'TB or not TB': the conundrum of pre-European contact tuberculosis in the Pacific.

Tuberculosis (TB) is a major global health threat, infecting one-third of the world's population. Despite this prominence, the age, origin and spread of the disease have been topics of contentious debate. Molecular studies suggest that Mycobacterium tuberculosis 'sensu stricto', the most common strain of TB infecting humans today, originated in Africa and from there spread into Europe and Asia. The M. tuberculosis strains most commonly found across the Pacific and the Americas today are most closely related to European strains, supporting a hypothesis that the disease only reached these regions relatively recently via European sailors or settlers. However, this hypothesis is inconsistent with palaeopathological evidence of TB-like lesions in human remains from across the Pacific that predate European contact. Similarly, genetic evidence from pre-European South American mummies challenges the notion of a European introduction of the disease into the Pacific. Here, we review the complex evidence for the age and origin of TB in the Pacific, and discuss key gaps in our knowledge and how these may be addressed. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions.

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H2 and CO2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions.IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions.

A decade of community MRSA in New Zealand.

In 1992, isolates with a distinctive phage pattern were identified amongst the 186 MRSA recovered in New Zealand. These unusual isolates were recovered in the Auckland region from individuals who came from or had visited Western Samoa, and were called Western Samoan phage pattern (WSPP) MRSA. They were almost exclusively community based and were mainly responsible for the alarming 15-fold increase in MRSA seen in New Zealand over the next 6 years. Since 2000, the number of infections attributable to WSPP MRSA appears to be declining. WSPP isolates are clonal, possess a unique type IV SCC mec element, and a distinctive multilocus sequence allelic profile (ST30). WSPP isolates are invariably not multiresistant with methicillin MICs generally

The intracellular pH of the thermophilic bacterium Thermoanaerobacter wiegelii during growth and production of fermentation acids.

The thermophilic glycolytic anaerobe Thermoanaerobacter wiegelii grows over the pH range 5.1-7.7, and no growth is observed below pH 5.0 or above 7.7. When T. wiegelii was grown in pH-uncontrolled batch culture, glucose was fermented to ethanol, acetate, and lactate. Small amounts of lactic acid were produced once the external pH reached 6.0, and a fructose-1.6-diphosphate (FDP) activated lactate dehydrogenase (LDH) was detected in cell-free crude extracts. Maximal activation of LDH by FDP was observed at pH 6.2. As the pH of the medium declined from 6.7 to 5.1 due to the production of acetate and lactate, the total protonmotive force (deltap) remained between - 110 and - 130mV, and the membrane potential (dekltapsi) decreased from -104 to -65mV. This decrease in deltapsi was paralleled by an increase in the chemical gradient of protons (ZdeltapH) from -31 to -62mV at pH 5.1. Based on these results, T. wiegelii maintained a small deltapH (0.3-0.9 units, inside alkaline) as the medium pH declined and interconverted deltapsi to ZdeltapH to maintain the total deltap relatively constant. Intracellular potassium decreased from 150 mM at pH 6.70 to 50 mM at pH 5.1, and this represented a 33-mV decline in the transmembrane chemical potential of potassium. The ability to synthesize ATP remained constant as the external pH declined, and therefore metabolic energy per se was not a critical aspect of pH sensitivity.

Sucrose transport by the alkaliphilic, thermophilic Bacillus sp. strain TA2.A1 is dependent on a sodium gradient.

An alkaliphilic Bacillus designated strain TA2.A1, isolated from a thermal spring in Te Aroha, New Zealand, grew optimally at pH 9.2 and 70 degrees C. Sodium chloride (>5mM) was an obligate requirement for the growth of strain TA2.A1 on sucrose, and growth on sucrose was inhibited by monensin, an ionophore that collapses the sodium gradient (ApNa+) across the cell membrane. Sucrose transport by strain TA2.A1 was sodium dependent and was inhibited by monensin. The Kt for sucrose transport was 33 microM and the Eadie-Hofstee plot was linear, suggesting one high-affinity uptake system for sucrose. The affinity for sodium was low (0.5 mM), and the Hill plot had a slope of 1.6, suggesting that sodium binding was noncooperative and that the sucrose transporter had more than one binding site for sodium. Based on these results, Bacillus strain TA2.A1 uses a sodium gradient for sucrose uptake, in addition to the sodium-dependent glutamate uptake system reported previously.

