by Campylobacter genus- and species-specific triplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA gene internal transcribed spacer (ITS) region. A total of 759 water, wastewater, and bird fecal dropping samples were tested. Positive amplification reactions for the genus Campylobacter were found for 454 (60%) samples incubated at 37°C, compared to 258 (34%) samples incubated at 42°C. C. jejuni (16%) and C. lari (12%) were detected significantly more frequently at the 42°C incubation temperature than at 37°C (8% and 5%, respectively). In contrast, significantly higher rates of C. coli (14%) and other Campylobacter spp. (36%) were detected at the 37°C incubation temperature than at 42°C (8% and 7%, respectively). These results were consistent across surface water, wastewater, and bird fecal dropping samples. At times, Campylobacter spp. were recovered and detected at 37°C (3% for C. jejuni, 10% for C. coli, and 3% for C. lari) when the same samples incubated at 42°C were negative. A significantly higher rate of other Campylobacter spp. was detected only at 37°C (32%) than only at 42°C (3%). These results indicate that incubation temperature can significantly influence the culturability and detection of thermophilic and other fastidious Campylobacter spp. and that a comprehensive characterization of the Campylobacter spp. in surface water, wastewaters, or bird fecal droppings will require incubation at both 37 and 42°C.     

Engraftment and differentiation of embryonic stem cell–derived neural progenitor cells in the cochlear nerve trunk: Growth of processes into the organ of corti

Hearing loss in mammals is irreversible because cochlear neurons and hair cells do not regenerate. To determine whether we could replace neurons lost to primary neuronal degeneration, we injected EYFP‐expressing embryonic stem cell–derived mouse neural progenitor cells into the cochlear nerve trunk in immunosuppressed animals 1 week after destroying the cochlear nerve (spiral ganglion) cells while leaving hair cells intact by ouabain application to the round window at the base of the cochlea in gerbils. At 3 days post transplantation, small grafts were seen that expressed endogenous EYFP and could be immunolabeled for neuron‐specific markers. Twelve days after transplantation, the grafts had neurons that extended processes from the nerve core toward the denervated organ of Corti. By 64–98 days, the grafts had sent out abundant processes that occupied a significant portion of the space formerly occupied by the cochlear nerve. The neurites grew in fasciculating bundles projecting through Rosenthal's canal, the former site of spiral ganglion cells, into the osseous spiral lamina and ultimately into the organ of Corti, where they contacted hair cells. Neuronal counts showed a significant increase in neuronal processes near the sensory epithelium, compared to animals that were denervated without subsequent stem cell transplantation. The regeneration of these neurons shows that neurons differentiated from stem cells have the capacity to grow to a specific target in an animal model of neuronal degeneration. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006     

Reduction of oxidized guanosine by dietary carotenoids: A pulse radiolysis study

Time-resolved pulse radiolysis investigations reported herein show that the carotenoids β-carotene, lycopene, zeaxanthin and astaxanthin (the last two are xanthophylls - oxygen containing carotenoids) are capable of both reducing oxidized guanosine as well as minimizing its formation. The reaction of the carotenoid with the oxidized guanosine produces the radical cation of the carotenoid. This behavior contrasts with the reactions between the amino acids and dietary carotenoids where the carotenoid radical cations oxidized the amino acids (tryptophan, cysteine and tyrosine) at physiological pH.     

