Analysis of a tuberculosis model with a case study in Uganda

We consider a four-compartment tuberculosis model including exogenous reinfection. We derive sufficient conditions, in terms of the parameters of the system, which guarantee the occurrence of backward bifurcation. We also discuss the global stability of the endemic state by using a generalization of the Poincaré–Bendixson criterion. An application is given for the case of Internally Displaced People's Camps in North Uganda. The study suggests how important it is to provide qualitative indications on the threshold value of the population density in the area occupied by the camps, in order to possibly eradicate the disease.     

Basic reproduction ratio for a fishery model in a patchy environment

We present a dynamical model of a multi-site fishery. The fish stock is located on a discrete set of fish habitats where it is catched by the fishing fleet. We assume that fishes remain on fishing habitats while the fishing vessels can move at a fast time scale to visit the different fishing sites. We use the existence of two time scales to reduce the dimension of the model : we build an aggregated model considering the habitat fish densities and the total fishing effort. We explore a regulation procedure, which imposes an average residence time in patches. Several equilibria exist, a Fishery Free Equilibria (FFEs) as well as a Sustainable Fishery Equilibria (SFEs). We show that the dynamics depends on a threshold which is similar to a basic reproduction ratio for the fishery. When the basic reproduction ratio is less or equal to 1, one of the FFEs is globally asymptotically stable (GAS), otherwise one of the SFEs is GAS.     

Stability of a melittin pore in a lipid bilayer: a molecular dynamics study

We have investigated the configuration and the stability of a single membrane pore bound by four melittin molecules and embedded in a fully hydrated bilayer lipid membrane. We used molecular dynamics simulations up to 5.8 ns. It is found that the initial tetrameric configuration decays with increasing time into a stable trimer and one monomer. This continuous transformation is accompanied by a lateral expansion of the aqueous pore exhibiting a final size comparable to experimental findings. The expansion-induced formation of an interface between the pore-lining acyl chains of the lipids and the pore water ("hydrophobic pore") is transformed into an energetically more favorable toroidal pore structure where some lipid heads are translocated from the rim to the central part of the interface ("hydrophilic pore"). The expansion of the pore is supported by the electrostatic repulsion among the alpha-helices. It is hypothesized that pore growth, and hence cell lysis, is induced by a melittin-mediated line tension of the pore.     

Evolutionary engineering of a beta-Lactamase activity on a D-Ala D-Ala transpeptidase fold

The beta-Lactamase hydrolytic activity has arisen several times from DD-transpeptidases. We have been able to replicate the evolutionary process of beta-Lactamase activity emergence on a PBP2X DD-transpeptidase. Some of the most interesting changes, like modifying the catalytic properties of an enzyme, may require several mutations in concert; therefore it is essential to explore efficiently sequence space by generating the right diversity. We designed a biased combinatorial library in which biochemical and structural information were incorporated by site directed mutagenesis on relevant residues and then subjected to random mutagenesis to allow for mutations in unforeseen positions. We isolated mutants from this library conferring 10-fold higher cefotaxime resistance levels than the background wild-type through mutations exclusively in the coding sequence. We demonstrate that only three substitutions in the DD-transpeptidase active site, two produced by the directed and one by the random mutagenesis, are sufficient to acquire this activity. The purified product of one mutant (MutE) had a 10(5)-fold increase in cefotaxime deacylation rate allowing it to hydrolyze beta-Lactams yet it has apparently conserved DD-peptidase activity. This work is the first to show a possible evolutionary intermediate between a beta-Lactamase and a DD-transpeptidase necessary for the development of antibiotic resistance.     

Isolation and sequence of a human gene encoding a potent inhibitor of leukocyte proteases.

We report the isolation of the human gene encoding an inhibitor of neutrophil elastase and cathepsin G. We have sequenced the gene and a cDNA clone isolated from human parotid tissue. The protein encoded by this gene appears to contain two functional domains, one having a trypsin inhibitory site and the other an elastase inhibitory site. The two-domain structure of the protein is reflected in the organization of the gene, with each domain represented by a separate exon. We have also noted that the intervening sequence separating the trypsin-inhibitor-exon and the elastase-inhibitor-exon is flanked by eleven base-pair direct repeats, suggesting that this intron may have been generated by a transposition-type event.     

