MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation

Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.

Validation and the Determination of Antibody Bioactivity Using MILKSHAKE and Sundae Protocols

To develop reproducible results, it is critical that all reagents used in an experiment be validated in an alternative or independent method. We present two such independent methods for determining the specificity of antibodies: (1) "MILKSHAKE," which can be used to validate the liability and specificity of antibodies directed against post-translationally-modified epitopes, and (2) "Sundae," which is a more complete alanine-like scanning method that can be used to better understand the binding and bioactivity of specific residues of a protein. We apply both of these methods to the interaction between an antibody and its antigen.

Epivolve: A Protocol for Site-Directed Antibodies

Researchers can often successfully generate antibodies to predicted epitopes. Especially when the epitopes are on the surface of a protein or in a hydrophilic loop. But it is difficult to direct recombinant antibodies to bind either to- or near a specific amino acid on a protein or peptide. We have developed a unique immune-targeting strategy, that we call "Epivolve," that enables us to make site-specific antibodies (Abs). Epivolve technology leverages a highly immunogenic modified amino acid that acts as a "pseudo-hapten" immuno-target and takes advantage of Ab affinity maturation technologies to make high-affinity site-specific antibodies. Epivolve functions by the evolution of an Ab paratope to either synonymous or especially non-synonymous amino acid (aa) binding. Here we describe the use of Epivolve technology in phage display and the protocols for developing site-specific antibodies.

MILKSHAKE: novel validation method for antibodies to post-translationally modified targets by surrogate Western blot

Antibody (Ab) validation is the procedure in which an Ab is thoroughly assayed for sensitivity and specificity in a given application. Validation of Abs against post-translationally modified (PTM) targets is particularly challenging because it requires specifically prepared antigen. Here we describe a novel validation method using surrogate proteins in a Western blot. The surrogate protein, which we termed 'MILKSHAKE,' is a modified maltose binding protein enzymatically conjugated to a peptide from the chosen target that is either modified or nonmodified at the residue of interest. The certainty of the residue's modification status can be used to confirm Ab specificity. This method also allows for Ab validation even in the absence or limited availability of treated cell lysates.

Mobilising vitamin D from adipose tissue: The potential impact of exercise

Vitamin D is lipophilic and accumulates substantially in adipose tissue. Even without supplementation, the amount of vitamin D in the adipose of a typical adult is equivalent to several months of the daily reference nutrient intake (RNI). Paradoxically, despite the large amounts of vitamin D located in adipose tissue, individuals with obesity are often vitamin D deficient according to consensus measures of vitamin D status (serum 25-hydroxyvitamin D concentrations). Thus, it appears that vitamin D can become 'trapped' in adipose tissue, potentially due to insufficient lipolytic stimulation and/or due to tissue dysfunction/adaptation resulting from adipose expansion. Emerging evidence suggests that exercise may mobilise vitamin D from adipose (even in the absence of weight loss). If exercise helps to mobilise vitamin D from adipose tissue, then this could have important ramifications for practitioners and policymakers regarding the management of low circulating levels of vitamin D, as well as chronically low levels of physical activity, obesity and associated health conditions. This perspective led us to design a study to examine the impact of exercise on vitamin D status, vitamin D turnover and adipose tissue vitamin D content (the VitaDEx project). The VitaDEx project will determine whether increasing physical activity (via exercise) represents a potentially useful strategy to mobilise vitamin D from adipose tissue.

Lateral Ge Diffusion During Oxidation of Si/SiGe Fins

This Letter reports on the unusual diffusion behavior of Ge during oxidation of a multilayer Si/SiGe fin. It is observed that oxidation surprisingly results in the formation of vertically stacked Si nanowires encapsulated in defect free epitaxial strained Si_xGe_1-x. High angle annular dark field scanning transmission electron microscopy (HAADF-STEM) shows that extremely enhanced diffusion of Ge occurs along the vertical Si/SiO₂ oxidizing interface and is responsible for the encapsulation process. Further oxidation fully encapsulates the Si layers in defect free single crystal Si_xGe_1-x (x up to 0.53), which results in Si nanowires with up to -2% strain. Atom probe tomography reconstructions demonstrate that the resultant nanowires run the length of the fin. We found that the oxidation temperature plays a significant role in the formation of the Si nanowires. In the process range of 800-900 °C, pure strained and rounded Si nanowires down to 2 nm in diameter can be fabricated. At lower temperatures, the Ge diffusion along the oxidizing Si/SiO₂ interface is slow, and rounding of the nanowire does not occur, while at higher temperatures, the diffusivity of Ge into Si is sufficient to result in dilution of the pure Si nanowire with Ge. The use of highly selective etchants to remove the SiGe could provide a new pathway for the creation of highly controlled vertically stacked nanowires for gate all around transistors.

