Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon.

Thermococcus kodakarensis is a hyperthermophilic Euryarchaeon that grows well under laboratory conditions and, being naturally competent for genetic transformation, it has become a widely studied experimental model species. With the genome sequence available since 2004, combining genetic, enzymological and structural biochemical approaches has revealed previously unknown and unanticipated features of archaeal molecular biology and metabolism. T. kodakarensis DNA polymerase is already commercialized and with the details of metabolism and hydrogenase available, generating H2 from biopolymers solubilized at high temperatures, most notably chitin, now seems a very attractive possibility as a renewable energy bioprocess.

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis.

Many aspects of and factors required for DNA replication are conserved across all three domains of life, but there are some significant differences surrounding lagging-strand synthesis. In Archaea, a 5'-to-3' exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS was identified and designated GAN (for GINS-associated nuclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation, and as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, and GINS) replication complex. We demonstrate here that, individually, either Fen1 or GAN can be deleted, with no discernible effects on viability and growth. However, deletion of both Fen1 and GAN was not possible, consistent with both enzymes catalyzing the same step in primer removal from Okazaki fragments in vivo RNase HII has also been proposed to participate in primer processing during Okazaki fragment maturation. Strains with both Fen1 and RNase HII deleted grew well. GAN activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it was not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. The ability to delete GAN demonstrates that GAN is not required for the activation or stability of the archaeal MCM replicative helicase.IMPORTANCE The mechanisms used to remove primer sequences from Okazaki fragments during lagging-strand DNA replication differ in the biological domains. Bacteria use the exonuclease activity of DNA polymerase I, whereas eukaryotes and archaea encode a flap endonuclease (Fen1) that cleaves displaced primer sequences. RNase HII and the GINS-associated exonuclease GAN have also been hypothesized to assist in primer removal in Archaea Here we demonstrate that in Thermococcus kodakarensis, either Fen1 or GAN activity is sufficient for viability. Furthermore, GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN.

Variable prey development time suppresses predator-prey cycles and enhances stability.

Although theoretical models have demonstrated that predator-prey population dynamics can depend critically on age (stage) structure and the duration and variability in development times of different life stages, experimental support for this theory is non-existent. We conducted an experiment with a host-parasitoid system to test the prediction that increased variability in the development time of the vulnerable host stage can promote interaction stability. Host-parasitoid microcosms were subjected to two treatments: Normal and High variance in the duration of the vulnerable host stage. In control and Normal-variance microcosms, hosts and parasitoids exhibited distinct population cycles. In contrast, insect abundances were 18-24% less variable in High- than Normal-variance microcosms. More significantly, periodicity in host-parasitoid population dynamics disappeared in the High-variance microcosms. Simulation models confirmed that stability in High-variance microcosms was sufficient to prevent extinction. We conclude that developmental variability is critical to predator-prey population dynamics and could be exploited in pest-management programs.

Patch-Burn Grazing Effects on the Ecological Integrity of Tallgrass Prairie Streams.

Conversion to agriculture, habitat fragmentation, and the loss of native grazers have made tallgrass prairie one of the most endangered ecosystems. One management option for the remaining prairie parcels, patch-burn grazing (PBG), applies a controlled burn to a portion of the prairie to attract cattle, creating a mosaic of more- and less-grazed patches. Although beneficial to cattle and grassland birds, the potential impacts of PBG on streams have not been studied, and a holistic approach is needed to ensure against adverse effects. We used a Before-After-Control-Impact design to assess potential impacts of PBG with and without riparian protection on tallgrass prairie headwater streams. We sampled stream macroinvertebrates and benthic organic matter 2 yr before and 2 yr during PBG treatments on two grazed watersheds with riparian fencing (fenced), two unfenced grazed watersheds (unfenced), and two ungrazed (control) watersheds. Very fine benthic organic matter increased significantly (51%) in unfenced streams compared with controls ( < 0.007), and fine particulate organic matter (<1 mm and >250 µm) increased 3-fold in the unfenced streams compared with controls ( = 0.008). The contribution of fine inorganic sediments to total substrata increased 28% in unfenced streams during PBG, which was significantly different from controls ( = 0.03). Additionally, the abundance of Ephemeroptera, Plecoptera, and Trichoptera taxa decreased from 7635 to 687 individuals m in unfenced streams, which was significantly lower than in control streams ( = 0.008). Our results indicate that PBG adversely influences prairie streams through sediment inputs and reductions in sensitive invertebrate taxa, but riparian fencing can alleviate these impacts.

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis.

