The molecular basis of drug selectivity for α5 subunit-containing GABAA receptors

α5 subunit-containing γ-aminobutyric acid type A (GABAA) receptors represent a promising drug target for neurological and neuropsychiatric disorders. Altered expression and function contributes to neurodevelopmental disorders such as Dup15q and Angelman syndromes, developmental epilepsy and autism. Effective drug action without side effects is dependent on both α5-subtype selectivity and the strength of the positive or negative allosteric modulation (PAM or NAM). Here we solve structures of drugs bound to the α5 subunit. These define the molecular basis of binding and α5 selectivity of the β-carboline, methyl 6,7-dimethoxy-4-ethyl-β-carboline-3-carboxylate (DMCM), type II benzodiazepine NAMs, and a series of isoxazole NAMs and PAMs. For the isoxazole series, each molecule appears as an 'upper' and 'lower' moiety in the pocket. Structural data and radioligand binding data reveal a positional displacement of the upper moiety containing the isoxazole between the NAMs and PAMs. Using a hybrid molecule we directly measure the functional contribution of the upper moiety to NAM versus PAM activity. Overall, these structures provide a framework by which to understand distinct modulator binding modes and their basis of α5-subtype selectivity, appreciate structure-activity relationships, and empower future structure-based drug design campaigns.

Effects of restricting energy during the gilt development period on growth and reproduction of lines differing in lean growth rate: Responses in reproductive performance and longevity

Longevity and reproductive performance are economically important traits in the swine industry that are largely influenced by nutrition and other environmental factors. Reproductive performance and longevity through 4 parities was assessed in gilts of 2 genetic lines developed on ad libitum access to feed or restricted to 75% of ad libitum intake. A total of 661 gilts were used in a 2 x 2 factorial with half of the gilts allocated to an ad libitum diet (AL; n = 330), while the other half were energy restricted by 25% (R; n = 331) from 123 to 235 d of age. All gilts were sired by an industry maternal line. Dams of the gilts were from either a Large White by Landrace industry maternal line or Nebraska Selection Line 45X, producing gilts designated as W x L (n = 355) and L45X (n = 306), respectively. Daily estrus detection began at 140 d of age to obtain age at puberty (AP). Gilts (n = 510) were mated on their second or later estrus, beginning at 240 d of age. Sow weight and backfat were recorded at 110 d of gestation and weaning of each parity. Number of live-born, stillborn, and mummified pigs per litter and piglet birth and weaning weights were recorded through 4 parities. More L45X than W x L and more AL than R gilts reached puberty by 230 d of age (P < 0.01). Dietary treatment did not affect probability to produce parities 1 to 4 or any litter trait analyzed. The L45X females tended to be more likely to produce parities 1 (P < 0.08) and 3 (P < 0.06), while W x L had heavier litters at birth (P < 0.01) and weaning (P = 0.01). Treatment by parity interactions (P < 0.01) existed for weight and backfat prior to farrowing and backfat at weaning, and weight at weaning exhibited a line by treatment by parity interaction (P = 0.04) as R sows had lower weights and backfats in earlier parities, but caught up to AL sows in later parities. A treatment by parity interaction (P < 0.01) was also present for backfat loss from farrowing to weaning as R gilts lost less backfat than AL in parities 1 and 2, but more in parities 3 and 4. No significant differences were detected between lines or treatments for lifetime production traits. The populations of pigs and data presented here provide a framework for a diverse array of further studies. Alternative approaches to restrict energy have been assessed in addition to methods of marker-assisted and genomic selection for improvement of litter size and sow longevity.

Factors that affect heat production in lactating Jersey cows

Heat production (HP) represents a major energy cost in lactating dairy cows. Better understanding of factors that affect HP will improve our understanding of energy metabolism. Our objective was to derive models to explain variation in HP of lactating Jersey cows. Individual animal-period data from 9 studies (n = 293) were used. The data set included cows with a wide range (min to max) in days in milk (44-410) and milk yield (7.8-43.0 kg/d). Diets included corn silage as the predominate forage source, but diets varied (min to max on DM basis) in crude protein (CP; 15.2-19.5%), neutral detergent fiber (NDF; 35.5-43.0%), starch (16.2-31.1%), and crude fat (2.2 to 6.4%) contents. Average HP was (mean ± standard deviation) 22.1 ± 2.86 Mcal/d, or 28.1 ± 3.70% of gross energy intake. Eight models were fit to explain variation in HP: (1) dry matter intake (DMI; INT); (2) milk fat, protein, and lactose yield (MILKCOMP); (3) INT and milk yield (INT+MY); (4) INT and MILKCOMP/DMI (INT+MILKCOMP); (5) mass of digested NDF, CP, and starch (DIG); (6) INT and digested energy (INT+DE); (7) INT and NDF, CP, and starch digestibility (INT+DIG); or (8) INT+MILKCOMP model plus urinary N excretion (INT+MILKCOMP+UN). For all HP models, metabolic body weight was included. All models were derived via a backward elimination approach and included the random effects of study, cow, and period within block within study. The INT models adequately explained variation in HP with a nonrandom effect-adjusted concordance correlation coefficient of 0.84. Similar adjusted concordance correlation coefficients (0.79-0.85) were observed for other HP models. The HP associated with milk protein yield and supply of digestible protein was greater than other milk production and nutrient digestibility variables. The HP associated with urinary N excretion was 5.32. Overall, HP can be adequately predicted from metabolic body weight and DMI. Milk component yield, nutrient digestibility, or urinary N excretion explained similar variation as DMI. Coefficients for milk protein and protein digestion suggest that digestion and metabolism of protein and synthesis of milk protein contribute substantially to HP of a dairy cow.

Development of feed composition tables using a statistical screening procedure

Millions of feed composition records generated annually by testing laboratories are valuable assets that can be used to benefit the animal nutrition community. However, it is challenging to manage, handle, and process feed composition data that originate from multiple sources, lack standardized feed names, and contain outliers. Efficient methods that consolidate and screen such data are needed to develop feed composition databases with accurate means and standard deviations (SD). Considering the interest of the animal science community in data management and the importance of feed composition tables for the animal industry, the objective was to develop a set of procedures to construct accurate feed composition tables from large data sets. A published statistical procedure, designed to screen feed composition data, was employed, modified, and programmed to operate using Python and SAS. The 2.76 million data received from 4 commercial feed testing laboratories were used to develop procedures and to construct tables summarizing feed composition. Briefly, feed names and nutrients across laboratories were standardized, and erroneous and duplicated records were removed. Histogram, univariate, and principal component analyses were used to identify and remove outliers having key nutrients outside of the mean ± 3.5 SD. Clustering procedures identified subgroups of feeds within a large data set. Aside from the clustering step that was programmed in Python to automatically execute in SAS, all steps were programmed and automatically conducted using Python followed by a manual evaluation of the resulting mean Pearson correlation matrices of clusters. The input data set contained 42, 94, 162, and 270 feeds from 4 laboratories and comprised 25 to 30 nutrients. The final database included 174 feeds and 1.48 million records. The developed procedures effectively classified by-products (e.g., distillers grains and solubles as low or high fat), forages (e.g., legume or grass-legume mixture by maturity), and oilseeds versus meal (e.g., soybeans as whole raw seeds vs. soybean meal expellers or solvent extracted) into distinct sub-populations. Results from these analyses suggest that the procedure can provide a robust tool to construct and update large feed data sets. This approach can also be used by commercial laboratories, feed manufacturers, animal producers, and other professionals to process feed composition data sets and update feed libraries.

Increasing the concentration of linolenic acid in diets fed to Jersey cows in late lactation does not affect methane production

Although the inclusion of fat has reduced methane production in ruminants, relatively little research has been conducted comparing the effects of source and profile of fatty acids on methane production in lactating dairy cows. A study using 8 multiparous (325 ± 17 DIM; mean ± SD) lactating Jersey cows was conducted to determine effects of feeding canola meal and lard versus extruded byproduct containing flaxseed as a high-C18:3 fat source on methane production and diet digestibility in late-lactation dairy cows. A crossover design with 32-d periods (28-d adaptation and 4-d collections) was used to compare 2 different fat sources. Diets contained approximately 50% forage mixture of corn silage, alfalfa hay, and brome hay; the concentrate mixture changed between diets to include either (1) a conventional diet of corn, soybean meal, and canola meal with lard (control) or (2) a conventional diet of corn and soybean meal with an extruded byproduct containing flaxseed (EXF) as the fat source. Diets were balanced to decrease corn, lard, and canola meal and replace them with soybean mean and EXF to increase the concentration of C18:3 (0.14 vs. 1.20% of DM). Methane production was measured using headbox-style indirect calorimeters. Cattle were restricted to 95% ad libitum feed intake during collections. Milk production (17.4 ± 1.04 kg/d) and dry matter intake (15.4 ± 0.71 kg/d) were similar among treatments. Milk fat (5.88 ± 0.25%) and protein (4.08 ± 0.14%) were not affected by treatment. For methane production, no difference was observed for total production (352.0 vs. 349.8 ± 16.43 L/d for control vs. EXF, respectively). Methane production per unit of dry matter intake was not affected and averaged 23.1 ± 0.57 L/kg. Similarly, methane production per unit of energy-corrected milk was not affected by fat source and averaged 15.5 ± 0.68 L/kg. Heat production was similar, averaging 21.1 ± 1.02 Mcal/d. Digestibility of organic matter, neutral detergent fiber, and crude protein was not affected by diet and averaged 69.9, 53.6, and 73.3%, respectively. Results indicated that increasing C18:3 may not affect methane production or digestibility of the diet in lactating dairy cows.

GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows

Genetic variants associated with traits such as age at puberty and litter size could provide insight into the underlying genetic sources of variation impacting sow reproductive longevity and productivity. Genomewide characterization and gene expression profiling were used using gilts from the University of Nebraska-Lincoln swine resource population ( = 1,644) to identify genetic variants associated with age at puberty and litter size traits. From all reproductive traits studied, the largest fraction of phenotypic variation explained by the Porcine SNP60 BeadArray was for age at puberty (27.3%). In an evaluation data set, the predictive ability of all SNP from high-ranked 1-Mb windows (1 to 50%), based on genetic variance explained in training, was greater (12.3 to 36.8%) compared with the most informative SNP from these windows (6.5 to 23.7%). In the integrated data set ( = 1,644), the top 1% of the 1-Mb windows explained 6.7% of the genetic variation of age at puberty. One of the high-ranked windows detected (SSC2, 12-12.9 Mb) showed pleiotropic features, affecting both age at puberty and litter size traits. The RNA sequencing of the hypothalami arcuate nucleus uncovered 17 differentially expressed genes (adjusted < 0.05) between gilts that became pubertal early (<155 d of age) and late (>180 d of age). Twelve of the differentially expressed genes are upregulated in the late pubertal gilts. One of these genes is involved in energy homeostasis (), a function in which the arcuate nucleus plays an important contribution, linking nutrition with reproductive development. Energy restriction during the gilt development period delayed age at puberty by 7 d but increased the probability of a sow to produce up to 3 parities ( < 0.05). Identification of pleotropic functional polymorphisms may improve accuracy of genomic prediction while facilitating a reduction in sow replacement rates and addressing welfare concerns.

Structural basis for GABAA receptor potentiation by neurosteroids

Type A γ-aminobutyric acid receptors (GABAARs) are the principal mediators of inhibitory neurotransmission in the human brain. Endogenous neurosteroids interact with GABAARs to regulate acute and chronic anxiety and are potent sedative, analgesic, anticonvulsant and anesthetic agents. Their mode of binding and mechanism of receptor potentiation, however, remain unknown. Here we report crystal structures of a chimeric GABAAR construct in apo and pregnanolone-bound states. The neurosteroid-binding site is mechanically coupled to the helices lining the ion channel pore and modulates the desensitization-gate conformation. We demonstrate that the equivalent site is responsible for physiological, heteromeric GABAAR potentiation and explain the contrasting modulatory properties of 3a versus 3b neurosteroid epimers. These results illustrate how peripheral lipid ligands can regulate the desensitization gate of GABAARs, a process of broad relevance to pentameric ligand-gated ion channels.

Structural basis of Smoothened regulation by its extracellular domains

Developmental signals of the Hedgehog (Hh) and Wnt families are transduced across the membrane by Frizzledclass G-protein-coupled receptors (GPCRs) composed of both a heptahelical transmembrane domain (TMD) and an extracellular cysteine-rich domain (CRD). How the large extracellular domains of GPCRs regulate signalling by the TMD is unknown. We present crystal structures of the Hh signal transducer and oncoprotein Smoothened, a GPCR that contains two distinct ligand-binding sites: one in its TMD and one in the CRD. The CRD is stacked a top the TMD, separated by an intervening wedge-like linker domain. Structure-guided mutations show that the interface between the CRD, linker domain and TMD stabilizes the inactive state of Smoothened. Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site. Mutations predicted to prevent cholesterol binding impair the ability of Smoothened to transmit native Hh signals. Binding of a clinically used antagonist, vismodegib, to the TMD induces a conformational change that is propagated to the CRD, resulting in loss of cholesterol from the CRD-linker domain-TMD interface. Our results clarify the structural mechanism by which the activity of a GPCR is controlled by ligand-regulated interactions between its extracellular and transmembrane domains.

Evaluation of collection method and diet effects on apparent digestibility and energy values of swine diets

Two experiments were conducted to investigate the effects of collection method and diet type on digestibility coefficients. In Exp. 1, 24 barrows were fed either a corn-soybean meal (CSBM) diet or CSBM with 20% dried distillers' grains with solubles (CSBM-DDGS). In Exp. 2, the effects of basal diet and collection method on determination of dried distillers' grains with solubles (DDGS) digestibility were studied using 24 barrows. The 4 diets used in Exp. 2 were: a CSBM (basal 1) , a barley-canola meal (BCM; basal 2), 80% basal 1 with 20% DDGS (CSBM-DDGS), and 80% basal 2 with 20% DDGS (BCM-DDGS). In both experiments, feces were collected using a time-based collection method (DY) or a "marker-to-marker" collection method (MM). Diets contained 0.5% of titanium dioxide (TiO) for estimating digestibility using the index marker approach (IM). The apparent total tract digestibility (ATTD) of DM and GE were lower ( < 0.05) in the CSBM-DDGS diet than in the CSBM diet in Exp. 1 but were not different in Exp. 2. All the estimates of BCM-based diets were consistently lower ( < 0.05) than those of CSBM-based diets. In Exp. 1, digestibility coefficients determined by the DY and MM were not different from each other, whereas those estimates were lower ( < 0.05) using the IM than those using the total collection approach (TC; DY and MM). In Exp. 2, interactions ( < 0.05) were observed between diet type and method for dietary digestibility coefficients. Digestibility and energy values estimated by the DY and MM were not different in pigs fed CSBM-based diets and the BCM-DDGS diet, whereas those estimates were greater ( < 0.05) using the DY than those using the MM in pigs fed the BCM. There were no interactions between basal diet and method for estimating DDGS digestibility. The ATTD of DM and GE of DDGS using the MM were greater ( < 0.05) than those using the IM, and ATTD of N tended to be greater ( < 0.10) using the MM than that using the IM. All estimates using the DY were not different from those using the MM or the IM, except that DE of DDGS was greater ( < 0.05) using the DY than when using the IM. Digestibility estimates of DDGS were not affected by basal diets. The mean DE and ME (as-fed basis) of DDGS were 3,994 and 3,688 kcal/kg, respectively, when estimated using the basal 1 diet and were 3,919 and 3,547 kcal/kg, respectively, when estimated using the basal 2 diet. In conclusion, both collection methods can be used to estimate energy and nutrient digestibility of diets and DDGS when using CSBM-based diets.

Body composition, tissue deposition, and lysine utilization for protein deposition of barrows and gilts fed crystalline or protein-bound lysine

An experiment with 2 trials (28 d/trial) was conducted to determine body composition, tissue deposition, and utilization of Lys for protein deposition (PD) of barrows and gilts fed -Lys·HCl (CLys) or protein-bound Lys in soybean meal (SBM). Thirty-two growing pigs (16 barrows and 16 gilts; average initial BW of 18.6 kg) were used in each of 2 trials. Four pigs (2 barrows and 2 gilts) were euthanized at the start of each trial to determine initial body composition. The remaining pigs were euthanized at the end of the trials to determine empty-body composition and deposition rates of water, protein, fat, ash, and AA. Pigs were randomly allotted to 1 of 7 dietary treatments. There were 2 replications per treatment in each trial for a total of 4 replications. Dietary treatments consisted of a corn-SBM basal diet (0.48% Lys) and diets containing 0.56%, 0.65%, and 0.74% standardized ileal digestible (SID) Lys that were achieved by adding Lys to the basal diet from either SBM or CLys. Pigs fed the CLys-supplemented diets at 0.65% SID Lys had more ( < 0.05) body water (663 vs. 624 g/kg) and less ( < 0.01) body protein (153 vs. 160 g/kg) than pigs fed the SBM-supplemented diets. Body fat content decreased ( < 0.01) as the dietary Lys increased similarly for pigs fed Lys from SBM and pigs fed CLys. Gilts had greater ( = 0.05) body Lys content in body protein than barrows (7.68 vs. 7.52 g/100 g). Empty-body ash contents were not different between pigs fed CLys or SBM-supplemented diets. Water deposition and PD increased linearly ( < 0.01) with dietary Lys and were least ( < 0.01) in pigs fed the basal diet but were similar when comparing pigs fed CLys and SBM-supplemented diets at the same dietary Lys concentration. Lysine deposition showed a linear increase ( < 0.01) with dietary Lys but was not different between pigs fed the 2 Lys sources at the same concentration. Barrows and gilts did not differ in tissue deposition rates. Overall, empty-body contents and deposition rates of essential and nonessential AA were not different between pigs fed CLys and pigs fed SBM-bound Lys. The amount of SID Lys required for PD ranged between 0.09 and 0.13 g/g for both sources of Lys. The Lys deposition:SID Lys intake ratio was greater ( < 0.01) in gilts than barrows (0.62 vs. 0.56). Body composition, tissue deposition, and utilization of Lys for PD and Lys deposition were not different in pigs fed diets supplemented with -Lys·HCl with respect to protein-bound Lys in SBM.