Roles of respiratory oxidases in protecting Escherichia coli K12 from oxidative stress.

Isogenic strains of Escherichia coli that were defective in either of the two major aerobic terminal respiratory oxidases (cytochromes bo' and bd) or in the putative third oxidase (cytochrome bd-II) were studied to elucidate role(s) for oxidases in protecting cells from oxidative stress in the form of H2O2 and paraquat. Exponential phase cultures of all three oxidase mutants exhibited a greater decline in cell viability when exposed to H2O2 stress compared to the isogenic parent wild-type strain. Cytochrome bo' mutants showed the greatest sensitivity to H2O2 under all conditions studied indicating that this oxidase was crucial for protection from H2O2 in E. coli. Cell killing of all oxidase mutants by H2O2 was by an uncharacterized mechanism (mode 2 killing) with cell growth rate affected. The expression of phi(katG-lacZ), an indicator of intracellular H2O2, was 2-fold higher in a cydAB::kan mutant compared to the wild-type strain at low H2O2 concentrations (< 100 microM) suggesting that cytochrome bd mutants were experiencing higher intracellular levels of H2O2. Protein fusions to the three oxidase genes demonstrated that expression of genes encoding cytochrome bd, but not cytochrome bo' or cytochrome bd-II was increased in the presence of external H2O2. This increase in expression of 4P(cydA-lacZ) by H2O2 was further enhanced in a cyo::kan mutant. The level of cytochrome bd determined spectrally and phi(cydA-lacZ) expression was 5-fold and 2-fold higher respectively in an rpoS mutant compared to isogenic wild-type cells suggesting that RpoS was a negative regulator of cytochrome bd. Whether the effect of RpoS is direct or indirect remains to be determined.

Enterococci with reduced susceptibility to vancomycin in New Zealand.

This study was conducted to determine the prevalence of vancomycin-resistant enterococci (VRE) in the stools of hospitalized patients with possible antibiotic-associated diarrhoea. From 176 faecal samples collected during 1997 and 1998, 66 strains of enterococci were recovered using vancomycin enrichment techniques. Only six of these displayed reduced susceptibility to vancomycin (MIC 8-12 mg/L). All VRE were positive for the presence of the vanC gene. Based on motility, pigment production and automated Gram-positive identification (GPI Vitek card), four of these six VRE isolates were identified as Enterococcus gallinarum. The remaining two isolates were non-motile and therefore were considered to be Enterococcus faecium. However, 16S rDNA sequence analysis and positive methyl-alpha-D-glucopyranoside tests indicated that they were non-motile species of E. gallinarum. This is consistent with the intrinsic, low-level vanC-1-mediated resistance associated with this species. Pulsed-field gel electrophoresis analysis comparisons between the VRE indicated genetic relatedness between some strains. This work confirms that vancomycin-resistant E. faecium and Enterococcus faecalis are rare in New Zealand.

Spinal nerve segmentation in the chick embryo: analysis of distinct axon-repulsive systems.

In higher vertebrates, the segmental organization of peripheral spinal nerves is established by a repulsive mechanism whereby sensory and motor axons are excluded from the posterior half-somite. A number of candidate axon repellents have been suggested to mediate this barrier to axon growth, including Sema3A, Ephrin-B, and peanut agglutinin (PNA)-binding proteins. We have tested the candidacy of these factors in vitro by examining their contribution to the growth cone collapse-inducing activity of somite-derived protein extracts on sensory, motor, and retinal axons. We find that Sema3A is unlikely to play a role in the segmentation of sensory or motor axons and that Ephrin-B may contribute to motor but not sensory axon segmentation. We also provide evidence that the only candidate molecule(s) that induces the growth cone collapse of both sensory and motor axons binds to PNA and is not Sema3A or Ephrin-B. By grafting primary sensory, motor, and quail retinal neurons into the chick trunk in vivo, we provide further evidence that the posterior half-somite represents a universal barrier to growing axons. Taken together, these results suggest that the mechanisms of peripheral nerve segmentation should be considered in terms of repellent molecules in addition to the identified molecules.