Habitat as a potential factor limiting the recovery of a population of nocturnal seabirds

We asked whether the lack of a population response by ancient murrelets (Synthliboramphus antiquus) to eradication of rats (Rattus spp.) at Langara Island could be due to a change in vegetative cover. We quantified ancient murrelet habitat associations on 12 islands and assessed changes in vegetation at Langara Island between 1981 and 2007. We found that ancient murrelets exhibit a high degree of flexibility in their use of available breeding habitats, and we noted no changes over time. Thus, recovery of ancient murrelets at Langara Island is unlikely to be limited by habitat quality. We propose artificial social attraction as a method to speed recovery. © 2011 The Wildlife Society.     

Retrieval of a Micra transcatheter pacing system in a heart with a preexisting lead

We report the case of a 74-year-old man with a previously implanted pacemaker lead. He had undergone Medtronic? Micra Transcatheter Pacing System (TPS, Medtronic plc, MN, USA) implantation because of lead fracture. We implanted a new TPS and retrieved the dislodged one. We used a multiple-loop snare (EN snare^®) and an 8.5F steerable sheath (Agilis NXT; St. Jude Medical, St Paul, MN, USA). The TPS was obstructed by the chordae tendineae of the tricuspid valve and the pacemaker lead. We pushed the TPS to the apex site; this enabled us to move the TPS away from the chordae tendineae and pacemaker lead. The TPS body was caught in the inferior vena cava and was successfully retrieved. To our knowledge, this is the first case reporting TPS retrieval in a heart with preexisting lead.     

Gender-specific differences in cannibalism between a laboratory strain and a field strain of a predatory mite

Many phytoseiid species, including Phytoseiulus persimilis, are known to engage in cannibalism when food is scarce and when there is no possibility to disperse. In nature adult females of P. persimilis are known to disperse when prey is locally depleted. Males, in contrast, are expected to stay and wait for potential mates to mature. During this phase, males can obtain food by cannibalizing. Therefore, we hypothesize that male P. persimilis exhibit a higher tendency to cannibalize than females. Because rearing conditions in the laboratory usually prevent dispersal, prolonged culturing may also affect cannibalistic behavior. We hypothesize that this should especially affect cannibalism by females, because they consume far more food. We tested these hypotheses by comparing males and females from two strains, one of which had been in culture for over 20 years, whereas the other was recently collected from the field. It is known that this predator can discriminate between kin and non-kin and prefers cannibalizing the latter, hence to construct lines with high relatedness we created isofemale lines of these two original strains. We subsequently tested to what extent the adult females and males of the original strains and the isofemale lines cannibalized conspecific larvae from the same strain/line in a closed system. Relatedness with the victims did not affect cannibalistic behavior, but males engaged more often in cannibalism than females, and females of the laboratory strain engaged more in cannibalism than those of the field strain, both in agreement with our ideas. We hypothesize that the difference in cannibalism between the two genders will increase when they have the alternative to disperse.     

Identification of a nuclear variant of MGEA5, a cytoplasmic hyaluronidase and a beta-N-acetylglucosaminidase

MGEA5 was originally identified to be a novel human hyaluronidase, which is immunogenic in meningioma patients. Recently an N-acetylglucosaminidase was reported with identical sequence. Here, we define the origin of a splice variant by determining the genomic organization of the mgea5 gene. We find the splice variant missing a putative acetyltransferase domain of MGEA5. As for evolutionary analysis, we show that the MGEA5 is highly conserved in higher eukaryotes. As for expression analysis, we find both mRNA variants ubiquitously expressed in various human tissues and throughout mouse development. We generated polyclonal antibodies against MGEA5s/5 and identified proteins of 75 and 130 kDa, indicating posttranslational modifications of the larger protein. Cell fractionation revealed the cytoplasmic/cytoskeletal localization of the 130-kDa protein and the nuclear localization of the 75-kDa protein. We propose a model in which MGEA5 functions both as a hyaluronidase and an N-acetylglucosaminidase.     