A cooperative study on the standardized total-tract digestible phosphorus requirement of twenty-kilogram pigs

A cooperative study comprising growth performance, bone mineralization, and nutrient balance experiments was conducted at 11 stations to determine the standardized total-tract digestible (STTD) P requirement of 20-kg pigs using broken-line regression analysis. Monocalcium phosphate and limestone were added to a corn-soybean meal-based diet at the expense of cornstarch to establish 6 concentrations of STTD P from 1.54 to 5.15 g/kg in increments of 0.62 g/kg at a constant Ca:total P of 1.52:1.0. Diets were fed to 936 pigs (average initial BW of 19 kg) in 240 pens for 20 replicate pens of barrows and 20 replicate pens of gilts per diet. As STTD P increased from 1.54 to 5.15 g/kg of the diet for d 0 to 14, 14 to 28, and 0 to 28, the ADG, ADFI, and G:F increased ( < 0.01). Barrows gained and ate more ( < 0.05) than gilts during d 14 to 28 and 0 to 28. There was no interaction between sex and STTD P concentration for any of the growth performance response criteria. There were both linear and quadratic increases ( < 0.05) in mineral density and content of ash, Ca, and P in the femur expressed as a percentage of dry, fat-free metacarpal as dietary STTD P increased. Furthermore, the maximum load of the femur and mineral density and content and maximum load as well as the Ca and P expressed as a percentage of metacarpal ash linearly increased ( < 0.01) with increasing dietary concentrations of STTD P. There were both linear and quadratic increases ( < 0.01) in apparent digestibility and retention of P with increasing concentrations of STTD P in the diets. Digestibility and retention of Ca linearly ( < 0.01) increased with increasing dietary concentrations of STTD P. Breakpoints determined from nonlinear broken-line regression analyses revealed estimates of 4.20 ± 0.102, 3.20 ± 0.036, or 3.87 ± 0.090 g/kg for ADG during d 0 to 14, 14 to 28, or 0 to 28, respectively. Corresponding estimates using G:F as the response criterion were 4.34 ± 0.146, 3.38 ± 0.139, or 4.08 ± 0.195 g/kg. When mineralization of the femur was used as criteria of response, estimates of STTD P requirement were 4.28, 4.28, or 4.34, g/kg for mineral density, mineral content, or maximum load, respectively. Using mineralization of the metacarpal as criteria of response, estimates of STTD P requirement ranged from 3.5 to 5.0 g/kg depending on the metacarpal response criteria. The study provided empirical estimates of STTD P requirements of 20- to 40-kg pigs.

Energy content of reduced-fat dried distillers grains with solubles for lactating dairy cows

Eight Holstein and 8 Jersey multiparous, lactating cows were used to complete 56 energy balances to determine the energy content of reduced-fat dried distillers grains with solubles (RFDDGS). A repeated switchback design was used to compare treatments with and without RFDDGS. Diets consisted of 24.2% corn silage, 18.4% alfalfa hay, 6.94% brome hay with either 22.9% rolled corn or 14.8% soybean meal (control), or 8.95% rolled corn, 28.8% RFDDGS, and 0% soybean meal [Co-P; dry-matter (DM) basis]. The inclusion of RFDDGS did not affect DM intake, averaging 21.4 ± 0.53 kg of DM for all cows, but milk production tended to increase from 29.8 to 30.9 ± 1.46 kg/d for control and Co-P treatments, respectively. Milk fat percentage and energy-corrected milk did not differ between treatments, averaging 4.33 ± 0.14% and 34.1 kg/d, respectively. Milk protein was significantly decreased by the Co-P treatment (3.56 and 3.41 ± 0.08% for control and Co-P treatments), but protein yield was not affected. Milk energies were 1.40 Mcal/d greater with Co-P. Energy lost as methane was reduced by 0.31 Mcal/d with the addition of RFDDGS to the diet. Heat loss averaged 29.9 ± 0.55 Mcal/d and was not different between diets. Average energy retained as tissue energy was -2.99 ± 0.93 Mcal/d and did not differ between treatments. Intake of digestible and metabolizable energy were not different between the control and Co-P treatments, averaging 2.68 and 2.31 Mcal/kg of DM, respectively. The net energy of lactation values of control and Co-P diets were calculated to be 1.43 and 1.47 Mcal/kg of DM, respectively. These energy estimates suggest greater energy content of diets containing RFDDGS than diets containing a mixture of corn and soybean meal in lactating dairy cows.

Targeting the human androgen receptor gene with platinated triplex-forming oligonucleotides

Platinum-derivatized homopyrimidine triplex-forming oligonucleotides (Pt-TFOs) consisting of 2'-O-methyl-5-methyluridine, 2'-O-methyl-5-methylcytidine, and a single 3'-N7-trans-chlorodiammine platinum(II)-2'-deoxyguanosine were designed to cross-link to the transcribed strand at four different sequences in the human androgen receptor (AR) gene. Fluorescence microscopy showed that a fluorescein-tagged Pt-TFO localizes in both the cytoplasm and nucleus when it is transfected into LAPC-4 cells, a human prostate cancer cell line, using Lipofectamine 2000. A capture assay employing streptavidin-coated magnetic beads followed by polymerase chain reaction (PCR) amplification was used to demonstrate that 5'-biotin-conjugated Pt-TFOs cross-link in vitro to their four designated AR gene targets in genomic DNA extracted from LAPC-4 cells. Similarly, the capture assay was used to examine cross-linking between the 5'-biotin-conjugated Pt-TFOs and the AR gene in LAPC-4 cells in culture. Three of the four Pt-TFOs cross-linked to their designated target, suggesting that different regions of the AR gene are not uniformly accessible to Pt-TFO cross-linking. LAPC-4 cells were transfected with fluorescein-tagged Pt-TFO or a control oligonucleotide that does not bind or cross-link to AR DNA. The levels of AR mRNA in highly fluorescent cells isolated by fluorescence-activated cell sorting were determined by RT-qPCR, and the levels of AR protein were monitored by immunofluorescence microscopy. Decreases in mRNA and protein levels of 40 and 30%, respectively, were observed for fluorescein-tagged Pt-TFO versus control treated cells. Although the levels of knockdown of AR mRNA and protein were modest, the results suggest that Pt-TFOs hold potential as agents for controlling gene expression by cross-linking to DNA and disrupting transcription.

Supplementation of organic and inorganic selenium to diets using grains grown in various regions of the United States with differing natural Se concentrations and fed to grower-finisher swine

Grains grown in various regions of the United States vary in their innate or natural Se contents. A regional study evaluated the effects of adding inorganic Se (sodium selenite) or organic Se (Se yeast) to diets with differing innate Se contents. A 2 × 2 + 1 factorial experiment evaluating 2 Se sources (organic or inorganic) at 2 Se levels (0.15 or 0.30 mg/kg) in 18 total replicates (n = 360 total pigs). A basal diet was fed without supplemental Se and served as the negative (basal) control. The study was conducted as a randomized complete block design in 9 states (Georgia, Illinois, Kentucky, Nebraska, North Carolina, Ohio, South Dakota, Texas, and Wisconsin) with each station conducting 2 replicates. Pigs were fed from 25 to approximately 115 kg BW. Similar dietary formulations were used at each station, incorporating a common source of trace mineral and Se premixes. Three pigs per treatment in 16 replicates (n = 240) were bled at 55, 85, and 115 kg BW and serum Se and glutathione peroxidase (GSH-Px) activities were determined. Three pigs (n = 260) from each treatment pen were killed at 115 kg BW and issues (liver, loin, and hair) were analyzed for Se. The corn Se content from the various states ranged from 0.026 to 0.283 mg Se/kg while the soybean meal Se content ranged from 0.086 to 0.798 mg Se/kg. Tissue and serum Se concentrations were greater (P < 0.01) when supplemental organic Se was fed, whereas serum GSH-Px was greater (P < 0.01) as Se level increased. There were linear increases (P < 0.01) in loin and quadratic increases (P < 0.01) in liver and hair Se concentrations as dietary Se level increased within each state. There was a source × level interaction (P < 0.01) for each tissue resulting in a greater increase when organic Se was fed. Serum Se and GSH-Px activity increased (P < 0.01) when both Se sources were fed and plateaued at each state at 0.15 mg Se/kg. There was a high and significant correlation between each tissue Se, serum Se, and GSH-Px activity to dietary Se level indicating that those states having greater grain natural Se contents also had greater tissue Se concentrations. These results indicate that a large difference in corn and soybean meal Se concentrations exists between states, that the addition of organic or inorganic Se to these grains increased tissue and serum Se in each state, and that organic Se was incorporated at greater concentrations in the loin, liver, and hair tissues of grower-finisher pigs than inorganic Se.

Crystal structure of a human GABAA receptor

Type-A γ-aminobutyric acid receptors (GABAARs) are the principal mediators of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signalling triggers hyperactive neurological disorders such as insomnia, anxiety and epilepsy. Here we present the first three-dimensional structure of a GABAAR, the human β3 homopentamer, at 3 Å resolution. This structure reveals architectural elements unique to eukaryotic Cys-loop receptors, explains the mechanistic consequences of multiple human disease mutations and shows an unexpected structural role for a conserved N-linked glycan. The receptor was crystallized bound to a previously unknown agonist, benzamidine, opening a new avenue for the rational design of GABAAR modulators. The channel region forms a closed gate at the base of the pore, representative of a desensitized state. These results offer new insights into the signalling mechanisms of pentameric ligand-gated ion channels and enhance current understanding of GABAergic neurotransmission.