Redundancy of aerobic respiratory chains in bacteria? Routes, reasons and regulation.

Bacteria are the most remarkable organisms in the biosphere, surviving and growing in environments that support no other life forms. Underlying this ability is a flexible metabolism controlled by a multitude of environmental sensors and regulators of gene expression. It is not surprising, therefore, that bacterial respiration is complex and highly adaptable: virtually all bacteria have multiple, branched pathways for electron transfer from numerous low-potential reductants to several terminal electron acceptors. Such pathways, particularly those involved in anaerobic respiration, may involve periplasmic components, but the respiratory apparatus is largely membrane-bound and organized such that electron flow is coupled to proton (or sodium ion) transport, generating a protonmotive force. It has long been supposed that the multiplicity of pathways serves to provide flexibility in the face of environmental stresses, but the existence of apparently redundant pathways for electrons to a single acceptor, say dioxygen, is harder to explain. Clues have come from studying the expression of oxidases in response to growth conditions, the phenotypes of mutants lacking one or more oxidases, and biochemical characterization of individual oxidases. Terminal oxidases that share the essential properties of substrate (cytochrome c or quinol) oxidation, dioxygen reduction and, in some cases, proton translocation, differ in subunit architecture and complement of redox centres. Perhaps more significantly, they differ in their affinities for oxidant and reductant, mode of regulation, and inhibitor sensitivity; these differences to some extent rationalize the presence of multiple oxidases. However, intriguing requirements for particular functions in certain physiological functions remain unexplained. For example, a large body of evidence demonstrates that cytochrome bd is essential for growth and survival under certain conditions. In this review, the physiological basis of the many phenotypes of Cyd-mutants is explored, particularly the requirement for this oxidase in diazotrophy, growth at low protonmotive force, survival in the stationary phase, and resistance to oxidative stress and Fe(III) chelators.

Orienting axon growth: spinal nerve segmentation and surround-repulsion.

The study of spinal nerve trajectories in higher vertebrate embryos has revealed an inherent polarity within somites along the antero-posterior axis, and provides a simple system in which to study the factors that influence axon pathfinding. We argue that the orientation of spinal axons is determined by the simultaneous operation of two distinct guidance mechanisms, contact repulsion and chemorepulsion. Motor and sensory axons traverse the anterior half of each somite because they are excluded by contact repulsion from the posterior half-somite, and the molecular nature of several candidate contact repellents is reviewed. In contrast, we find that the dorsoventral trajectory of primary sensory axons is oriented by diffusible repellents originating from the notochord medially and dermamyotome laterally. In this system, therefore, repulsion by surrounding tissues ('surround-repulsion') is the main force directing axon growth in three dimensions.

Survival of Streptococcus pyogenes under stress and starvation.

The ability of Streptococcus pyogenes to enter a quiescent state, similar to the stationary phase of lab cultures, is believed to be an important factor in its ability to persist within the host and to subsequently cause disease. Using a model broth system, we determined that after entering the stationary phase, there was a 99.99% reduction in cell viability over a 4-day period, following which the cells appeared to enter a resistant starvation state where cell numbers remained constant over the subsequent 3-4 weeks. This starvation response was induced by carbon or phosphorous limitation, but not by nitrogen limitation in the form of amino acids where cells became non-culturable after 4 days. Amino acid utilization in the absence of a carbon source may be an essential factor for the long-term survival of this bacterium in the stationary phase. Early stationary phase cells showed a greater resistance to oxidative and pH stress compared to 24-h-starved cultures. There was evidence for the formation of a viable but non-culturable state as indicated by a comparison of the numbers of cells with a functional membrane potential (rhodamine 123) against culturable cells on either Todd Hewitt broth agar or sheep blood agar. Long-term survival of S. pyogenes was dependent on both cell wall and protein synthesis, suggesting that starving cultures are a dynamic cell population.

Embryonic lens repels retinal ganglion cell axons.

