Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity.

Despite investment in toxicogenomics, nonclinical safety studies are still used to predict clinical liabilities for new drug candidates. Network-based approaches for genomic analysis help overcome challenges with whole-genome transcriptional profiling using limited numbers of treatments for phenotypes of interest. Herein, we apply co-expression network analysis to safety assessment using rat liver gene expression data to define 415 modules, exhibiting unique transcriptional control, organized in a visual representation of the transcriptome (the 'TXG-MAP'). Accounting for the overall transcriptional activity resulting from treatment, we explain mechanisms of toxicity and predict distinct toxicity phenotypes using module associations. We demonstrate that early network responses complement traditional histology-based assessment in predicting outcomes for longer studies and identify a novel mechanism of hepatotoxicity involving endoplasmic reticulum stress and Nrf2 activation. Module-based molecular subtypes of cholestatic injury derived using rat translate to human. Moreover, compared to gene-level analysis alone, combining module and gene-level analysis performed in sequence identifies significantly more phenotype-gene associations, including established and novel biomarkers of liver injury.

Protein interaction networks at the host-microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen.

The Asian citrus psyllid (Diaphorina citri) is the insect vector responsible for the worldwide spread of 'Candidatus Liberibacter asiaticus' (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the D. citri immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host-microbe relationships. Using protein interaction reporter technology, a D. citri haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a D. citri myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with D. citri proteins. These co-evolved protein interaction networks at the host-microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.

Overview of worldwide diversity of Diaphorina citri Kuwayama mitochondrial cytochrome oxidase 1 haplotypes: two Old World lineages and a New World invasion.

Relationships among worldwide collections of Diaphorina citri (Asian citrus psyllid) were analyzed using mitochondrial cytochrome oxidase I (mtCOI) haplotypes from novel primers. Sequences were produced from PCR amplicons of an 821bp portion of the mtCOI gene using D. citri specific primers, derived from an existing EST library. An alignment was constructed using 612bps of this fragment and consisted of 212 individuals from 52 collections representing 15 countries. There were a total of eight polymorphic sites that separated the sequences into eight different haplotypes (Dcit-1 through Dcit-8). Phylogenetic network analysis using the statistical parsimony software, TCS, suggests two major haplotype groups with preliminary geographic bias between southwestern Asia (SWA) and southeastern Asia (SEA). The recent (within the last 15 to 25 years) invasion into the New World originated from only the SWA group in the northern hemisphere (USA and Mexico) and from both the SEA and SWA groups in the southern hemisphere (Brazil). In only one case, Reunion Island, did haplotypes from both the SEA and SWA group appear in the same location. In Brazil, both groups were present, but in separate locations. The Dcit-1 SWA haplotype was the most frequently encountered, including ~50% of the countries sampled and 87% of the total sequences obtained from India, Pakistan and Saudi Arabia. The second most frequently encountered haplotype, Dcit-2, the basis of the SEA group, represented ~50% of the countries and contained most of the sequences from Southeast Asia and China. Interestingly, only the Caribbean collections (Puerto Rico and Guadeloupe) represented a unique haplotype not found in other countries, indicating no relationship between the USA (Florida) and Caribbean introductions. There is no evidence for cryptic speciation for D. citri based on the COI region included in this study.

Comparison of laboratory colonies and field populations of Tamarixia radiata, an ectoparasitoid of the Asian citrus psyllid, using internal transcribed spacer and cytochrome oxidase subunit I DNA sequences.

The genetic diversity of Tamarixia radiata Waterston (Hymenoptera: Eulophidae) laboratory colonies derived from collections in China, northern Vietnam, Pakistan, and a mixed colony from Taiwan and southern Vietnam was evaluated using the internal transcribed spacer (ITS) region 1, ITS-2, and the 5' end of the cytochrome oxidase subunit I gene. The strains share the same ITS sequence, consistent with the morphological hypothesis that the collections represent a single species. The COI marker was variable and could distinguish the northern Vietnam and Pakistan colonies from each other and from the other colonies. Comparison of COI sequences from field-collected populations of Puerto Rico, Guadeloupe, and Texas indicates that Florida is not a likely source of the introduction into Puerto Rico but is a likely source of the introduction into Texas.