A novel sortase, SrtC2, from Streptococcus pyogenes anchors a surface protein containing a QVPTGV motif to the cell wall

The important human pathogen Streptococcus pyogenes (group A streptococcus GAS), requires several surface proteins to interact with its human host. Many of these are covalently linked by a sortase enzyme to the cell wall via a C-terminal LPXTG motif. This motif is followed by a hydrophobic region and charged C terminus, which are thought to retard the protein in the cell membrane to facilitate recognition by the membrane-localized sortase. Previously, we identified two sortase enzymes in GAS. SrtA is found in all GAS strains and anchors most proteins containing LPXTG, while SrtB is present only in some strains and anchors a subset of LPXTG-containing proteins. We now report the presence of a third sortase in most strains of GAS, SrtC. We show that SrtC mediates attachment of a protein with a QVPTGV motif preceding a hydrophobic region and charged tail. We also demonstrate that the QVPTGV sequence is a substrate for anchoring of this protein by SrtC. Furthermore, replacing this motif with LPSTGE, found in the SrtA-anchored M protein of GAS, leads to SrtA-dependent secretion of the protein but does not lead to its anchoring by SrtA. We conclude that srtC encodes a novel sortase that anchors a protein containing a QVPTGV motif to the surface of GAS.     

Extreme population differentiation in a vulnerable slavemaking ant with a fragmented distribution

Understanding levels of population differentiation and inbreeding are important issues in conservation biology, especially for social Hymenoptera with fragmented and small population sizes. Isolated populations are more vulnerable to genetic loss and extinction than those with extended continuous distributions. However, small populations are not always a consequence of a recent reduction of their habitat. Thus, determining the history of population isolation and current patterns of genetic variation of a species is crucial for its conservation. Rossomyrmex minuchae is a slave-making ant with patchy distribution in South Eastern Spain and is classified as vulnerable by the IUCN. In contrast, the other three known species of the genus are presumed to show more uniform distributions. Here we investigate the genetic diversity and population structure of R. minuchae and compare it with that found in two other species of the genus: R. anatolicus and R. quandratinodum. We conclude that although genetic diversity of R. minuchae is low, there is no evidence of a recent bottleneck, suggesting a gradual and natural fragmentation process. We also show extreme population differentiation at nuclear and mitochondrial markers, and isolation by distance at a local scale. Despite some evidence for inbreeding and low genetic variation within populations, we found almost no diploid males, a finding which contrasts with that expected in inbred Hymenoptera with single locus complementary sex determination. This could mean that sex is determined by another mechanism. We argue that continued low population size means that detrimental effects of inbreeding and low genetic variation are likely in the future. We suggest that a policy of artificial gene flow aimed at increasing within population variation is considered as a management option.     

Highly potent dUTPase inhibition by a bacterial repressor protein reveals a novel mechanism for gene expression control

Transfer of phage-related pathogenicity islands of Staphylococcus aureus (SaPI-s) was recently reported to be activated by helper phage dUTPases. This is a novel function for dUTPases otherwise involved in preservation of genomic integrity by sanitizing the dNTP pool. Here we investigated the molecular mechanism of the dUTPase-induced gene expression control using direct techniques. The expression of SaPI transfer initiating proteins is repressed by proteins called Stl. We found that Φ11 helper phage dUTPase eliminates SaPIbov1 Stl binding to its cognate DNA by binding tightly to Stl protein. We also show that dUTPase enzymatic activity is strongly inhibited in the dUTPase:Stl complex and that the dUTPase:dUTP complex is inaccessible to the Stl repressor. Our results disprove the previously proposed G-protein-like mechanism of SaPI transfer activation. We propose that the transfer only occurs if dUTP is cleared from the nucleotide pool, a condition promoting genomic stability of the virulence elements.     