BACKGROUND: Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present in the model hyperthermophilic Archaeon, Thermococcus kodakarensis, under different physiological conditions. RESULTS: Sequencing cDNA libraries, generated from RNA isolated from cells under different growth and metabolic conditions has identified >2,700 sites of transcription initiation, established a genome-wide map of transcripts, and consensus sequences for transcription initiation and post-transcription regulatory elements. The primary transcription start sites (TSS) upstream of 1,254 annotated genes, plus 644 primary TSS and their promoters within genes, are identified. Most mRNAs have a 5'-untranslated region (5'-UTR) 10 to 50 nt long (median = 16 nt), but ~20% have 5'-UTRs from 50 to 300 nt long and ~14% are leaderless. Approximately 50% of mRNAs contain a consensus ribosome binding sequence. The results identify TSS for 1,018 antisense transcripts, most with sequences complementary to either the 5'- or 3'-region of a sense mRNA, and confirm the presence of transcripts from all three CRISPR loci, the RNase P and 7S RNAs, all tRNAs and rRNAs and 69 predicted snoRNAs. Two putative riboswitch RNAs were present in growing but not in stationary phase cells. The procedure used is designed to identify TSS but, assuming that the number of cDNA reads correlates with transcript abundance, the results also provide a semi-quantitative documentation of the differences in T. kodakarensis genome expression under different growth conditions and confirm previous observations of substrate-dependent specific gene expression. Many previously unanticipated small RNAs have been identified, some with relative low GC contents (≤ 50%) and sequences that do not fold readily into base-paired secondary structures, contrary to the classical expectations for non-coding RNAs in a hyperthermophile. CONCLUSION: The results identify >2,700 TSS, including almost all of the primary sites of transcription initiation upstream of annotated genes, plus many secondary sites, sites within genes and sites resulting in antisense transcripts. The T. kodakarensis genome is small (~2.1 Mbp) and tightly packed with protein-encoding genes, but the transcriptomes established also contain many non-coding RNAs and predict extensive RNA-based regulation in this model Archaeon.

Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis.

Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in Bacteria and Pol D exists only in Archaea. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all Archaea, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of Thermococcus kodakarensis strains with mutations that delete or inactivate key functions of Pol B. T. kodakarensis strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in T. kodakarensis and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of Archaea contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in Archaea, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.

BACKGROUND: Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. RESULTS: Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. CONCLUSIONS: The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.

Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability.

Proliferating cell nuclear antigen (PCNA) monomers assemble to form a ring-shaped clamp complex that encircles duplex DNA. PCNA binding to other proteins tethers them to the DNA providing contacts and interactions for many other enzymes essential for DNA metabolic processes. Most eukarya and euryarchaea have only one PCNA homolog but Thermococcus kodakarensis uniquely has two, designated PCNA1 and PCNA2, encoded by TK0535 and TK0582, respectively. Here, we establish that both PCNA1 and PCNA2 form homotrimers that stimulate DNA synthesis by archaeal DNA polymerases B and D and ATP hydrolysis by the replication factor C complex. In exponentially growing cells, PCNA1 is abundant and present at an ~100-fold higher concentration than PCNA2 monomers. Deletion of TK0582 (PCNA2) had no detectable effects on viability or growth whereas repeated attempts to construct a T. kodakarensis strain with TK0535 (PCNA1) deleted were unsuccessful. The implications of these observations for PCNA1 function and the origin of the two PCNA-encoding genes in T. kodakarensis are discussed.

Estimation of the diffusion rate and crossing probability for biased edge movement between two different types of habitat.

One of the fundamental goals of ecology is to examine how dispersal affects the distribution and dynamics of insects across natural landscapes. These landscapes are frequently divided into patches of habitat embedded in a matrix of several non-habitat regions, and dispersal behavior could vary within each landscape element as well as the edges between elements. Reaction-diffusion models are a common way of modeling dispersal and species interactions in such landscapes, but to apply these models we also need methods of estimating the diffusion rate and any edge behavior parameters. In this paper, we present a method of estimating the diffusion rate using the mean occupancy time for a circular region. We also use mean occupancy time to estimate a parameter (the crossing probability) that governs one type of edge behavior often used in these models, a biased random walk. These new methods have some advantages over other methods of estimating these parameters, including reduced computational cost and ease of use in the field. They also provide a method of estimating the diffusion rate for a particular location in space, compared to existing methods that represent averages over large areas. We further examine the statistical properties of the new method through simulation, and discuss how mean occupancy time could be estimated in field experiments.

Thermococcus kodakarensis encodes three MCM homologs but only one is essential.