Utilization of crystalline or protein-bound lysine for growth and carcass traits of barrows and gilts fed individually or in groups

An experiment consisting of two 4-wk trials was conducted to determine Lys use for growth and carcass traits in barrows and gilts fed individually or in groups. One hundred twelve growing pigs (56 barrows and 56 gilts; average initial BW of 18.6 kg) were used in each trial. Pigs were fed individually or in groups of 3. There were 28 pigs individually penned, and 84 pigs in 28 pens (3 pigs/pen). There were 2 replications per treatment in each trial for a total of 4 replications. Dietary treatments consisted of a corn-soybean meal (SBM) basal diet (0.48% Lys) and diets containing 0.56%, 0.65%, and 0.74% standardized ileal digestible (SID) Lys that were achieved by adding Lys to the basal diet from either SBM or crystalline source as L-Lys HCL (CLys). At the end of each trial, all pigs were scanned using real-time ultrasound to determine 10th-rib back fat depth and LM area, and fat-free lean gain (FFLG) was calculated. Blood samples were taken from all pigs weekly to determine plasma urea N (PUN). Pigs fed CLys and Lys from SBM were not different in final BW, ADG, ADFI, or G:F. The ADG and G:F increased linearly (P < 0.01) as dietary Lys concentration increased. The SID Lys intake increased linearly (P < 0.01) as dietary Lys concentration increased and was not different when comparing pigs fed diets with CLys or SBM. The amount of SID Lys required per unit of growth or BW gain increased linearly (about 13 to 15.50 g/kg) in pigs fed either CLys or SBM Lys. Pigs fed individually had a greater (P < 0.05) ADG (0.59 vs. 0.57 kg) and ADFI (1.36 vs. 1.29 kg) than pigs fed in groups. The SID Lys intake was greater (P < 0.05) in pigs fed individually in comparison with pigs fed in a group (8.51 vs. 8.06 g/d). Fat-free lean gain and LM area increased (P < 0.01) as dietary Lys concentration increased regardless of Lys source. Pigs fed CLys diets had a greater (P < 0.05) LM area than pigs fed SBM at 0.74% SID Lys. Gilts had a greater (P < 0.01) LM area (14.28 vs. 13.58 cm(2)) and FFLG (264 vs. 245 g/d) than barrows. Pigs fed individually with CLys had less (P < 0.01) PUN than pigs fed Lys from SBM. Barrows fed individually had less (sex × feeding method, P < 0.01) PUN than gilts (26.75 vs. 29.32 g/100 mL). The results indicate that Lys from SBM-bound and CLys source were utilized similarly for growth and carcass traits regardless of sex or feeding method.

Synthesis of building blocks and oligonucleotides with {T}N3-alkylene-N3{T} cross-links

This unit describes two methods to directly prepare oligonucleotide duplexes containing an N3thymidine-alkylene-N3thymidine inter-strand cross-link. The inter-strand cross-link can be engineered into the duplex with a number of possible orientations. Both methods require the preparation of a protected thymidine dimer where the N3 atoms of the two nucleosides are covalently attached by an alkyl linker. This linker is prepared starting from a protected diol using two successive alkylation reactions under basic conditions to accomplish the alkylation selectively at the N3 atom of the nucleoside. The chain length of the cross-link can be varied based on the selection of the diol used in the dimer synthesis. The solid-phase mono-phosphoramidite approach involves oligonucleotide synthesis with 3'-O-phosphoramidites, on-column removal of a 3'-O-tert-butyldimethylsilyl protecting group, and continued oligonucleotide synthesis with 5'-O-phosphoramidites. The bis-phosphoramidite approach does not require synthesis with 5'-O-phosphoramidites. At the end of synthesis using either method, the N3thymidine-alkylene-N3thymidine inter-strand cross-linked oligonucleotides can be removed from the solid-support and purified using standard techniques (ion-exchange HPLC) in yields sufficient for various structural studies and repair assays.

Genome-wide prediction of age at puberty and reproductive longevity in sows

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1-Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27-28 Mb), SSC8 (36-37 Mb) and SSC12 (1.2-2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities by up to 1.36. The region located on SSC5 harbors non-synonymous alleles in the arginine vasopressin receptor 1A (AVPR1A) gene, a G-protein-coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker-assisted selection programs across populations to increase sow reproductive longevity.

Effect of dietary acids on growth performance of nursery pigs: a cooperative study

An experiment involving 854 crossbred pigs (20 replicate pens of 4 to 8 pigs per pen) was conducted at 8 experiment stations to determine the effects of acids in nursery pig diets and their inclusion amounts on growth performance using diets and weaning ages typical of those used in the United States commercial pork industry. Diets were formulated to have constant a ME and contain 1.45, 1.45, and 1.30% standardized ileal digestible Lys for phases 1, 2, and 3, respectively. The basal diets were supplemented with various types and concentrations of acid at the expense of corn (Zea mays). Treatment diets included 0% acid (control), 0.1 or 0.2% phosphoric acid, 1 or 2% organic acids, and 0.1% phosphoric acid plus 1% organic acids with or without an antibiotic. The organic acids consisted of 50% citric acid and 50% fumaric acid by weight. All but the final diet contained the antibiotic carbadox. All diets contained 3,000 mg of Zn/kg diet from zinc oxide during phases 1 and 2 and had limited acid buffering capacity, ranging from 142, 127, and 122 mEq/kg of feed for phases 1, 2, and 3, respectively. At each participating station, pigs were randomly allotted to dietary treatments on the basis of their initial BW. Sex and ancestry were equally distributed across the treatments. Results indicated that treatment effects on pig performance were observed in phases 1 and 2 but not in phase 3. In phase 1, ADG of pigs fed 0.2% phosphoric acid was greater than that of pigs fed the combination of acids with no antibiotic (P = 0.041). In phase 2, pigs fed treatments containing an antibiotic had a greater ADG than those fed the combination of acids without antibiotic (P < 0.05). Addition of acids to diets did not affect growth performance during any phase or the overall period. Over the 4-wk study, growth rate was slowest on the treatment without antibiotic, with specific differences that were often statistically significant (P < 0.05). In summary, under the conditions of this experiment, the acid treatments had no effect but the antibiotic improved growth performance.

Inhibition of transcription by platinated triplex-forming oligonucleotides

Platinated triplex-forming oligonucleotides (TFOs) consisting of 2'-methoxythymidine and 2'-methoxy-5-methylcytidine and an N-7 platinated deoxyguanosine ((Pt)G) at the 5'-((Pt)G-TFO), 3'-(TFO-G(Pt)), or 3'- and 5'-((Pt)G-TFO-G(Pt)) ends of the TFO form mono-((Pt)G-TFO and TFO-G(Pt)) and interstrand ((Pt)G-TFO-G(Pt)) cross-links with target DNA as a result of reaction of the (Pt)G with guanines adjacent to the homopurine TFO binding site in the target. The extent of cross-linking is greatest when the (Pt)G is located on the 3' end of the TFO and the target guanine is on the same strand as the TFO binding site. Multiple, contiguous deoxyguanosines in the TFO binding site or a cytosine adjacent to the G(Pt) of the TFO significantly reduce cross-linking. DNA reporter plasmids in which platinated TFOs were cross-linked at a site in the transcribed region between a CMV promoter and a luciferase reporter gene were transfected into Chinese hamster ovary cells, and luciferase expression was compared with that for the corresponding non-cross-linked plasmid. Luciferase expression was inhibited 95 % when TFO-G(Pt) was bound and cross-linked to the transcribed strand, demonstrating that the cross-linked TFO was able to block transcription elongation. Further inhibition (99 %) was observed in nucleotide excision repair (NER) deficient cells, suggesting that NER may repair this lesion. The 3'-G(Pt) group of TFO-G(Pt) protects the TFO from degradation by exonucleases found in mammalian serum. Taken together, these results suggest that platinated TFOs of the type TFO-G(Pt) may find applications as agents for suppressing DNA transcription and consequently inhibiting gene expression in mammalian cells.