The Relationship Between FST and the Frequency of the Most Frequent Allele

F_ST is frequently used as a summary of genetic differentiation among groups. It has been suggested that F_ST depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of F_ST on allele frequencies, however, has been elusive. Here, we examine the relationship between F_ST and the frequency of the most frequent allele, demonstrating that the range of values that F_ST can take is restricted considerably by the allele-frequency distribution. For a two-population model, we derive strict bounds on F_ST as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum F_ST is ∼0.3585. Further, F_ST is restricted to values much less than 1 when M is low or high, and the contribution to the maximum F_ST made by the most frequent allele is on average ∼0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on F_ST in terms of the homozygosity of the total population, finding that the mean maximum F_ST given this homozygosity is 1 − ln 2 ≈ 0.3069. Our results provide a conceptual basis for understanding the dependence of F_ST on allele frequencies and genetic diversity and for interpreting the roles of these quantities in computations of F_ST from population-genetic data. Further, our analysis suggests that many unusual observations of F_ST, including the relatively low F_ST values in high-diversity human populations from Africa and the relatively low estimates of F_ST for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of F_ST on the properties of allele-frequency distributions.DIFFERENTIATION among groups is one of the fundamental subjects of the field of population genetics. Comparisons of the level of variation among subpopulations with the level of variation in the total population have been employed frequently in population-genetic theory, in statistical methods for data analysis, and in empirical studies of distributions of genetic variation. Wright’s (Wright 1951) fixation indices, and F_ST in particular, have been central to this effort.Wright’s F_ST was originally defined as the correlation between two randomly sampled gametes from the same subpopulation when the correlation of two randomly sampled gametes from the total population is set to zero. Several definitions of F_ST or F_ST-like quantities are now available, relying on a variety of different conceptual formulations but all measuring some aspect of population differentiation (e.g., Charlesworth 1998; Holsinger and Weir 2009). Many authors have claimed that one or another formulation of F_ST is affected by levels of genetic diversity or by allele frequencies, either because the range of F_ST is restricted by these quantities or because these quantities affect the degree to which F_ST reflects population differentiation (e.g., Charlesworth 1998; Nagylaki 1998; Hedrick 1999, 2005; Long and Kittles 2003; Jost 2008; Ryman and Leimar 2008; Long 2009; Meirmans and Hedrick 2011). For example, Nagylaki (1998) and Hedrick (1999) argued that measures of F_ST may be poor measures of genetic differentiation when the level of diversity is high. Charlesworth (1998) suggested that F_ST can be inflated when diversity is low, arguing that F_ST might not be appropriate for comparing loci with substantially different levels of variation. In a provocative recent article, Jost (2008) used the diversity dependence of forms of F_ST to question their utility as differentiation measures at all.One definition that is convenient for mathematical assessment of the relationship of an F_ST-like quantity and allele frequencies is the quantity labeled G_ST by Nei (1973), which for a given locus measures the difference between the heterozygosity of the total (pooled) population, h_T, and the mean heterozygosity across subpopulations, h_S, divided by the heterozygosity of the total population:GST=hT−hShT.(1)In terms of the homozygosity of the total population, H_T = 1 − h_T, and the mean homozygosity across subpopulations, H_S = 1 − h_S, we can writeGST=HS−HT1−HT.(2)The Wahlund (1928) principle guarantees that H_S ≥ H_T and, therefore, because H_S ≤ 1 and for a polymorphic locus with finitely many alleles, 0 < H_T < 1, G_ST lies in the interval [0,1].Using G_ST for their definition of F_ST, Hedrick (1999, 2005) and Long and Kittles (2003) pointed out that because h_T < 1, F_ST cannot exceed the mean homozygosity across subpopulations, H_S:F_ST = 1 ? h_S/h_T < 1 ? h_S = H_S.(3)Hedrick (2005) obtained this result by considering a set of K equal-sized subpopulations, in which each allele is private to a single subpopulation. In the limit as K → ∞, a stronger upper bound on F_ST as a function of H_S and K reduces to Equation 3 (see also Jin and Chakraborty 1995 and Long and Kittles 2003).While Hedrick (1999, 2005) and Long and Kittles (2003) have clarified the relationship between F_ST and the mean homozygosity H_S across subpopulations, their approaches do not easily illuminate the connection between F_ST and allele frequencies themselves. A formal understanding of the relationship between F_ST and allele frequencies would make it possible to more fully understand the behavior of F_ST in situations where markers of interest differ substantially in allele frequencies or levels of genetic diversity. Our recent work on the relationship between homozygosity and the frequency of the most frequent allele (Rosenberg and Jakobsson 2008; Reddy and Rosenberg 2012) provides a mathematical approach for formal investigation of bounds on population-genetic statistics in terms of allele frequencies. In this article, we therefore seek to thoroughly examine the dependence of F_ST on allele frequencies by investigating the upper bound on F_ST in terms of the frequency M of the most frequent allele across a pair of populations. We derive bounds on F_ST given the frequency of the most frequent allele and bounds on the frequency of the most frequent allele given F_ST. We consider loci with arbitrarily many alleles in a pair of subpopulations. Using theory for the bounds on homozygosity given the frequency of the most frequent allele, we obtain strict bounds on F_ST given the homozygosity of the total population. Our analysis clarifies the relationships among F_ST, allele frequencies, and homozygosity, providing explanations for peculiar observations of F_ST that can be attributed to allele-frequency dependence.