Epidemics and vaccination on weighted graphs

A Reed-Frost epidemic with inhomogeneous infection probabilities on a graph with prescribed degree distribution is studied. Each edge (u, v) in the graph is equipped with two weights W_(u,v) and W_(v,u) that represent the (subjective) strength of the connection and determine the probability that u infects v in case u is infected and vice versa. Expressions for the epidemic threshold are derived for i.i.d. weights and for weights that are functions of the degrees. For i.i.d. weights, a variation of the so called acquaintance vaccination strategy is analyzed where vertices are chosen randomly and neighbors of these vertices with large edge weights are vaccinated. This strategy is shown to outperform the strategy where the neighbors are chosen randomly in the sense that the basic reproduction number is smaller for a given vaccination coverage.     

The inbreeding effective number and the effective number of alleles in a population that varies in size

Consider a population that does not change in size. If it is assumed that there are an infinite number of possible neutral alleles at a locus and u is the probability that a particular gene mutates to some other gene in one generation, the effective number of alleles n_e is computed to be 4N_eu + 1, where N_e is the inbreeding effective population number. It is assumed in this paper that the number of individuals in a monoecious population, or the numbers of males and females in a dioecious population, are states in a finite irreducible Markov chain. In general it is impossible to obtain a single value of n_e. In some cases where the computation of n_e is possible, the results are as follows. When the population is monoecious, N_e is the reciprocal of the asymptotic average, over population sizes, of the probabilities that two gametes uniting to form an individual came from the same individual one generation earlier. In dioecious populations, N_e is the reciprocal of the long-run average of the probabilities that two homologous genes in separate individuals of one generation came from the same individual one generation earlier. Special cases are discussed.     

The Plasmodesmal Protein PDLP1 Localises to Haustoria-Associated Membranes during Downy Mildew Infection and Regulates Callose Deposition

The downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) is a filamentous oomycete that invades plant cells via sophisticated but poorly understood structures called haustoria. Haustoria are separated from the host cell cytoplasm and surrounded by an extrahaustorial membrane (EHM) of unknown origin. In some interactions, including Hpa-Arabidopsis, haustoria are progressively encased by host-derived, callose-rich materials but the molecular mechanisms by which callose accumulates around haustoria remain unclear. Here, we report that PLASMODESMATA-LOCATED PROTEIN 1 (PDLP1) is expressed at high levels in Hpa infected cells. Unlike other plasma membrane proteins, which are often excluded from the EHM, PDLP1 is located at the EHM in Hpa-infected cells prior to encasement. The transmembrane domain and cytoplasmic tail of PDLP1 are sufficient to convey this localization. PDLP1 also associates with the developing encasement but this association is lost when encasements are fully mature. We found that the pdlp1,2,3 triple mutant is more susceptible to Hpa while overexpression of PDLP1 enhances plant resistance, suggesting that PDLPs enhance basal immunity against Hpa. Haustorial encasements are depleted in callose in pdlp1,2,3 mutant plants whereas PDLP1 over-expression elevates callose deposition around haustoria and across the cell surface. These data indicate that PDLPs contribute to callose encasement of Hpa haustoria and suggests that the deposition of callose at haustoria may involve similar mechanisms to callose deposition at plasmodesmata.     

Functional RelBE-Family Toxin-Antitoxin Pairs Affect Biofilm Maturation and Intestine Colonization in Vibrio cholerae

Toxin–antitoxin (TA) systems are small genetic elements that typically encode a stable toxin and its labile antitoxin. These cognate pairs are abundant in prokaryotes and have been shown to regulate various cellular functions. Vibrio cholerae, a human pathogen that is the causative agent of cholera, harbors at least thirteen TA loci. While functional HigBA, ParDE have been shown to stabilize plasmids and Phd/Doc to mediate cell death in V. cholerae, the function of seven RelBE-family TA systems is not understood. In this study we investigated the function of the RelBE TA systems in V. cholerae physiology and found that six of the seven relBE loci encoded functional toxins in E. coli. Deletion analyses of each relBE locus indicate that RelBE systems are involved in biofilm formation and reactive oxygen species (ROS) resistance. Interestingly, all seven relBE loci are induced under the standard virulence induction conditions and two of the relBE mutants displayed a colonization defect, which was not due to an effect on virulence gene expression. Although further studies are needed to characterize the mechanism of action, our study reveals that RelBE systems are important for V. cholerae physiology.     