During development of the vertebrate visual system, retinal ganglion cell (RGC) axons follow a precise path toward their midbrain targets. Although much is known about the cues that direct RGC axons once they have left the optic disc, less is known about the guidance of axons at earlier stages, when RGCs first send out their axons to navigate within the developing retina. Using collagen gel coculture experiments, we find that the embryonic lens produces a powerful diffusible repulsive activity for RGC axons. We also find that this activity is localized to the lens epithelium and not the lens fiber layer, while the pigmented epithelium and vitreous humour are devoid of activity. The further observation that the lens also chemorepels primary sensory axons, but does not repel olfactory bulb axons, shows that this activity is specific for subsets of axons. Our experiments have excluded two candidate repellents for RGC axons (collapsin-1/sema III and chondroitin sulfate proteoglycans). These results implicate the lens in the earliest stages of RGC axon guidance. One function of the lens repellent may be to prevent aberrant targeting toward the lens, and it may also be involved in the directional guidance of RGC axons toward the optic disc.

Sodium-dependent glutamate uptake by an alkaliphilic, thermophilic Bacillus strain, TA2.A1.

A strain of Bacillus designated TA2.A1, isolated from a thermal spring in Te Aroha, New Zealand, grew optimally at pH 9.2 and 70 degrees C. Bacillus strain TA2.A1 utilized glutamate as a sole carbon and energy source for growth, and sodium chloride (>5 mM) was an obligate requirement for growth. Growth on glutamate was inhibited by monensin and amiloride, both inhibitors that collapse the sodium gradient (DeltapNa) across the cell membrane. N, N-Dicyclohexylcarbodiimide inhibited the growth of Bacillus strain TA2.A1, suggesting that an F1F0-ATPase (H type) was being used to generate cellular ATP needed for anabolic reactions. Vanadate, an inhibitor of V-type ATPases, did not affect the growth of Bacillus strain TA2.A1. Glutamate transport by Bacillus strain TA2.A1 could be driven by an artificial membrane potential (DeltaPsi), but only when sodium was present. In the absence of sodium, the rate of DeltaPsi-driven glutamate uptake was fourfold lower. No glutamate transport was observed in the presence of DeltapNa alone (i.e., no DeltaPsi). Glutamate uptake was specifically inhibited by monensin, and the Km for sodium was 5.6 mM. The Hill plot had a slope of approximately 1, suggesting that sodium binding was noncooperative and that the glutamate transporter had a single binding site for sodium. Glutamate transport was not affected by the protonophore carbonyl cyanide m-chlorophenylhydrazone, suggesting that the transmembrane pH gradient was not required for glutamate transport. The rate of glutamate transport increased with increasing glutamate concentration; the Km for glutamate was 2.90 microM, and the Vmax was 0.7 nmol. min-1 mg of protein. Glutamate transport was specifically inhibited by glutamate analogues.

The 1999 Crafoord Prize lectures. Neo-Lamarckian experimentalism in America: origins and consequences.

The 1890s and the first decades of the twentieth century saw a vigorous debate about the mechanisms of evolutionary change. On one side, August Weismann defended the selectionist hypothesis; on the other, Herbert Spencer defended neo-Lamarckian theory. Supporters of Spencer, notably the American paleontologist and evolutionary theorist Henry Fairfield Osborn, recognized that the questions raised by Weismann and Spencer could only be settled experimentally. They called for the application of experimental methods, and the establishment of a new institution for the purpose of confirming the inheritance of acquired characters. To a great extent, the experimental program championed by Osborn and others was implemented and, although it failed to reveal soft inheritance and was soon eclipsed by Mendelian and chromosomal genetics, it did make significant and lasting contributions to evolutionary biology. Thus the importance of methodological and institutional innovation and theoretical pluralism to the progress of science is illustrated and underscored.

Identification and characterization of aarF, a locus required for production of ubiquinone in Providencia stuartii and Escherichia coli and for expression of 2'-N-acetyltransferase in P. stuartii.