The minichromosome maintenance (MCM) complex is thought to function as the replicative helicase in archaea and eukaryotes. In eukaryotes, this complex is an assembly of six different but related polypeptides (MCM2-7) but, in most archaea, one MCM protein assembles to form a homohexameric complex. Atypically, the Thermococcus kodakarensis genome encodes three archaeal MCM homologs, here designated MCM1-3, although MCM1 and MCM2 are unusual in having long and unique N-terminal extensions. The results reported establish that MCM2 and MCM3 assemble into homohexamers and exhibit DNA binding, helicase and ATPase activities in vitro typical of archaeal MCMs. In contrast, MCM1 does not form homohexamers and although MCM1 binds DNA and has ATPase activity, it has only minimal helicase activity in vitro. Removal of the N-terminal extension had no detectable effects on MCM1 but increased the helicase activity of MCM2. A T. kodakarensis strain with the genes TK0096 (MCM1) and TK1361 (MCM2) deleted has been constructed that exhibits no detectable defects in growth or viability, but all attempts to delete TK1620 (MCM3) have been unsuccessful arguing that that MCM3 is essential and is likely the replicative helicase in T. kodakarensis. The origins and possible function(s) of the three MCM proteins are discussed.

A novel DNA nuclease is stimulated by association with the GINS complex.

Chromosomal DNA replication requires the spatial and temporal coordination of the activities of several complexes that constitute the replisome. A previously uncharacterized protein, encoded by TK1252 in the archaeon Thermococcus kodakaraensis, was shown to stably interact with the archaeal GINS complex in vivo, a central component of the archaeal replisome. Here, we document that this protein (TK1252p) is a processive, single-strand DNA-specific exonuclease that degrades DNA in the 5' → 3' direction. TK1252p binds specifically to the GINS15 subunit of T. kodakaraensis GINS complex and this interaction stimulates the exonuclease activity in vitro. This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed.

An archaeal histone is required for transformation of Thermococcus kodakarensis.

Archaeal histones wrap DNA into complexes, designated archaeal nucleosomes, that resemble the tetrasome core of a eukaryotic nucleosome. Therefore, all DNA interactions in vivo in Thermococcus kodakarensis, the most genetically versatile model species for archaeal research, must occur in the context of a histone-bound genome. Here we report the construction and properties of T. kodakarensis strains that have TK1413 or TK2289 deleted, the genes that encode HTkA and HTkB, respectively, the two archaeal histones present in this archaeon. All attempts to generate a strain with both TK1413 and TK2289 deleted were unsuccessful, arguing that a histone-mediated event(s) in T. kodakarensis is essential. The HTkA and HTkB amino acid sequences are 84% identical (56 of 67 residues) and 94% similar (63 of 67 residues), but despite this homology and their apparent redundancy in terms of supporting viability, the absence of HTkA and HTkB resulted in differences in growth and in quantitative and qualitative differences in genome transcription. A most surprising result was that the deletion of TK1413 (ΔhtkA) resulted in a T. kodakarensis strain that was no longer amenable to transformation, whereas the deletion of TK2289 (ΔhtkB) had no detrimental effects on transformation. Potential roles for the archaeal histones in regulating gene expression and for HTkA in DNA uptake and recombination are discussed.

Deletion of alternative pathways for reductant recycling in Thermococcus kodakarensis increases hydrogen production.

Hydrogen (H2) production by Thermococcus kodakarensis compares very favourably with the levels reported for the most productive algal, fungal and bacterial systems. T. kodakarensis can also consume H2 and is predicted to use several alternative pathways to recycle reduced cofactors, some of which may compete with H2 production for reductant disposal. To explore the reductant flux and possible competition for H2 production in vivo, T. kodakarensis TS517 was mutated to precisely delete each of the alternative pathways of reductant disposal, H2 production and consumption. The results obtained establish that H2 is generated predominantly by the membrane-bound hydrogenase complex (Mbh), confirm the essential role of the SurR (TK1086p) regulator in vivo, delineate the roles of sulfur (S°) regulon proteins and demonstrate that preventing H2 consumption results in a substantial net increase in H2 production. Constitutive expression of TK1086 (surR) from a replicative plasmid restored the ability of T. kodakarensis TS1101 (ΔTK1086) to grow in the absence of S° and stimulated H2 production, revealing a second mechanism to increase H2 production. Transformation of T. kodakarensis TS1101 with plasmids that express SurR variants constructed to direct the constitutive synthesis of the Mbh complex and prevent expression of the S° regulon was only possible in the absence of S° and, under these conditions, the transformants exhibited wild-type growth and H2 production. With S° present, they grew slower but synthesized more H2 per unit biomass than T. kodakarensis TS517.