Abstract C19: Targeting the human androgen receptor gene with platinum-conjugated triplex-forming oligonucleotides

Androgen receptor (AR) gene expression is required to maintain prostrate tumor cell growth and inhibition of this gene would be expected to prevent prostate tumor cell proliferation. The human AR gene contains numerous homopurine tracts that can serve as binding sites for triplex-forming oligonucleotides (TFOs), a class of oligonucleotides that have significant potential as antigene agents. We have developed a novel type of TFO that is comprised of 2′-O-methylribonucleotides and contains a N7-trans-diamminechloroplatinumdeoxygu anosine residue at either its 5′- (Pt-mrTFO) or 3′-end (mrTFO-Pt). When bound to a homopurine tract in double-stranded DNA, the platinum group of the Pt-mrTFO can cross-link with suitably positioned guanine residues adjacent to the TFO binding site, a reaction that irreversibly anchors the TFO to its DNA target. Such cross-link formation would be expected to interfere with transcription and/or replication of the target DNA. We have identified 27 different homopurine tracts in the transcribed region of the human AR gene whose sequences are compatible with cross-link formation by Pt-mrTFOs or mrTFO-Pt. In preliminary studies, we have synthesized a mrTFO-Pt whose sequence (mr−TTTCTTCTTTTCTCTCTTGPt; T = 2′-O-methylribothymine; C = 2′-O-methylribo-5-methylcytosine; GPt = N7-trans-diammin echloroplatinumdeoxyguanosine) targets a 19 nucleotide homopurine sequence on the transcribed strand in the 2nd intron of the human AR gene. At physiological pH and temperature, the mrTFO lacking GPt forms a stable triplex (melting temperature = 45.2°C) with a 24 bp DNA duplex whose sequence corresponds to the TFO binding site in the AR gene. The mrTFO-Pt cross-links to this duplex to the extent of 80% under physiological conditions as shown by gel electrophoretic mobility shift assays. To test its ability to inhibit transcription, the mrTFO-Pt was cross-linked (91%) to a firefly luciferase reporter plasmid that contained a single copy of the AR target gene sequence placed in the transcribed region between the plasmid's CMV promoter and luciferase reporter gene. The cross-linked plasmid was co-transfected with a Renilla luciferase reporter plasmid (to monitor transfection efficiency) into HeLa cells in culture and luciferase activity was determined 24 hrs after transfection using a dual luciferase assay (Promega Inc.). Luciferase expression decreased 43% compared to that from a non-cross-linked control plasmid. The mrTFO-Pt was found to be resistant to degradation when incubated at 37.C for a period of 24 hrs with cell culture medium containing 10% fetal calf serum. Transfection of a human prostate cancer cell line (LAPC4) with a Lipofectamine complex of the fluorescein-labeled TFO (Fl-mrTFO-Pt*, where Pt* is an inert N7-diethelentraimineplatinum-deoxyguanosine residue) resulted in nuclear localization of the label in 69% of the cells as revealed by fluorescence microscopy of the live cells. Cell viability as monitored by an MTT assay decreased 24% when LAPC4 cells were treated for 24 hrs with a Lipofectamine complex containing 0.2 μg of the mrTFO-Pt compared to cells that were treated with 0.2 μg of scrambled inert mrTFO-Pt*/Lipofectamine complex under the same conditions. The ability of the mrTFO-Pt to cross-link effectively with its target, inhibit DNA transcription and decrease the viability of LAPC4 cells in culture suggest that these compounds may have potential as therapeutic agents to disrupt AR signaling in androgen-resistant prostate cancer.

Citation Format: Mindy Kim Graham, Terry R. Brown, Paul S. Miller. Targeting the human androgen receptor gene with platinum-conjugated triplex-forming oligonucleotides [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C19.

Hydrolysis of bulged nucleotides in hybrids formed by RNA and imidazole-derivatized oligo-2'-O-methylribonucleotides

In order to enhance the efficacy of small antisense molecules, we examined a series of antisense oligonucleotides derivatized with functional groups designed to enable them to hydrolyze their RNA target. Solid phase synthetic methods were used to prepare imidazole-derivatized antisense oligo-2'-O-methylribonucleotides. Upon binding, these oligonucleotides create internal bulged bases in the target RNA that serve as sites for hydrolysis. We observed that an oligonucleotide derivatized with a side chain containing two imidazole groups was capable of hydrolyzing 58% of its RNA target when incubated with the target for 48 hours at 37°C and physiological pH.

Corn distillers dried grains with solubles in diets for growing-finishing pigs: a cooperative study

An experiment involving 560 crossbred pigs (28 replications of 4 to 6 pigs per pen) was conducted at 9 research stations to assess the effects of dietary concentrations of corn distillers dried grains with solubles (DDGS) on pig performance and belly firmness. Fortified corn-soybean meal diets containing 0, 15, 30, or 45% DDGS were fed in 3 phases from 33 to 121 kg of BW. A common source of DDGS containing 90.1% DM, 26.3% CP, 0.96% Lys, 0.18% Trp, 9.4% crude fat, 34.6% NDF, 0.03% Ca, and 0.86% P was used at each station. Diets were formulated to contain 0.83, 0.70, and 0.58% standardized ileal digestible (SID) Lys during the 3 phases with diets changed at 60 and 91 kg of BW, respectively. The DDGS replaced corn and soybean meal, and up to 0.172% Lys and 0.041% Trp were added to maintain constant SID concentrations of Lys and Trp in each phase. At each station, 2 pigs from each pen in 2 replications were killed and a midline backfat core was obtained for fatty acid analysis and iodine value. In most instances, there were differences among stations (P < 0.01), but the station × treatment interactions were few. Body weight gain was linearly reduced in pigs fed the greater amounts of DDGS (0 to 45%) during phase I (950, 964, 921, and 920 g/d; P < 0.01) and over the entire experimental period (944, 953, 924, and 915 g/d; P = 0.03), but ADFI (2.73, 2.76, 2.68, and 2.70 kg) and G:F (347, 347, 345, and 341 g/kg) were not affected (P = 0.15 and P = 0.33, respectively) during the entire test. Backfat depth was reduced (linear, P < 0.02) by increasing amounts of DDGS (22.5, 22.7, 21.4, and 21.6 mm), but LM area (47.4, 47.4, 46.1, and 45.4 cm(2)) was not affected (P = 0.16) by treatments. Estimated carcass fat-free lean was 51.9, 52.2, 52.4, and 52.1% for 0 to 45% DDGS, respectively (linear, P = 0.06). Flex measures obtained at 6 stations indicated less firm bellies as dietary DDGS increased (lateral flex: 11.9, 8.6, 8.4, and 6.6 cm; linear, P < 0.001; vertical flex: 26.1, 27.4, 28.2, and 28.7 cm; linear, P < 0.003). Saturated and monounsaturated fatty acid concentrations in subcutaneous fat decreased linearly (P < 0.001) and PUFA concentrations increased linearly (P < 0.001) with increasing DDGS in the diet. Iodine values in inner (61.1, 68.2, 74.7, and 82.2) and outer (67.9, 73.6, 79.6, and 85.8) backfat increased linearly (P < 0.001) as DDGS in the diet increased. In this study, feeding diets with 30 or 45% DDGS did not have major effects on growth performance, but resulted in softer bellies. Regression analysis indicated that iodine values increased 4.3 units for every 10 percentage unit inclusion of DDGS in the diet.

Syntheses of DNA duplexes that contain a N⁴C-alkyl-N⁴C interstrand cross-link

This unit describes a simple procedure for preparing short DNA duplexes that contain a single N(4)C-alkyl-N(4)C interstrand cross-link. The synthesis is carried out on an automated DNA synthesizer using standard phosphoramidite chemistry. The cross-link is introduced during the synthesis of the duplex. The method can be used to prepare milligram quantities of cross-linked duplexes suitable for physical studies and for the preparation of larger DNA molecules that can be used as substrates to study DNA repair in whole cell extracts and in living cells in culture.

XPB, a subunit of TFIIH, is a target of the natural product triptolide

Triptolide (1) is a structurally unique diterpene triepoxide isolated from a traditional Chinese medicinal plant with anti-inflammatory, immunosuppressive, contraceptive and antitumor activities. Its molecular mechanism of action, however, has remained largely elusive to date. We report that triptolide covalently binds to human XPB (also known as ERCC3), a subunit of the transcription factor TFIIH, and inhibits its DNA-dependent ATPase activity, which leads to the inhibition of RNA polymerase II-mediated transcription and likely nucleotide excision repair. The identification of XPB as the target of triptolide accounts for the majority of the known biological activities of triptolide. These findings also suggest that triptolide can serve as a new molecular probe for studying transcription and, potentially, as a new type of anticancer agent through inhibition of the ATPase activity of XPB.

Unique dynamic properties of DNA duplexes containing interstrand cross-links

Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand cross-linked (ICL) structures that are potent cytotoxins. Because it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem, we have synthesized and characterized several homogeneous ICL DNAs containing site-specific staggered N4-cytosine-ethyl-N4-cytosine cross-links. Staggered cross-links were introduced in two ways, in a manner that preserves the overall structure of B-form duplex DNA and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by (1)H NMR line width or imino proton solvent exchange showed that the guanine base opposite the cross-linked cytosine opened at least 1 order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the cross-link to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross-link, which extended over the entire DNA sequence. Because DNA duplexes containing the B-form and non-B-form ICL cross-links have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model in which destabilized ICL duplexes serve to energetically facilitate binding of DNA repair factors that must induce bubbles or other distortions in the duplex. However, the essential requirement for incision is an immobile Y-junction where the repair factors are stably bound at the site of the ICL, and the two DNA strands are unpaired.

Extremophile-inspired strategies for enzymatic biomass saccharification

Domestic ethanol production in the USA relies on starch feedstocks using a first generation bioprocess. Enzymes that contribute to this industry remain of critical value in new and established markets as commodity additives and for in planta production. A transition to non-food feedstocks is both desirable and essential to enable larger scale production. This objective would relieve dependence on foreign oil and strengthen the national economy. Feedstocks derived from corn stover, wheat straw, perennial grasses and timber require pretreatment to increase the accessibility of the cellulosic and hemicellulosic substrates to commodity enzymes for saccharification, which is followed by fermentation-based conversion of monosaccharides to ethanol. Hot acid pretreatment is the industrial standard method used to achieve deconstruction of lignocellulosic biomass. Therefore, enzymes that tolerate both acid and heat may contribute toward the improvement of lignocellulosic biomass processing. These enzymes are produced naturally by extremely thermophilic microbes, sometimes called extremophiles. This review summarizes information on enzymes from selected (acido)thermophiles that mediate saccharification of alpha- and beta-linked carbohydrates of relevance to biomass processing.