Cytogenetics of the South American DROSOPHILA MULLERI Complex: The MARTENSIS Cluster. More Interspecific Sharing of Inversions

Three Drosophila mulleri complex species have been found to be endemic to the cactus regions of northern South America. The three species are morphologically distinct, and no hybridization between species has been found in either the laboratory or nature. An analysis of their salivary gland chromosomes revealed that they evolved from a single cytological population, subspecies F of the ancestor of the D. mulleri complex, and comprise a cluster of sister species that are homozygous for inversions not found elsewhere. Within the martensis cluster are also found several inversions that are unique for these species, but have segregated out among the three species. Thus 2f² is found in martensis and starmeri, but not in uniseta, while 2t⁶, 3v and 3w are found in starmeri and uniseta, but not in martensis. This is analogous to the situation found within the remainder of the mulleri complex species, all the members of which share homozygosity for six other inversions. An interpretation of the cytological evolution of the martensis cluster is proposed.     

ON THE EXCITATION OF TISSUE BY MEANS OF CONDENSER DISCHARGES

Equations are derived for the capacity-voltage relations for stimulation of tissue by condenser discharges, using the hypothesis that the local excitatory process p grows under the influence of an applied potential V according to the equation, See PDF for Equation where K and k are constants. It is further assumed that the local excitatory process becomes adequate when it attains a value h ± α V where h and α are constants and V is the applied potential at the particular instant that the adequate value is attained. The equations so obtained are applied to the data of several authors on several types of tissue and the agreements obtained are sufficiently good. It is shown in one case that the direct current equation and the condenser discharge equation each derived from the above bases are consistent when applied to data from the same preparation.     

Transposases are responsible for the target specificity of IS1397 and ISKpn1 for two different types of palindromic units (PUs)

Insertion sequences (IS)1397 and ISKpn1, found in Escherichia coli and Klebsiella pneumoniae, respectively, are IS3 family members that insert specifically into short palindromic repeated sequences (palindromic units or PUs). In this paper, we first show that although PUs are naturally absent from extrachromosomal elements, both ISs are able to transpose from the chromosome or from a plasmid into PUs artificially introduced into target plasmids. We also show that ISKpn1 target specificity is restricted to K.pneumoniae Z¹ PU type, whereas IS1397 target specificity is less stringent since the IS targets the three E.coli Y, Z¹ and Z² PU types indifferently. Experiments of transposition of both ISs driven by both transposases demonstrate that the inverted repeats flanking the ISs are not responsible for this target specificity, which is entirely due to the transposase itself. Implications on ISs evolution are presented.     

Nimbya and Embellisia revisited, with nov. comb for Alternaria celosiae and A. perpunctulata

Previous phylogenetic analyses revealed that species within the genera Nimbya and Embellisia reside within a large monophyletic clade that also includes the genera Alternaria, Ulocladium, Undifilum, Sinomyces, and Crivellia with Stemphylium as the sister taxon. This study expands upon previous work by including many contemporary species of each genus and utilizes molecular and morphological characters to further examine relationships. Maximum parsimony and Bayesian analysis reveals that Nimbya is not a monophyletic genus but is split into two phylogenetically distant clades, which have different and distinct conidial morphologies. One of these clades resides completely within Alternaria. Phylogenetic analyses also reveals that Embellisia does not form a monophyletic genus but is split into four monophyletic lineages. Moreover, several species of Embellisia cluster individually with clades that are predominantly Alternaria, Ulocladium, or Stemphylium, yet these Embellisia spp. possess morphological characters that are diagnostically Embellisia. Thus, these data reveal that both Nimbya and Embellisia are polyphyletic as currently defined and taxonomic restructuring is necessary in order to resolve conflict between historical morphological and contemporary molecular-based phylogenies.     