Effects of temperature and salinity on bioconcentration and toxicokinetics of permethrin in pyrethroid-resistant Hyalella azteca.

Recent studies demonstrated pyrethroid resistance associated with voltage-gated sodium channel mutations in populations of the epibenthic amphipod, Hyalella azteca. Resistant populations were able to tolerate and bioconcentrate pyrethroids at concentrations significantly higher than toxic levels for non-resistant populations. In conjunction with elevated bioconcentration potential, environmental alteration particularly as a result of global climate change is anticipated to significantly alter abiotic parameters including temperature and salinity. These changes are expected to influence uptake and biotransformation of contaminants. Thus, the aims of the current study were a) to examine the bioconcentration potential of permethrin in two pyrethroid-resistant clades of H. azteca and b) assess the influence of temperature and salinity changes on toxicokinetic parameters. Two pyrethroid-resistant clades of H. azteca were exposed to 14C-permethrin at three salinities (0.2, 1.0 and 6.0 practical salinity units (PSU)) and temperatures (18, 23 and 28 °C). Tests were conducted for up to 36 h and uptake, elimination and biotransformation rates were calculated. Both populations demonstrated bioconcentration factors (BCFs) between five and seven times greater than published data for non-resistant H. azteca, with significant differences between clades. Calculated BCF values were comparable to field populations of resistant H. azteca, emphasizing the potential for elevated pyrethroid bioconcentration in the natural environment and increased exposure for predators consuming pyrethroid-resistant aquatic invertebrates. Alterations to temperature and salinity had no statistically significant effect on uptake or parent compound half-life in either population, though biotransformation was elevated at higher temperatures in both populations. Salinity had a variable effect between the two populations, with lower BCF values at 1.0 PSU in clade D H. azteca and greater BCFs at 6.0 PSU in clade C H. azteca. This is the first study to demonstrate the potential for future climate scenarios to influence toxicokinetics in pyrethroid-resistant aquatic organisms.

The time is now: Achieving FH paediatric screening across Europe - The Prague Declaration.

Familial hypercholesterolaemia (FH) is the most common inherited metabolic disorder characterized by high cholesterol and if left untreated leads to premature cardiovascular disease, such as heart attacks. Treatment that begins early in life, particularly in childhood, is highly efficacious in preventing cardiovascular disease and cost-effective, thus early detection of FH is crucial. However, in Europe, less than 10% of people living with FH are diagnosed and even less receive life-saving treatment. The Prague Declaration is a call to action for national and European Union policymakers and decision-makers and a result of the Czech EU Presidency meeting on FH Paediatric Screening (early detection of inherited high cholesterol) at the Czech Senate in Prague on 6th September 2022. It builds on a considerable body of evidence which was discussed at the Technical Meeting under the auspices of the Slovenian EU Presidency in October 2021. The Prague meeting addressed the outstanding barriers to the systematic implementation of FH paediatric screening across Europe. In this article, we present the key points from the Prague meeting and concrete actions needed to move forward.

Deletion of switch 3 results in an archaeal RNA polymerase that is defective in transcript elongation.

Switch 3 is a polypeptide loop conserved in all multisubunit DNA-dependent RNA polymerases (RNAPs) that extends into the main cleft of the RNAP and contacts each base in a nascent transcript as that base is released from the internal DNA-RNA hybrid. Plasmids have been constructed and transformed into Thermococcus kodakaraensis, which direct the constitutive synthesis of the archaeal RNAP subunit RpoB with an N-terminal His(6) tag and the Switch 3 loop either intact (wild-type) or deleted (DeltaS3). RNAPs containing these plasmid-encoded RpoB subunits were purified, and, in vitro, the absence of Switch 3 had no negative effects on transcription initiation or elongation complex stability but reduced the rate of transcript elongation. The defect in elongation occurred at every template position and increased the sensitivity of the archaeal RNAP to intrinsic termination. Comparing these properties and those reported for a bacterial RNAP lacking Switch 3 argues that this loop functions differently in the RNAPs from the two prokaryotic domains. The close structural homology of archaeal and eukaryotic RNAPs would predict that eukaryotic Switch 3 loops likely conform to the archaeal rather than bacterial functional paradigm.

Olfactory experience modifies semiochemical responses in a bark beetle predator.