Analysis of host preference and geographical distribution of Anastrepha suspensa (Diptera: Tephritidae) using phylogenetic analyses of mitochondrial cytochrome oxidase I DNA sequence data.

Anastrepha suspensa (Loew) is an economically important pest, restricted to the Greater Antilles and southern Florida. It infests a wide variety of hosts and is of quarantine importance in citrus, a multi-million dollar industry in Florida. The observed recent increase in citrus infested with A. suspensa in Florida has raised questions regarding host-specificity of certain populations and genetic diversity of the pest throughout its geographical distribution. Cytochrome oxidase I (COI) DNA sequence data was used to characterize the genetic diversity of A. suspensa from Florida and Caribbean populations reared from different host plants. Maximum likelihood and Bayesian phylogenetic methods were used to analyse COI data. Sequence variation among mitochondrial COI genes from 107 A. suspensa samples collected throughout Florida and the Caribbean ranged between 0 and 10% and placed all A. suspensa as a monophyletic group that united all A. suspensa in a clade sister to a Central American group of the A. fraterculus paraphyletic species complex. The most likely tree of the COI locus indicated that COI sequence variation was too low to provide resolution at the subspecies level, therefore monophyletic groups based on host-plant use, geography (Florida, Jamaica, Cayman Islands, Puerto Rico or Dominican Republic) or population sampled are not supported. This result indicates that either no population segregation has occurred based on these biological or geographical distinctions and that this is a generalist, polyphagous invasive genotype. Alternatively, if populations are distinct, the segregation event was more recent than can be distinguished based on COI sequence variation.

Reduced oviposition by Diaprepes abbreviatus (Coleoptera: Curculionidae) and growth enhancement of citrus by Surround particle film.

Regularly applied sprays of a particle film, Surround WP, greatly enhanced the growth of citrus trees on a poorly drained Winder soil at Fort Pierce, FL. After 3 yr of applications every 3 or 4 wk, Surround-treated trees had at least 5 times the mass, 6 times the canopy volume, and approximately 4 times the cross-sectional area of the tree stems at the graft union compared with untreated trees. The larger Surround-treated trees attracted a higher number of adult weevil Diaprepes abbreviatus (L.) and to a lesser extent citrus root weevil, Pachnaeus litus (Germar), per tree, but there was an equivalent number of egg masses per tree compared with the control trees. The number of egg masses per female weevil oviposited on Surround-treated trees was significantly less than either the control trees or trees treated biannually with an entomopathogenic nematode, BioVector. The number of larvae per tree recovered from the roots of excavated trees was greater from trees treated with Surround once every 3 wk compared with control trees. The data suggest that Surround particle film greatly enhanced the growth of citrus trees grown in a poorly drained soil. The reduction in oviposition by D. abbreviatus was insufficient to significantly reduce the number of root weevil larvae per tree feeding on the roots. However, the more vigorous trees resulting from Surround applications may be more resistant or tolerant to root weevil feeding.

Field comparison of chemical attractants and traps for Caribbean fruit fly (Diptera: Tephritidae) in Florida citrus.