Conformational spread in a ring of proteins: a stochastic approach to allostery

We recently suggested that the sensitivity and range of a cluster of membrane receptors in bacteria would be enhanced by cooperative interactions between neighbouring proteins. Here, we examine the consequences of this "conformational spread" mechanism for an idealised one-dimensional system comprising a closed ring of identical allosteric protomers (protein molecules, or a group of protein domains operating as a unit). We show analytically and by means of Monte Carlo simulations that a ring of allosteric protomers can exhibit a switch-like response to changes in ligand concentration. We derive expressions for the sensitivity and cooperativity of switching and show that the maximum sensitivity is proportional to the number of protomers in the ring. A ring of this kind can reproduce the sensitivity and kinetics of the switch complex of a bacterial flagellar motor, for example, which is based on a ring of 34 FliM proteins. We also compare smaller rings of conformationally coupled protomers to classical allosteric proteins such as haemoglobin and show that the canonical MWC and KNF models arise naturally as limiting cases. Conformational spread appears to be a natural extension of the familiar mechanism of allostery: a physically realistic mechanism that should apply widely to many structures built from protein molecules.     

Behavior as a key component of integrative biology in a human-altered world

A major grand challenge in biology is to understand the interactions between an organism and its environment. Behavior resides in the central core of this association as it affects and is affected by development, physiology, ecological dynamics, environmental choice, and evolution. We present this central role of behavior in a diagram illustrating the multifaceted program emphasizing the necessity for understanding this nexus and to fully appreciate the organism in its environment given the ongoing changes affected by contemporary human induced, rapid environmental change (HIREC). We call for the consideration of educational and research focuses to concentrate on the interdisciplinary role that behavior plays in the integration of biological processes.     

Using a genetic algorithm to drive a microbial ecosystem in a desirable direction

The functioning of natural microbial ecosystems is influenced by various biotic and abiotic conditions. The careful experimental manipulation of environmental conditions can drive microbial ecosystems toward exhibiting desirable types of functionality. Such manipulations can be systematically approached by viewing them as a combinatorial optimization problem, in which the optimal configuration of environmental conditions is sought. Such an effort requires a sound optimization technique. Genetic algorithms are a class of optimization methods that should be suitable for such a task because they can deal with multiple interacting variables and with experimental noise and because they do not require an intricate understanding or modelling of the ecosystem of interest. We propose the use of genetic algorithms to drive undefined microbial ecosystems in desirable directions by combinatorially optimizing sets of environmental conditions. We tested this approach in a model system where the microbial ecosystem of a human saliva sample was manipulated in successive steps to display increasing amounts of azo dye decoloration. The results of our experiments indicated that a genetic algorithm was capable of optimizing ecosystem function by manipulating the presence or absence of a set of 10 chemical supplements. Genetic algorithms hold promise for use as a tool in environmental microbiology for the efficient control of the functioning of natural and undefined microbial ecosystems.     

Industrial Ecology as a Cultural Phenomenon: On Objectivity as a Normative Position

Taking a recent column by Braden Allenby in this journal as a starting point, we argue the need for researchers in the field of industrial ecology to reflect upon its normative aspects. We argue that the field will advance through an explicit discourse on such issues as epistemological positions, the inherent normative nature of using metaphors, and the way in which the field of study relates to the field of practice.
In "Culture and Industrial Ecology," Allenby raises, and begins to address, some critical questions that define the field of industrial ecology. We suggest that his arguments dismiss too lightly issues that are central to this developing field. The purpose of this reply is to open up for further discussion what industrial ecology is, and what it is not.
We begin by summarizing Allenby's line of reasoning. We explore his arguments around the notion of objectivity and the questions he raises about the relationship among objective science, normative positions, opinions, and fads. While Allenby makes a strong plea for industrial ecology to maintain objectivity and avoid normative positions, we contend that any positions on what should or should not be included in a field of study carry normative intent. Although science might seek to be objective in its method, scientists are rarely free of such normative positions. These positions need to be explicit and open to debate. Also, Allenby's position implies that industrial ecology as a field of study should be separated from industrial ecology as a field of practice. We argue that the interrelation of these fields provides important advantages.
Our main concern is that Allenby's position forestalls discussion on important issues at the heart of the field of study. We examine some key issues around the concept of objectivity and propose an agenda for research on the cultural and ideological aspects of industrial ecology.