Initiation of DNA interstrand cross-link repair in mammalian cells

Interstrand cross-links (ICLs) are among the most cytotoxic DNA lesions to cells because they prevent the two DNA strands from separating, thereby precluding replication and transcription. Even though chemotherapeutic cross-linking agents are well established in clinical use, and numerous repair proteins have been implicated in the initial events of mammalian ICL repair, the precise mechanistic details of these events remain to be elucidated. This review will summarize our current understanding of how ICL repair is initiated with an emphasis on the context (replicating, transcribed or quiescent DNA) in which the ICL is recognized, and how the chemical and physical properties of ICLs influence repair. Although most studies have focused on replication-dependent repair because of the relation to highly replicative tumor cells, replication-independent ICL repair is likely to be important in the circumvention of cross-link cytotoxicity in nondividing, terminally differentiated cells that may be challenged with exogenous or endogenous sources of ICLs. Consequently, the ICL repair pathway that should be considered "dominant" appears to depend on the cell type and the DNA context in which the ICL is encountered. The ability to define and inhibit distinct pathways of ICL repair in different cell cycle phases may help in developing methods that increase cytotoxicity to cancer cells while reducing side-effects in nondividing normal cells. This may also lead to a better understanding of pathways that protect against malignancy and aging.

Cross-link structure affects replication-independent DNA interstrand cross-link repair in mammalian cells

DNA interstrand cross-links (ICLs) are cytotoxic products of common anticancer drugs and cellular metabolic processes, whose mechanism(s) of repair remains poorly understood. In this study, we show that cross-link structure affects ICL repair in nonreplicating reporter plasmids that contain a mispaired N(4)C-ethyl-N(4)C (C-C), N3T-ethyl-N3T (T-T), or N1I-ethyl-N3T (I-T) ICL. The T-T and I-T cross-links obstruct the hydrogen bond face of the base and mimic the N1G-ethyl-N3C ICL created by bis-chloroethylnitrosourea, whereas the C-C cross-link does not interfere with base pair formation. Host-cell reactivation (HCR) assays in human and hamster cells showed that repair of these ICLs primarily involves the transcription-coupled nucleotide excision repair (TC-NER) pathway. Repair of the C-C ICL was 5-fold more efficient than repair of the T-T or I-T ICLs, suggesting the latter cross-links hinder lesion bypass following initial ICL unhooking. The level of luciferase expression from plasmids containing a C-C cross-link remnant on either the transcribed or nontranscribed strand increased in NER-deficient cells, indicating NER involvement occurs at a step prior to remnant removal, whereas expression from similar T-T remnant plasmids was inhibited in NER-deficient cells, demonstrating NER is required for remnant removal. Sequence analysis of repaired plasmids showed a high proportion of C residues inserted at the site of the T-T and I-T cross-links, and HCR assays showed that Rev1 was likely responsible for these insertions. In contrast, both C and G residues were inserted at the C-C cross-link site, and Rev1 was not required for repair, suggesting replicative or other translesion polymerases can bypass the C-C remnant.

Transplatin-conjugated triplex-forming oligonucleotides form adducts with both strands of DNA

Triplex-forming oligonucleotides (TFOs) can bind to polypurine x polypyrimidine tracts in DNA and, as a consequence, perturb the normal functioning of a targeted gene. The effectiveness of such antigene TFOs can potentially be enhanced by covalent attachment of the TFO to its DNA target. Here, we report that attachment of N-7-platinated guanine nucleosides to the 3'- and/or 5'-ends of oligopyrimidine TFOs enables these TFOs to form highly stable adducts with target DNA deoxyguanosines or deoxyadenosines that are adjacent to the TFO binding site. Such adduct formation stably anchors the TFO to its target. Depending on the sequences adjacent to the TFO binding site, adduct formation can occur on either strand of the DNA. Adduct formation by 3',5'-bis-platinated TFOs can result in the formation of an interstrand cross-link between both strands of the DNA duplex. Formation of the adducts, which could be reversed by treatment with sodium cyanide, was dependent upon the ability of the TFO to bind to DNA and appeared to occur at a rate slower than that at which the TFO bound to the DNA duplex. The extent of adduct formation at 37 degrees C by platinated deoxyribo-TFOs diminished as the pH was increased from 6.5 to 7.4. In contrast, high levels (approximately 86%) of adduct formation by platinated 2'-O-methylribo-TFOs were observed at both pH 6.5 and pH 7.4. Platinated 2'-O-methylribo-TFOs were also shown to bind to plasmid DNA and inhibit transcription in vitro, and to inhibit plasmid replication in E. coli cells. These results suggest that platinum-conjugated TFOs may be good candidates for use as antigene agents.

Binding, activation and modulation of Cys-loop receptors

It is over forty years since the major neurotransmitters and their protein receptors were identified, and over twenty years since determination of the first amino-acid sequences of the Cys-loop receptors that recognize acetylcholine, serotonin, GABA and glycine. The last decade has seen the first structures of these proteins (and related bacterial and molluscan homologues) determined to atomic resolution. Hopefully over the next decade, more detailed molecular structures of entire Cys-loop receptors in drug-bound and drug-free conformations will become available. These, together with functional studies, will provide a clear picture of how these receptors participate in neurotransmission and how structural variations between receptor subtypes impart their unique characteristics. This insight should facilitate the design of novel and improved therapeutics to treat neurological disorders. This review considers our current understanding about the processes of agonist binding, receptor activation and channel opening, as well as allosteric modulation of the Cys-loop receptor family.

Effect of phytase on apparent total tract digestibility of phosphorus in corn-soybean meal diets fed to finishing pigs

Five experiments were conducted to investigate the ability of different phytase products to improve P digestibility in finishing pigs. A corn-soybean meal basal diet containing 0.50% Ca, 0.32% P, and 0.40% Cr(2)O(3) was used to calculate apparent P and GE digestibility. Pigs were individually penned and fed their respective diet for ad libitum intake for 12 d before fecal sampling on d 13 and 14 and blood collection on d 14 for plasma P determination. Experiments 1 through 4 used gilts with across-trial average initial and final BW of 84 and 97 kg, respectively. Pigs were fed Natuphos (Exp. 1), OptiPhos (Exp. 2), Phyzyme (Exp. 3), or RonozymeP (Exp. 4) at 0, 200, 400, 600, 800, or 1,000 phytase units (FTU)/kg (where 1 FTU is defined as the quantity of enzyme required to liberate 1 micromol of inorganic P per min, at pH 5.5, from an excess of 15 micromol/L of sodium phytate at 37 degrees C). Experiment 5 used barrows with initial and final BW of 98 and 111 kg, respectively, and were fed diets containing 0, 500, or 1,000 FTU/kg of Natuphos, OptiPhos, Phyzyme, or RonozymeP. Pigs fed Natuphos (Exp. 1) and OptiPhos (Exp. 2) exhibited a linear and quadratic (P < 0.01) improvement in P digestibility with increasing levels of dietary phytase, whereas pigs fed Phyzyme (Exp. 3) and RonozymeP (Exp. 4) exhibited a linear (P < 0.01) improvement in apparent P digestibility with increasing levels of dietary phytase. In Exp. 5, the improvement in apparent P digestibility with increasing levels of dietary phytase was linear (P < 0.01) for Natuphos, Phyzyme, and RonozymeP, but was linear and quadratic (P < 0.01) for OptiPhos. Based on regression analysis, inorganic P release at 500 FTU/kg was predicted to be 0.070, 0.099, 0.038, and 0.030% for Natuphos, OptiPhos, Phyzyme, and RonozymeP, respectively. These estimates are comparable with those of pigs in Exp. 5, for which the estimated inorganic P release at 500 FTU/kg was 0.102, 0.039, and 0.028% for OptiPhos, Phyzyme, and RonozymeP, respectively, but not for the 0.034% value determined for Natuphos. The effect of dietary phytase on GE digestibility was inconsistent with a linear (P < 0.01) improvement in GE digestibility noted for OptiPhos (Exp. 2 and 5) and RonozymeP (Exp. 4), but the quadratic (P < 0.01) improvement for Natuphos. There was no effect of dietary phytase on plasma inorganic P. The data presented show clear improvements in P digestibility, with the estimated level of inorganic P release being dependent on phytase source and level.