Field studies in citrus were conducted to compare the following as attractants for the Caribbean fruit fly, Anastrepha suspensa (Loew): torula yeast-borax; propylene glycol (10%); a two-component lure consisting of ammonium acetate and putrescine; a two-component lure consisting of ammonium bicarbonate and putrescine; and a three-component lure consisting of ammonium bicarbonate, methylamine hydrochloride, and putrescine. Various combinations of these attractants in glass McPhail, plastic McPhail-type (Multi-Lure), and sticky panel traps were investigated in two replicated studies. In one study on wild flies, the most effective and least complex trap-lure combination tested was the Multi-Lure with propylene glycol baited with ammonium acetate and putrescine. This trap-lure combination captured significantly more female and male flies than the standard glass McPhail baited with torula yeast-borax in water. All of the trap-lure combinations were female biased, with an overall average of 80.8% (SEM 1.4) flies captured being female. A second study on laboratory-reared, irradiated flies indicated no significant differences among these trap-lure combinations with respect to number of flies recaptured, although rankings based on mean number of flies recovered per trap per day supported results of the first study. The percentage of flies recaptured that were female (83.0%, SEM 0.9) was statistically the same as in the first study. Weekly percentage recovery of flies during the second study was low, possibly due to our fly release strategy. Future release/recovery studies with laboratory-reared flies would benefit from some basic research on release strategies by using different trap densities and on relating recapture rates of laboratory-reared flies (nonsterile and sterile) to capture rates of wild flies.

Morphology, immunohistochemistry, and genetic alterations in dog astrocytomas.

Astrocytoma is one of the most common tumors of the central nervous system in animals. Of the domesticated animal species, most examples are seen in dogs, and the spectrum that has been described is quiet broad. Previous studies have revealed morphologic similarities between human and animal astrocytomas. Human astrocytomas are often associated with genetic alterations that determine the clinical behavior and therapy outcome. The purpose of this study was to further characterize astrocytomas in dogs and to determine whether there are genetic changes similar to those in the human counterpart.

Sampling methods as abundance indices for adult Diaprepes abbreviatus (Coleoptera: Curculionidae) in citrus.

Beat sampling and two type of traps, cup traps and Tedders traps, were evaluated as sampling methods to detect and estimate population densities of adult Diaprepes abbreviatus L. weevils newly colonizing young citrus trees. The study was conducted over a 65-wk period across a 0.25-ha area of 80 citrus trees [Citrus sinensis (L.) Osbeck] (1.2-1.5 m tall). Beat samples were taken weekly to determine the number of trees infested and number of new adult weevils per tree. Sixteen of the 80 trees studied were each monitored weekly using one of the following trapping methods: cup traps in trees, cup traps on a stake in the ground within the tree drip line, cup traps on a stake in the ground outside of the drip line, Tedders traps on the ground within the drip line, and Tedders traps on the ground outside of the drip line. Weevils collected each week from trees and traps were removed from the study site. Based on the coefficients associated with Taylor's power law, the optimum numbers of trees to sample for an SEM equal to 25% of the mean estimate decreased from 50 trees at a mean of 0.5 new weevils per tree to 30 trees at a mean of 0.8 new weevils per tree. A significant relationship was found between the weekly mean number of new weevils per tree and the proportion of trees infested, a binomial relationship that could be further explored in the search for a sampling program for adult D. abbreviatus. Regression analyses indicated that three of the trapping methods served at least as weak indices of the presence and abundance of new weevils: cup traps in trees, Tedders traps inside the dripline and Tedders traps outside the dripline. Cup traps in trees and Tedders traps inside the dripline captured the most weevils and most frequently detected weevils. Although relatively inefficient as abundance indices of populations of new weevils, these two trapping methods appeared to have some value with respect to signaling when weevils first appeared in trees during the spring.

A national audit of retail lamb loin quality in Australia.

A retail audit of lamb loin tenderness was conducted over a 12-month period to determine the variation in tenderness of Australian lamb. Tenderness was objectively measured using Warner-Bratzler (WB) shear force. Muscle pH and cooking loss were determined on all samples and colour was measured on a sub-sample of loins. A total of 909 midloins from retail butcher shops and supermarkets located in four Australian capital cities (Sydney, Canberra, Melbourne, and Perth) were evaluated at four sampling times (December 1997 and March, June, and October 1998). Overall, 20.3% of all midloins purchased had a WB shear force value above the threshold level of 5 kg. Generic samples from Melbourne butcher shops were similar for WB shear force on average to the generic samples from Canberra and Sydney, whereas those from Melbourne supermarkets had significantly (P<0.001) higher WB shear force and were in line with generic samples from Perth. In both Canberra and Perth, alliance (branded) lamb had a greater WB shear force (P<0.05) than generic lamb. No relationship was found between price per kg and shear force (r=0.02) for loins purchased in Sydney (n=220). Price per kg differed between months (P<0.001) and suburbs (P<0.001), but not between retail butcher shops and supermarkets. Of the midloins tested, 10.3% had a pH above the critical point of 5.8. Midloins from the December 1997 sampling had a lower pH (P<0.01) than those sampled at other months. Those sampled in Melbourne and Perth had a similar mean pH, which were lower (P<0.001) than Canberra and Sydney samples. The findings from this quality audit suggest that there is room to improve the tenderness of Australian lamb sold in the domestic market. A lamb eating quality assurance system, based on set protocols, is one approach that is currently being investigated in Australia to ensure the supply of consistently high eating quality lamb to consumers.