Genetics of yeast hexokinase

Two independent isolates of Saccharomyces cerevisiae lacking hexokinase activity (EC 2.7.1.1) are described. Both mutant strains grow on glucose but are unable to grow on fructose, and contain two mutant genes hxk1 and hxk2 each. The mutations are recessive and noncomplementing. Genetic analysis suggests that these two unlinked genes hxk1 and hxk2 determine, independently of each other, the synthesis of hexokinase isozymes P1 and P2, respectively. hxk1 is located on chromosome VIR distal to met10, and hxk2 is on chromosome IIIR distal to MAL2. Of four hexokinase-positive spontaneous reversions, one is very tightly linked to hxk1 and the other three to the hxk2 locus. The reverted enzymes are considerably more thermolabile than the respective wild-type enzymes, and in one case show altered immunological properties. Data are presented which suggest that the hxk1 and hxk2 mutations are missense mutations in the structural genes of hexokinase P1 and hexokinase P2, respectively. These are presumably the only enzymes that allow S. cerevisiae to grow on fructose.     

Do Hybrid Trees Inherit Invasive Characteristics? Fruits of Corymbia torelliana X C. citriodora Hybrids and Potential for Seed Dispersal by Bees

Tree invasions have substantial impacts on biodiversity and ecosystem functioning, and trees that are dispersed by animals are more likely to become invasive. In addition, hybridisation between plants is well documented as a source of new weeds, as hybrids gain new characteristics that allow them to become invasive. Corymbia torelliana is an invasive tree with an unusual animal dispersal mechanism: seed dispersal by stingless bees, that hybridizes readily with other species. We examined hybrids between C. torelliana and C. citriodora subsp. citriodora to determine whether hybrids have inherited the seed dispersal characteristics of C. torelliana that allow bee dispersal. Some hybrid fruits displayed the characteristic hollowness, resin production and resin chemistry associated with seed dispersal by bees. However, we did not observe bees foraging on any hybrid fruits until they had been damaged. We conclude that C. torelliana and C. citriodora subsp. citriodora hybrids can inherit some fruit characters that are associated with dispersal by bees, but we did not find a hybrid with the complete set of characters that would enable bee dispersal. However, around 20,000 hybrids have been planted in Australia, and ongoing monitoring is necessary to identify any hybrids that may become invasive.     

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Euonymeae (∼230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.     

The Evolution of One- and Two-Locus Systems. II

Weak selection in a monoecious population is studied in two multiallelic panmictic models. In the first, a single locus is considered with continuous time and age-independent fertilities and mortalities. If the fertilities of the various matings and the genotypic mortalities may be expressed with an error at most of the second order in s (i.e., O(s ²)), where s is the intensity of selection, as sums of terms corresponding to the different genotypes and alleles, respectively, then after several generations the deviations from Hardy-Weinberg proportions are of O(s²). In the second model, two loci are treated with discrete nonoverlapping generations. It is shown that if the epistatic parameters are of O(s²), then after several generations the linkage disequilibria are reduced to O(s²). Assuming only weak selection, it is proved that in both models, after several generations, the total change in mean fitness is generally positive. It is likely that the exclusion of the initial period is usually unnecessary in natural populations. Exceptions are discussed.     