Effect of cross-link structure on DNA interstrand cross-link repair synthesis

DNA interstrand cross-links (ICLs) are products of chemotherapeutic agents and cellular metabolic processes that block both replication and transcription. If left unrepaired, ICLs are extremely toxic to cells, and ICL repair mechanisms contribute to the survival of certain chemotherapeutic resistance tumors. A critical step in ICL repair involves unhooking the cross-link. In the absence of a homologous donor sequence, the resulting gap can be filled in by a repair synthesis step involving bypass of the cross-link remnant. Here, we examine the effect of cross-link structure on the ability of unhooked DNA substrates to undergo repair synthesis in mammalian whole cell extracts. Using 32P incorporation assays, we found that repair synthesis occurs efficiently past the site of damage when a DNA substrate containing a single N4C-ethyl-N4C cross-link is incubated in HeLa or Chinese hamster ovary cell extracts. This lesion, which can base pair with deoxyguanosine, is readily bypassed by both Escherichia coli DNA polymerase I and T7 DNA polymerase in a primer extension assay. In contrast, bypass was not observed in the primer extension assay or in mammalian cell extracts when DNA substrates containing a N3T-ethyl-N3T or N1I-ethyl-N3T cross-link, whose linkers obstruct the hydrogen bond face of the bases, were used. A modified phosphorothioate sequencing method was used to analyze the ICL repair patches created in the mammalian cell extracts. In the case of the N4C-ethyl-N4C substrate, the repair patch spanned the site of the cross-link, and the lesion was bypassed in an error-free manner. However, although the N3T-ethyl-N3T and N1I-ethyl-N3T substrates were unhooked in the extracts, bypass was not detected. These and our previous results suggest that although the chemical structure of an ICL may not affect initial cross-link unhooking, it can play a significant role in subsequent processing of the cross-link. Understanding how the physical and chemical differences of ICLs affect repair may provide a better understanding of the cytotoxic and mutagenic potential of specific ICLs.

Cross-linking to an interrupted polypurine sequence with a platinum-modified triplex-forming oligonucleotide

Triplex-forming oligonucleotides (TFOs) can bind specifically to polypurine sequences in double-stranded DNA. A single interruption of this polypurine tract can greatly destabilize triplex formation. The stability of triplexes can be significantly enhanced by covalently linking the TFO to its DNA target with reactive functional groups conjugated to the TFO. Covalently cross-linked TFOs are effective inhibitors of transcription of the target DNA sequence. We have designed a TFO with a platinum-modified base that can interact with and cross-link to a cytosine interruption in the polypurine tract of a target DNA duplex. The TFO contains an N(4)-(aminoalkyl)cytosine derivatized with cis-diamminediaquaplatinum(II) or trans-diamminediaquaplatinum(II). When bound to its target, the tethered platinum of the TFO can reach across the major groove and form an adduct with the guanine N7 of the interrupting C.G base pair. The optimal tether length is five methylene groups, and cross-linking is most efficient when the tether is modified with trans-diamminediaquaplatinum(II). Cross-linking requires that the TFO is bound to its designated DNA target. Addition of cyanide to the cross-linked TFO product reversed the cross-link, behavior that is consistent with the presence of a platinum-guanine adduct. The kinetics of the cross-linking reaction were studied and the half-life of the cross-linking reaction was approximately 3 h. Our results demonstrate that platinum-conjugated TFOs can be designed to cross-link with DNA targets that contain a single pyrimidine interruption. Modifications of this type may prove useful for expanding the DNA sequences that can be targeted by TFOs and increasing the stability of the resulting triplexes.

Phosphodiester-mediated reaction of cisplatin with guanine in oligodeoxyribonucleotides

The cancer chemotherapeutic agent cis-diamminedichloroplatinum(II) or cisplatin reacts primarily with guanines in DNA to form 1,2-Pt-GG and 1,3-Pt-GNG intrastrand cross-links and, to a lesser extent, G-G interstrand cross-links. Recent NMR evidence has suggested that cisplatin can also form a coordination complex with the phosphodiester internucleotide linkage of DNA. We have examined the effects of the phosphodiester backbone on the reactions of cisplatin with oligodeoxyribonucleotides that lack or contain a GTG sequence. Cisplatin forms a stable adduct with TpT that can be isolated by reversed phase HPLC. The cis-Pt-TpT adduct contains a single Pt, as determined by atomic absorption spectroscopy (AAS) and by electrospray ionization mass spectrometry (ESI-MS), and is resistant to digestion by snake venom phosphodiesterase. Treatment of the adduct with sodium cyanide regenerates TpT. Similar adduct formation was observed when T(pT)(8) was treated with cisplatin, but not when the phosphodiester linkages of T(pT)(8) were replaced with methylphosphonate groups. These results suggest that the platinum may be coordinated with the oxygens of the thymine and possibly with those of the phosphodiester group. As expected, reaction of a 9-mer containing a GTG sequence with cisplatin yielded an adduct that contained a 1,3-Pt-GTG intrastrand cross-link. However, we found that the number and placement of phosphodiesters surrounding a GTG sequence significantly affected intrastrand cross-link formation. Increasing the number of negatively charged phosphodiesters in the oligonucleotide increased the amount of GTG platination. Surrounding the GTG sequence with nonionic methylphosphonate linkages inhibited or eliminated cross-link formation. These observations suggest that interactions between cisplatin and the negatively charged phosphodiester backbone may play an important role in facilitating platination of guanine nucleotides in DNA.

Selectivity and affinity of DNA triplex forming oligonucleotides containing the nucleoside analogues 2'-O-methyl-5-(3-amino-1-propynyl)uridine and 2'-O-methyl-5-propynyluridine

Triplex forming oligonucleotides (TFOs) containing the nucleoside analogues 2'-O-methyl-5-propynyluridine (1) and 2'-O-methyl-5-(3-amino-1-propynyl)uridine (2) were synthesized. The affinity and selectivity of triplex formation by these TFOs were studied by gel shift analysis, T(m) value measurement, and association rate assays. The results show that the introduction of 1 and 2 into TFOs can improve the stability of the triplexes under physiological conditions. Optimized distribution of 1 or 2 in the TFOs combined with a cluster of contiguous nucleosides with 2'-aminoethoxy sugars resulted in formation of triplexes with further enhanced stability and improved selectivity.

Distortion-dependent unhooking of interstrand cross-links in mammalian cell extracts

Interstrand cross-links (ICLs) are formed by many chemotherapeutic agents and may also arise endogenously. The mechanisms used to repair these lesions remain unclear in mammalian cells. Repair in Escherichia coli and Saccharomyces cerevisiae requires an initial unhooking step to release the tethered DNA strands. We used a panel of linear substrates containing different site-specific ICLs to characterize how structure affects ICL processing in mammalian cell extracts. We demonstrate that ICL-induced distortions affect NER-dependent and -independent processing events. The NER-dependent pathway produces dual incisions 5' to the site of the ICL as described previously [Bessho, T., et al. (1997) Mol. Cell. Biol. 17 (12), 6822-6830] but does not release the cross-link. Surprisingly, we also found that the interstrand cross-linked duplexes were unhooked in mammalian cell extracts in a manner independent of the NER pathway. Unhooking occurred identically in extracts prepared from human and rodent cells and is dependent on ATP hydrolysis and metal ions. The structure of the unhooked product was characterized and was found to contain the remnant of the cross-link. Both the NER-mediated dual 5' incisions and unhooking reactions were greatly stimulated by ICL-induced distortions, including increased local flexibility and disruption of base pairs surrounding the site of the ICL. These results suggest that in DNA not undergoing transcription or replication, distortions induced by the presence of an ICL could contribute significantly to initial cross-link recognition and processing.

End modification of a linear DNA duplex enhances NER-mediated excision of an internal Pt(II)-lesion

The study of DNA repair has been facilitated by the development of extract-based in vitro assay systems and the use of synthetic DNA duplexes that contain site-specific lesions as repair substrates. Unfortunately, exposed DNA termini can be a liability when working in crude cell extracts because they are targets for DNA end-modifying enzymes and binding sites for proteins that recognize DNA termini. In particular, the double-strand break repair protein Ku is an abundant DNA end-binding protein that has been shown to interfere with nucleotide excision repair (NER) in vitro. To facilitate the investigation of NER in whole-cell extracts, we explored ways of modifying the exposed ends of synthetic repair substrates to prevent Ku binding and improve in vitro NER efficiency. Replacement of six contiguous phosphodiester linkages at the 3'-ends of the duplex repair substrate with nuclease-resistant nonionic methylphosphonate linkages resulted in a 280-fold decrease in binding affinity between Ku and the modified duplex. These results are consistent with the published crystal structure of a Ku/DNA complex [Walker et al. (2001) Nature 412, 607-614] and show that the 3'-terminal phosphodiester linkages of linear DNA duplexes are important determinants in DNA end-binding by Ku. Using HeLa whole-cell extracts and a 149-base pair DNA duplex repair substrate, we tested the effects of modification of exposed DNA termini on NER-mediated in vitro excision of a 1,3-GTG-Pt(II) intrastrand cross-link. Methylphosphonate modification at the 3'-ends of the repair substrate resulted in a 1.6-fold increase in excision. Derivatization of the 5'-ends of the duplex with biotin and subsequent conjugation with streptavidin to block Ku binding resulted in a 2.3-fold increase excision. By combining these modifications, we were able to effectively reduce Ku-derived interference of NER excision in vitro and observed a 4.4-fold increase in platinum lesion excision. These modifications are easy to incorporate into synthetic oligonucleotides and may find general utility whenever synthetic linear duplex DNAs are used as substrates to investigate DNA repair in whole-cell extracts.