Energy transfer at optical frequencies to silicon-based waveguiding structures.

For decades, crystalline silicon (Si) has been the semiconductor of choice for the majority of applications in microelectronics. Recent advances in material science have focused attention on the silicon-on-insulator (SOI) platform, a submicrometer-thick layer of single crystal Si resting on an insulating silicon dioxide (SiO2) layer. Here we calculate the lifetime of an electric dipole moment oscillating in the cover region of several canonical Si waveguiding structures. We show that the vicinity just above SOI produces the most dramatic changes to the radiative lifetime and thus the power spectrum of the emitting dipole. We demonstrate that SOI stands apart from other Si-based optoelectronic platforms in its ability to transport energy, in the form of light, away from an oscillating electric dipole via highly localized, optical- and IR-frequency guided waves.

Solid-phase synthesis of cleavable N-arylmaleimides: applications in 1,3-dipolar cycloaddition and in thiol scavenging.

[reaction: see text]. An efficient solid-phase synthesis of polymer-supported N-arylmaleimides has been developed. Various N-arylmaleimidobenzoic acids (MBA) were elaborated onto Rink and SASRIN resins by reaction of the aniline precursors with maleic anhydride followed by facile cyclative dehydration of the resulting maleimic acids. Applications of these acid-cleavable MBA resins in the solid-phase synthesis of highly decorated pyrrolidines and as thiol scavengers are presented.

Direct mono-N-methylation of solid-supported amino acids: a useful application of the Matteson rearrangement of alpha-aminoalkylboronic esters.

[reaction: see text] A novel solid-phase method for the mono-N-methylation of resin-supported amino acids was developed on the basis of Matteson's 1,2-carbon-to-nitrogen migration of boron in alpha-aminoalkylboronic esters. Amino acids supported on either Wang resin or the highly acid-sensitive SASRIN resin can be methylated by reaction with pinacol chloromethylboronic ester, followed by rearrangement of the resulting aminomethylboronate and subsequent cleavage of the boronate group. This direct method requires only a simple and expedient oxidative resin wash to repair overalkylated sites.

A mild and general solid-phase method for the synthesis of chiral polyamines. Solution studies on the cleavage of borane-amine intermediates from the reduction of secondary amides.

A mild oxidative workup protocol using iodine in an acetic acid-acetate buffer solution is described for the cleavage of borane-amine adducts arising from the borane-promoted reduction of polyamides supported onto practical trityl-based resins. Chiral polyamines with diverse side-chain functionalities can be generated as free bases without premature release from the solid support and with essentially no racemization using this method. A series of model oligomeric secondary diamides 6 containing various alpha-amino acid residues (Val, Phe, Tyr, Ser, Cys, Met, Gln, Trp) provided triamine products 8 in high yields and good to excellent purity. On the other hand, a substrate containing a tertiary amide (15) formed a rather unusual triaminoborane intermediate that required more stringent workup conditions to liberate the polyamine product 20. The reduction of oligomeric tertiary amides such as 9 was found sluggish, but these compounds could nonetheless be obtained in high purity from in situ reductive amination of the corresponding secondary amines. Control studies, carried out in solution with model secondary amide 23, confirmed the efficiency of the buffered iodine solution and highlighted several advantages (no heating necessary, no need for strong bases or acids) over existing methods for the cleavage of borane-amine adducts. A possible mechanism involving all buffer components (iodine, acetic acid, and acetate ion) is proposed in which borane-amine adducts are transformed first to the monoiodoborane-amine and then to the corresponding acetoxyborane-amine adduct of much weaker coordination affinity. The latter would dissociate readily and get trapped by the acetic acid to provide the desired secondary amine. This reduction/oxidative workup protocol is useful as a general method for the facile solid-phase synthesis of polyamines for eventual release in solution and use in various applications. It is also potentially very useful toward the synthesis and screening of bead-supported libraries of free oligoamines assembled through split-pool methods.