Providencia stuartii contains a chromosomal 2'-N-acetyltransferase [AAC(2')-Ia] involved in the O acetylation of peptidoglycan. The AAC(2')-Ia enzyme is also capable of acetylating and inactivating certain aminoglycosides and confers high-level resistance to these antibiotics when overexpressed. We report the identification of a locus in P. stuartii, designated aarF, that is required for the expression of AAC(2')-Ia. Northern (RNA) analysis demonstrated that aac(2')-Ia mRNA levels were dramatically decreased in a P. stuartii strain carrying an aarF::Cm disruption. The aarF::Cm disruption also resulted in a deficiency in the respiratory cofactor ubiquinone. The aarF locus encoded a protein that had a predicted molecular mass of 62,559 Da and that exhibited extensive amino acid similarity to the products of two adjacent open reading frames of unknown function (YigQ and YigR), located at 86 min on the Escherichia coli chromosome. An E. coli yigR::Kan mutant was also deficient in ubiquinone content. Complementation studies demonstrated that the aarF and the E. coli yigQR loci were functionally equivalent. The aarF or yigQR genes were unable to complement ubiD and ubiE mutations that are also present at 86 min on the E. coli chromosome. This result indicates that aarF (yigQR) represents a novel locus for ubiquinone production and reveals a previously unreported connection between ubiquinone biosynthesis and the regulation of gene expression.

"Spray, Spray, Spray!": insecticides and the making of applied entomology in Canada, 1871-1914.

As insecticides were adopted by Canadian farmers and fruit-growers after 1871, the resources conferred on economic entomology by the Dominion and Ontario governments grew. In 1886, with the establishment of the Experimental Farms system, James Fletcher, the Dominion entomologist and botanist, and his colleagues inherited the task of promoting insecticides to orchardists and others. In 1898-1900, in response to the arrival in Ontario of the San Jose scale, Canada and Ontario adopted laws mandating the use of insecticides, as sprays and fumigants, in orchards and at plant quarantine stations. To meet the resulting demand for trained technicians and scientifically-minded farmers, the institutions of applied entomology federally and at the Ontario Agricultural College were further developed. In 1910, after a decade of rapid diffusion of insecticides, Parliament adopted the Destructive Insects and Pest Act, thus creating a national system of horticultural hygiene.

Axon guidance and somites.

The segmental arrangement of spinal nerves in higher vertebrate embryos provides a simple system in which to study the factors that influence axon pathfinding. Developing motor and sensory axons are intimately associated with surrounding tissues that direct axon guidance. We argue that two distinct guidance mechanisms, viz. contact repulsion and chemorepulsion, act simultaneously to prescribe spinal axon trajectories by 'surround-repulsion'. Motor and sensory axons grow freely within the anterior half of each mesodermal somite, because they are excluded from posterior half-somites by contact repulsion. By contrast, the dorsoventral trajectory that bipolar sensory axons of the dorsal root ganglia follow is governed by diffusible repellents originating from the notochord medially and dermamyotome laterally. Even though spinal nerve development appears to be a simple system for elucidating axon guidance mechanisms, many distinct candidate guidance molecules have been implicated and their relative contributions remain to be evaluated.

Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors.

The expression of the cydDC operon was investigated by using a chromosomal phi(cydD-lacZ) transcriptional fusion and primer extension analysis. A single transcriptional start site was found for cydD located 68 bp upstream of the translational start site, and Northern blot analysis confirmed that cydDC is transcribed as a polycistronic message independently of the upstream gene trxB. cydDC was highly expressed under aerobic growth conditions and during anaerobic growth with alternative electron acceptors. Aerobic expression was independent of ArcA and Fnr, but induction of cydDC by nitrate and nitrite was dependent on NarL and Fnr.

Surround repulsion of spinal sensory axons in higher vertebrate embryos.

We have tested whether the orientation of axons sprouting from bipolar dorsal root ganglion neurons is influenced by diffusible cues from surrounding tissues. Surface ectoderm, dermomyotome, and notochord exert strong chemorepulsion on axons growing in collagen gels, operating at separations beyond those found in vivo and active in cocultures of chick and mouse tissues. Basal and alar plates of the neural tube are devoid of activity, as is the posterior-half-sclerotome, which repels in a contact-dependent manner. When ganglia are sandwiched between dermomyotome and notochord placed at a distance, axon growth is channeled in a bipolar trajectory. These results show that gradients of diffusible repulsion molecules flanking axon pathways can generate linear patterns of axon growth. We suggest that such "surround repulsion" may function generally, in concert with contact-dependent guidance mechanisms, to guide axons in the developing nervous system.