Small-scale extracts for the study of nucleotide excision repair and non-homologous end joining

The repair of DNA by nucleotide excision repair (NER) and non-homologous end joining (NHEJ) is essential for maintenance of genomic integrity and cell viability. Examination of NHEJ and NER in vitro using cell-free extracts has led to a deeper understanding of the biochemical mechanisms that underlie these processes. Current methods for production of whole-cell extracts (WCEs) to investigate NER and NHEJ start with one or more liters of culture containing 1–5 × 10⁹ cells. Here, we describe a small-scale method for production of WCE that can be used to study NER. We also describe a rapid, small-scale method for the preparation of WCE that can be used in the study of NHEJ. These methods require less time, 20- to 1000-fold fewer cells than large-scale extracts, facilitate examination of numerous samples and are ideal for such applications as the study of host–virus interactions and analysis of mutant cell lines.

Allosteric inhibition of the HIV-1 Rev/RRE interaction by a 3'-methylphosphonate modified antisense oligo-2'-O-methylribonucleotide

The HIV-1 Rev response element (RRE), a highly structured RNA sequence consisting of five stemloops, is found in all spliced and partially spliced human immunodeficiency virus (HIV) mRNA transcripts. The RRE interacts with HIV-encoded Rev protein, which facilitates exit of the transcripts from the nucleus to the cytoplasm. Because the Rev/RRE interaction is critical to virus function, it is considered a potential target for therapeutic drugs. We have investigated the interactions of antisense oligonucleotides with stem-loop II, a region that contains the high-affinity binding site for Rev. Oligo-2'-O-methylribonucleotides terminating in a nuclease resistant 3'-methylphosphonate internucleotide linkage were targeted to the 5'- or 3'-side of stem-loop IIB, which is adjacent to the Rev binding site. Thermal denaturation experiments showed that oligonucleotides of this type form highly stable duplexes with complementary single-stranded RNA. Gel electrophoretic mobility shift assays (EMSA) showed that the oligonucleotides bound with high affinity and specificity at 37 degrees C to RRE stem-loop II RNA with apparent dissociation constants, K(D), in the low nM range. A 16-mer, 2-1mp, whose K(D) is 46 nM, competitively inhibited binding of Rev peptide to RRE stem-loop II RNA as shown by EMSA experiments. When transfected into HEK 293T cells, 2-1mp inhibited RRE mediated expression of chloramphenicol acetyl transferase (CAT) by 60% at a concentration of 300 nM oligonucleotide. These results are consistent with a mechanism by which 2-1mp blocks access of Rev to the RRE/CAT transcript thus preventing nuclear export and subsequent translation.

Performance of growing-finishing pigs fed diets containing YieldGard Rootworm corn (MON 863), a nontransgenic genetically similar corn, or conventional corn hybrids

Two studies were conducted at two locations to evaluate growth performance and carcass characteristics of growing-finishing pigs fed diets containing either YieldGard Rootworm corn (MON 863), a non-transgenic genetically similar corn (RX670), or two conventional nontransgenic corn hybrids (DK647 and RX740). A randomized complete block design with a 2 x 4 factorial arrangement of treatments (two genders and four corn hybrids) was used. Study 1 used 72 barrows and 72 gilts (progeny of Danbred sires x [Danbred x NE White line] dams grown from 22.7 to 117.0 kg BW). Pigs were housed in a modified open-front building in single-gender groups of six (six pens per dietary treatment). Study 2 used 80 barrows and 80 gilts (progeny of PIC 337 sires x C22 dams) grown from 29.5 to 114.9 kg BW. Pigs were housed in an environmentally controlled finishing building in single-gender groups of five (eight pens per dietary treatment). The test corns were included at a fixed proportion of the diet in both studies. Animals had ad libitum access to feed and water. Pigs were slaughtered at the end of the growth period using standard procedures, and carcass measurements were taken. There were no diet x gender interactions for growth performance or carcass measurements in either study. In both studies, overall ADG, ADFI, and G:F were not affected by corn hybrid. There was no effect of corn hybrid on carcass or LM quality measurements in Study 1. In Study 2, LM protein content was less (P< 0.05) for pigs fed RX740 compared with those fed either MON 863 or RX670; however, there was no effect of corn hybrid on other LM composition measures or on quality traits. In both studies, differences between barrows and gilts for growth and carcass traits were similar to previous research. These results suggest that the YieldGard Rootworm corn (MON 863) results in equivalent growth performance and carcass quality to nontransgenic corn hybrids in growing-finishing pigs.

Evaluating the effects of supplemental B vitamins in practical swine diets during the starter and grower-finisher periods—A regional study1,2

Two experiments were conducted to evaluate dietary fortification levels of a B vitamin pre-mix for starter and grower-finisher pigs on subsequent performance responses. The objective was to determine whether the modern pig requires higher dietary levels of B vitamins than estimated by the NRC (1998). Both experiments added fat-soluble vitamins at the requirement levels (NRC, 1998) in all diets, whereas the B vitamins were added at 0, 100, 200, or 400% of the total NRC (1998) requirement levels for the starter and grower pig. Indigenous vitamin contributions from the feed grains were not included in the estimates. Each station used the same vitamin premixes but incorporated its own grain sources in the diets. The first experiment was conducted across 7 stations (Indiana, Ohio, Oklahoma, Michigan, Missouri, Nebraska, Texas) and involved 660 pigs in a randomized complete block design in 30 replicates. Complex nursery diets were fed in 2 phases. The first phase (0 to 14 d postweaning) and second phase (15 to 35 d postweaning) diets were formulated to Lys (total) levels of 1.50 and 1.30%, respectively. The results demonstrated no performance response to addition of B vitamins from 0 to 14 d post-weaning, but performances increased quadratically (P < 0.01) to the 100% NRC level from 14 to 35 d postweaning and for the overall 35-d period. The second experiment was conducted across 3 stations (Ohio, Nebraska, and South Dakota) and involved 216 pigs in a randomized complete block design in 10 replicates. Corn-soybean meal mixtures were fed in 3 phases formulated to total Lys levels of 1.30% (23 to 55 kg of BW), 1.00% (55 to 85 kg of BW), and 0.78% (85 to 120 kg of BW). Pig performances increased (P < 0.01) to the 100% B vitamin level from 23 to 85 kg of BW, but there was no response to any level from 85 to 120 kg of BW. Carcass measurements demonstrated a greater LM area (P < 0.01) and a lower backfat depth (P < 0.01) to the 100% B vitamin level. One station evaluated an additional treatment (3 replicates) in which each replicate was fed a fifth diet containing the 100% dietary level of B vitamins from 23 to 85 kg of BW whereupon the B vitamins were removed from 85 to 120 kg of BW. This removal did not reduce pig performance responses for the final period or for the overall period. The results demonstrated that supplementation of B vitamins at the 100% total NRC levels for starter and grower pigs was sufficient to meet their needs, and there was no further improvement to or deleterious effect to greater dietary levels.

Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo

We are developing triple helix forming oligonucleotides (TFOs) for gene targeting. Previously, we synthesized bioactive TFOs containing 2'-O-methylribose (2'-OMe) and 2'-O-aminoethylribose (2'-AE) residues. Active TFOs contained four contiguous 2'-AE residues and formed triplexes with high thermal stability and rapid association kinetics. In an effort to further improve bioactivity, we synthesized three series of TFOs containing the 2'-AE patch and additional ribose modifications distributed throughout the remainder of the oligonucleotide. These were either additional 2'-AE residues, the conformationally locked BNA/LNA ribose with a 2'-O,4'-C-methylene bridge, or the 2'-O,4'-C-ethylene analogue (ENA). The additionally modified TFOs formed triplexes with greater thermal stability than the reference TFO, and some had improved association kinetics. However, the most active TFOs in the biochemical and biophysical assays were the least active in the bioassay. We measured the thermal stability of triplexes formed by the TFOs in each series on duplex targets containing a change in sequence at a single position. The Tm value of the variant sequence triplexes increased as the number of all additional modifications increased. A simple explanation for the failure of the improved TFOs in the bioassay was that the increased affinity for nonspecific targets lowered the effective nuclear concentration. Enhancement of TFO bioactivity will require chemical modifications that improve interaction with the specific targets while retaining selectivity against mismatched sequences.

Tools and techniques for disease risk assessment in threatened wildlife conservation programmes

Disease plays a significant role as a risk factor in wildlife conservation programmes involving animal movements, such as translocation, transportation among zoos or reintroduction. However, the traditional 'zero-risk tolerance' approach to the assessment of disease risk in these programmes is unattainable and unmanageable, often leading to an excessively cautious attitude towards the risks that are involved. It is therefore critically important to develop a comprehensive, unified and broadly applicable set of descriptive and analytical tools that can more realistically and accurately assess disease-based risks in conservation-based animal-movement programmes. The Conservation Breeding Specialist Group, of the IUCN - World Conservation Union, has brought together an international team of wildlife medicine professionals to construct a set of qualitative and quantitative tools to assess disease risk. The tools are flexible, intuitive and span a broad range of complexities. These tools are designed to enable professionals to incorporate not only published, statistically valid data but also to make reasonable decisions under conditions of uncertainty, and to capture valuable information from more basic field or clinical experience. Selected tools from the larger 'toolkit' are described here, with examples from actual case studies where available.