The slug parasitic nematode Phasmarhabditis hermaphrodita associates with complex and variable bacterial assemblages that do not affect its virulence

Phasmarhabditis hermaphrodita is a nematode parasite of slugs that is commercially reared in monoxenic culture with the bacterium Moraxella osloensis and sold as a biological molluscicide. However, its bacterial associations when reared in vivo in slugs are unknown. We show that when reared in vivo in slugs, P. hermaphrodita does not retain M. osloensis and associates with complex and variable bacterial assemblages that do not influence its virulence. This is in marked contrast to the entomopathogenic nematodes that form highly specific mutualistic associations with Enterobacteriaceae that are specifically retained during in vivo growth.     

A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata

The segmentation gene hierarchy of Drosophila melanogaster represents one of the best understood of the gene networks that generate pattern during embryogenesis. Some components of this network are ancient, while other parts of the network have evolved within the higher Diptera. To further understand the evolution of this gene network, we are studying the role of gap genes in a representative of a basally diverging dipteran lineage, the moth midge Clogmia albipunctata. We have isolated orthologues of all of the Drosophila trunk gap genes from Clogmia, and determined their domains of expression during the blastoderm stage of development, in relation to one another, and in relation to the expression of even-skipped (Calb-eve), a component of the pair-rule system that is directly regulated by the gap genes in Drosophila. We find that hunchback (Calb-hb), Krüppel (Calb-Kr), knirps (Calb-knl), giant (Calb-gt) and tailless (Calb-tll) are all expressed in patterns consistent with a gap segmentation role during blastoderm formation, but huckebein (Calb-hkb) is not. In the anterior half of the embryo, the relative positions of the gap gene expression domains in relation to one another, and in relation to the eve stripes, are rather well conserved. In the posterior half of the embryo, there are significant differences. Posteriorly, Calb-gt is expressed only transiently and very weakly, in a domain that overlaps entirely with that of Calb-knl. At late blastoderm stages, none of the candidate genes we have tested is expressed in the region between the posterior Calb-knl domain and Calb-tll. It is likely that the regulation of Calb-eve expression in this posterior region depends on combinations of gap gene factors that differ from those utilised for the same stripes in Drosophila. Both the gap and the pair-rule patterns of gene expression are dynamic in Clogmia, as they are in Drosophila, shifting anteriorly as blastoderm development proceeds.     

The silkworm glutathione S-transferase gene noppera-bo is required for ecdysteroid biosynthesis and larval development

Insect molting and metamorphosis are tightly controlled by ecdysteroids, which are important steroid hormones that are synthesized from dietary sterols in the prothoracic gland. One of the ecdysteroidogenic genes in the fruit fly Drosophila melanogaster is noppera-bo (nobo), also known as GSTe14, which encodes a member of the epsilon class of glutathione S-transferases. In D. melanogaster, nobo plays a crucial role in utilizing cholesterol via regulating its transport and/or metabolism in the prothoracic gland. However, it is still not known whether the orthologs of nobo from other insects are also involved in ecdysteroid biosynthesis via cholesterol transport and/or metabolism in the prothoracic gland. Here we report genetic evidence showing that the silkworm Bombyx mori ortholog of nobo (nobo-Bm; GSTe7) is essential for silkworm development. nobo-Bm is predominantly expressed in the prothoracic gland. To assess the functional importance of nobo-Bm, we generated a B. mori genetic mutant of nobo-Bm using TALEN-mediated genome editing. We show that loss of nobo-Bm function causes larval arrest and a glossy cuticle phenotype, which are rescued by the application of 20-hydroxyecdysone. Moreover, the prothoracic gland cells isolated from the nobo-Bm mutant exhibit an abnormal accumulation of 7-dehydrocholesterol, a cholesterol metabolite. These results suggest that the nobo family of glutathione S-transferases is essential for development and for the regulation of sterol utilization in the prothoracic gland in not only the Diptera but also the Lepidoptera. On the other hand, loss of nobo function mutants of D. melanogaster and B. mori abnormally accumulates different sterols, implying that the sterol utilization in the PG is somewhat different between these two insect species.