Young children's use of syntactic cues to learn proper names and count nouns.

In 6 experiments, 144 toddlers were tested in groups ranging in mean age from 20 to 37 months. In all experiments, children learned a novel label for a doll or a stuffed animal. The label was modeled syntactically as either a count noun (e.g., "This is a ZAV") or a proper name (e.g., "This is ZAV"). The object was then moved to a new location in front of the child, and a second identical-looking object was placed nearby. The children's task was to choose 1 of the 2 objects as a referent for the novel word. By 24 months, both girls (Experiment 2) and boys (Experiment 5) were significantly more likely to select the labeled object if they heard a proper name than if they heard a count noun. At 20 months, neither girls (Experiments 1 and 6) nor boys (Experiment 1) demonstrated this effect. By their 2nd birthdays, children can use syntactic information to distinguish appropriately between labels for individual objects and those for object categories.

Meat quality of mixed sex lambs grazing pasture and supplemented with, roughage, oats or oats and sunflower meal.

The meat quality of 8-9-month-old cryptorchid, wether and ewe lambs (Poll Dorset×Border Leicester×Merino) was assessed. These lambs were grazed over summer and autumn from weaning (November) on lucerne (Medicago sativa) or ryegrass/clover (Lolium rigidum/trifolium subterranean) pasture at two locations (A or B). After 72 days lambs grazed on lucerne were supplemented with either ad lib clover hay or clover silage. Those grazed on the ryegrass/clover pasture were supplemented from weaning with either oat grain (400-600 g/h day and clover hay ad lib) or oat grain (200-400 g/h day) plus sunflower seed meal (200 g/h day) and clover hay ad lib. Lambs were slaughtered in April and May after they reached 48 kg liveweight. Lambs supplemented solely with roughage produced muscle (m. longissimus thoracis et lumborum; LTL) with a higher (P<0.05) pH, but there was no effect of nutrition or sex on meat colour or tenderness. Slaughter day affected tenderness of the topside (m. semimembranosus). Assessment of aroma, flavour and acceptability was undertaken on the m. biceps femoris from wether and cryptorchid lambs using an experienced taste panel. There was no clear effect of sex or nutrition on the assessment of the sensory attributes. However, panellists considered meat from cryptorchid lambs fed the oats/sunflower supplement and grazed at location B, to have a stronger aroma and flavour (P<0.05) and in some cases to be less acceptable than meat from other combinations of sex, diet and location. The most acceptable meat came from lambs supplemented with oats, irrespective of sex or location. As such, these effects could not be attributed solely to either the diet or sex, but suggest there are conditions where meat from cryptorchids can be less acceptable.

Energy transfer at optical frequencies to silicon-on-insulator structures.

The refractive-index distribution that is intrinsic to the silicon-on-insulator (SOI) material system makes it possible for optical-frequency guided waves to be confined by the SOI silicon layer. The same refractive-index distribution is unusual among nonmetals in that it is possible for those SOI guided waves to interact strongly with nearby optical-frequency radiators, absorbers, and scatterers (e.g., atoms, molecules, and nanoparticles). We calculate the guided-mode excitation efficiency for an exterior particle near the SOI surface and show that it can attain values greater than 80% under appropriate conditions, thus showing that the SOI waveguide system is an attractive platform for the study of optical-frequency surface interactions.