Flexible Resource Allocation: A Comparison Of Linear Diophantine Analysis And Integer Programming

To help production managers cope with an ever changing and complex business environment, we investigate a flexible methodology for solving integer resource allocation problems. Solutions obtained to an example problem using the Linear Diophantine Equation (LDE) methodology presented are compared to solutions produced using Integer Programming. Tradeoffs are examined and discussed, and suggestions are made for managers facing resource decisions similar to the example studied

T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors

The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50-80 min with burst sizes of 44-65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84-92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal beta-helices connecting loops.Peer reviewe

T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors

The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50–80 min with burst sizes of 44–65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84–92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops

Detecting Majorana bound states

We propose a set of interferometric methods on how to detect Majorana bound states induced by a topological insulator. The existence of these states can be easily determined by the conductance oscillations as function of magnetic flux and/or electric voltage. We study the system in the presence and absence of Majorana bound states and observe strikingly different behaviors. Importantly, we show that the presence of coupled Majorana bound states can induce a persistent current in absence of any external magnetic field.Comment: 7 pages, 6 figures, 1 table, revised and expanded, accepted for publication in Phys. Rev.

Bacteriophage-Resistant Mutants in Yersinia pestis: Identification of Phage Receptors and Attenuation for Mice

Background: Bacteriophages specific for Yersinia pestis are routinely used for plague diagnostics and could be an alternative to antibiotics in case of drug-resistant plague. A major concern of bacteriophage therapy is the emergence of phageresistant mutants. The use of phage cocktails can overcome this problem but only if the phages exploit different receptors. Some phage-resistant mutants lose virulence and therefore should not complicate bacteriophage therapy. Methodology/Principal Findings: The purpose of this work was to identify Y. pestis phage receptors using site-directed mutagenesis and trans-complementation and to determine potential attenuation of phage-resistant mutants for mice. Six receptors for eight phages were found in different parts of the lipopolysaccharide (LPS) inner and outer core. The receptor for R phage was localized beyond the LPS core. Most spontaneous and defined phage-resistant mutants of Y. pestis were attenuated, showing increase in LD 50 and time to death. The loss of different LPS core biosynthesis enzymes resulted in the reduction of Y. pestis virulence and there was a correlation between the degree of core truncation and the impact on virulence. The yrbH and waaA mutants completely lost their virulence. Conclusions/Significance: We identified Y. pestis receptors for eight bacteriophages. Nine phages together use at least seven different Y. pestis receptors that makes some of them promising for formulation of plague therapeutic cocktails. Most phage-resistant Y. pestis mutants become attenuated and thus should not pose a serious problem for bacteriophag

HldE Is Important for Virulence Phenotypes in Enterotoxigenic <i>Escherichia coli</i>

Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of diarrheal illness in third world countries and it especially affects children and travelers visiting these regions. ETEC causes disease by adhering tightly to the epithelial cells in a concerted effort by adhesins, flagella, and other virulence-factors. When attached ETEC secretes toxins targeting the small intestine host-cells, which ultimately leads to osmotic diarrhea. HldE is a bifunctional protein that catalyzes the nucleotide-activated heptose precursors used in the biosynthesis of lipopolysaccharide (LPS) and in post-translational protein glycosylation. Both mechanisms have been linked to ETEC virulence: Lipopolysaccharide (LPS) is a major component of the bacterial outer membrane and is needed for transport of heat-labile toxins to the host cells, and ETEC glycoproteins have been shown to play an important role for bacterial adhesion to host epithelia. Here, we report that HldE plays an important role for ETEC virulence. Deletion of hldE resulted in markedly reduced binding to the human intestinal cells due to reduced expression of colonization factor CFA/I on the bacterial surface. Deletion of hldE also affected ETEC motility in a flagella-dependent fashion. Expression of both colonization factors and flagella was inhibited at the level of transcription. In addition, the hldE mutant displayed altered growth, increased biofilm formation and clumping in minimal growth medium. Investigation of an orthogonal LPS-deficient mutant combined with mass spectrometric analysis of protein glycosylation indicated that HldE exerts its role on ETEC virulence both through protein glycosylation and correct LPS configuration. These results place HldE as an attractive target for the development of future antimicrobial therapeutics

Evolutionary exploration of a bacterial LPS genotype to phenotype map with phages

The evolution of bacterial resistance-to-phage strategies, and the mechanisms by which phages adapt to overcome these strategies, are usually studied via evolution experiments in which phages are added to sensitive bacteria and allowed to co-evolve. While this top-down approach has improved our understanding of co-evolutionary dynamics, it underestimates the diversity of available evolutionary pathways. In this thesis work, I propose an evolutionary bottom-up approach to study the natural lipopolysaccharide (LPS) structure diversity in resistant E. coli C strains and the corresponding ΦX174 adaptation process. I first investigated the mutational causes responsible for ΦX174-resistance using whole-genome sequencing. All phage-resistant mutants carry at least one mutation in genes linked to core LPS biosynthesis, assembly or regulation. Based on which genes are mutated and the current knowledge of LPS biology, I predicted that these bacterial strains collectively produce eight different LPS structures. Then, I used serial transfer experiments to evolve ΦX174 against each resistant mutant and determined the set of mutations required to overcome resistance. ΦX174 overcomes LPS-based resistance via mutations in only two genes: the F gene involved in host recognition and the H gene involved in DNA injection. Finally, I tested my predicted LPS genotype to phenotype maps using multiple phage infection assays to qualitatively determine the host range of each evolved phage. I showed that my evolved ΦX174 strains are great biosensor tools that can discriminate different E. coli C resistant strains. I also demonstrated that the LPS diversity is much greater than predicted. Instead of eight LPS structures, my phage analysis suggests that there are at least 14 distinct LPS phenotypes. My approach allows a deeper understanding of bacteria-phage interactions essential for developing efficient phage therapies in the future