A typical feature of forest insect pests is their tendency to undergo large fluctuations in abundance, which can jeopardize the persistence of their predaceous natural enemies. One strategy that these predators may adopt to cope with these fluctuations would be to respond to sensory cues for multiple prey species. Another possible adaptation to temporal variation in the prey community could involve the learning of prey cues and switching behavior. We conducted three experiments to investigate the ability of the generalist bark beetle predator Thanasimus dubius (F.) (Coleoptera: Cleridae) to respond to different prey signals and to investigate the effect of olfactory experience. We first conducted a field choice test and a wind tunnel experiment to examine the kairomonal response of individual predators toward prey pheromone components (frontalin, ipsenol, ipsdienol, sulcatol) along with the pine monoterpene α-pinene, which is a volatile compound from the host of the prey. We also presented semiochemically naive predators with two prey pheromone components, frontalin and ipsenol, alone or associated with a reward. Our results showed that T. dubius populations are composed of generalists that can respond to a broad range of kairomonal signals. Naive T. dubius also were more attracted to ipsenol following its association with a reward. This work constitutes the first evidence that the behavior of a predatory insect involved in bark beetle population dynamics is influenced by previous olfactory experience, and provides a potential explanation for the pattern of prey switching observed in field studies.

Genetic heterogeneity in a cyclical forest pest, the southern pine beetle, Dendroctonus frontalis, is differentiated into east and west groups in the southeastern United States.

The southern pine beetle, Dendroctonus frontalis Zimmerman (Coleoptera: Curculionidae) is an economically important pest species throughout the southeastern United States, Arizona, Mexico, and Central America. Previous research identified population structure among widely distant locations, yet failed to detect population structure among national forests in the state of Mississippi. This study uses microsatellite variation throughout the southeastern United States to compare the southern pine beetle's pattern of population structure to phylogeographic patterns in the region, and to provide information about dispersal. Bayesian clustering identified east and west genetic groups spanning multiple states. The east group had lower heterozygosity, possibly indicating greater habitat fragmentation or a more recent colonization. Significant genetic differentiation (θ(ST) = 0.01, p < 0.0001) followed an isolation-by-distance pattern (r = 0.39, p < 0.001) among samples, and a hierarchical AMOVA indicated slightly more differentiation occurred between multi-state groups. The observed population structure matches a previously identified phylogeographic pattern, division of groups along the Appalachian Mountain/Apalachicola River axis. Our results indicate that the species likely occurs as a large, stable metapopulation with considerable gene flow among subpopulations. Also, the relatively low magnitude of genetic differentiation among samples suggests that southern pine beetles may respond similarly to management across their range.

Thermococcus kodakarensis genetics: TK1827-encoded beta-glycosidase, new positive-selection protocol, and targeted and repetitive deletion technology.

Inactivation of TK1761, the reporter gene established for Thermococcus kodakarensis, revealed the presence of a second beta-glycosidase that we have identified as the product of TK1827. This enzyme (pTK1827) has been purified and shown to hydrolyze glucopyranoside but not mannopyranoside, have optimal activity at 95 degrees C and from pH 8 to 9.5, and have a functional half-life of approximately 7 min at 100 degrees C. To generate a strain with both TK1761 and TK1827 deleted, a new selection/counterselection protocol has been developed, and the levels of beta-glycosidase activity in T. kodakarensis strains with TK1761 and/or TK1827 deleted and with these genes expressed from heterologous promoters are described. Genetic tools and strains have been developed that extend the use of this selection/counterselection procedure to delete any nonessential gene from the T. kodakarensis chromosome. Using this technology, TK0149 was deleted to obtain an agmatine auxotroph that grows on nutrient-rich medium only when agmatine is added. Transformants can therefore be selected rapidly, and replicating plasmids can be maintained in this strain growing in rich medium by complementation of the TK0149 deletion.

Developmental variability and stability in continuous-time host-parasitoid models.

Insect host-parasitoid systems are often modeled using delay-differential equations, with a fixed development time for the juvenile host and parasitoid stages. We explore here the effects of distributed development on the stability of these systems, for a random parasitism model incorporating an invulnerable host stage, and a negative binomial model that displays generation cycles. A shifted gamma distribution was used to model the distribution of development time for both host and parasitoid stages, using the range of parameter values suggested by a literature survey. For the random parasitism model, the addition of biologically plausible levels of developmental variability could potentially double the area of stable parameter space beyond that generated by the invulnerable host stage. Only variability in host development time was stabilizing in this model. For the negative binomial model, development variability reduced the likelihood of generation cycles, and variability in host and parasitoid was equally stabilizing. One source of stability in these models may be aggregation of risk, because hosts with varying development times have different vulnerabilities. High levels of variability in development time occur in many insects and so could be a common source of stability in host-parasitoid systems.