AAV1/2-mediated BDNF gene therapy in a transgenic rat model of Huntington's disease

Reduced expression and disrupted corticostriatal transportation of brain-derived neurotrophic factor (BDNF) is proposed to contribute to the selective vulnerability of medium spiny striatal projection neurons (MSNs) in Huntington's disease (HD). We have previously demonstrated that BDNF overexpression in the quinolinic acid lesioned rat striatum attenuates motor impairment and reduces the extent of MSN cell loss. To further investigate the potential therapeutic properties of BDNF for HD, the current study examines the effect of bilateral AAV1/2-mediated BDNF expression in the striatum of a transgenic rat model of HD. Transfer of the BDNF gene to striatal neurons using an AAV1/2 serotype vector enhanced BDNF protein levels in the striatum. Bilateral BDNF expression attenuated the impairment of both motor and cognitive function when compared with AAV1/2-vehicle- or YFP-treated transgenic HD rats. Interestingly, a gender effect was apparent with female transgenic HD rats exhibiting less functional impairment than males. Quantification of NeuN and DARRP32 immunoreactivity and striatal volume revealed limited disease phenotype between wild type and transgenic HD animals. However, AAV1/2-BDNF-treated transgenic HD rats showed evidence of greater striatal volume and increased NeuN+ cell numbers compared with wild-type vehicle- and AAV1/2-vehicle- or YFP-treated transgenic HD rats. We propose BDNF holds considerable therapeutic potential for alleviating behavioral dysfunction and neuronal degeneration in HD, with further work required to examine the role of BDNF-TrkB signaling and the preservation of axonal and synaptic function.

Vitamin D binding protein genotype is associated with plasma 25OHD concentration in West African children

Vitamin D is well known for its role in promoting skeletal health. Vitamin D status is determined conventionally by circulating 25-dihydroxyvitamin D (25OHD) concentration. There is evidence indicating that circulating 25OHD concentration is affected by variation in Gc, the gene encoding the vitamin D binding protein (DBP). The composite genotype of two single nucleotide polymorphisms (rs7041 and rs4588) results in different DBP isotypes (Gc1f, Gc1s and Gc2). The protein configurational differences among DBP isotypes affect DBP substrate binding affinity. The aims of this study were to determine 1) Gc variant frequencies in a population from an isolated rural region of The Gambia, West Africa (n=3129) with year-round opportunity for cutaneous vitamin D synthesis and 2) the effects of Gc variants on 25OHD concentration (n=237) in a genetically representative sub-group of children (mean (SD) age: 11.9 (4.8) years). The distribution of Gc variants was Gc1f: 0.86, Gc1s: 0.11 and Gc2: 0.03. The mean (SD) concentration of 25OHD was 59.6 (12.9) nmol/L and was significantly higher in those homozygous for Gc1f compared to other Gc variants (60.7 (13.1) vs. 56.6 (12.1) nmol/L, P=0.03). Plasma 25OHD and 1,25(OH)2D concentration was significantly associated with parathyroid hormone in Gc1f-1f but not in the other Gc variants combined. This study demonstrates that different Gc variants are associated with different 25OHD concentrations in a rural Gambian population. Gc1f-1f, thought to have the highest affinity for 25OHD, had the highest 25OHD concentration compared with lower affinity Gc variants. The considerable difference in Gc1f frequency observed in Gambians compared with other non-West African populations and associated differences in plasma 25OHD concentration, may have implications for the way in which vitamin D status should be interpreted across different ancestral groups.

Predictors of 25(OH)D half-life and plasma 25(OH)D concentration in The Gambia and the UK

Predictors of 25(OH)D3 half-life were factors associated with vitamin D metabolism, but were different between people in The Gambia and the UK. Country was the strongest predictor of plasma 25(OH)D concentration, probably as a marker of UVB exposure. 25(OH)D3 half-life may be applied as a tool to investigate vitamin D expenditure.

INTRODUCTION

The aim of this study was to investigate predictors of 25(OH)D3 half-life and plasma 25(OH)D concentration.

METHODS

Plasma half-life of an oral tracer dose of deuterated-25(OH)D3 was measured in healthy men aged 24-39 years, resident in The Gambia, West Africa (n = 18) and in the UK during the winter (n = 18), countries that differ in calcium intake and vitamin D status. Plasma and urinary markers of vitamin D, calcium, phosphate and bone metabolism, nutrient intakes and anthropometry were measured.

RESULTS

Normally distributed data are presented as mean (SD) and non-normal data as geometric mean (95% CI). Gambian compared to UK men had higher plasma concentrations of 25(OH)D (69 (13) vs. 29 (11) nmol/L; P < 0.0001); 1,25(OH)2D (181 (165, 197) vs. 120 (109, 132) pmol/L; P < 0.01); and parathyroid hormone (PTH) (50 (42, 60) vs. 33 (27, 39); P < 0.0001). There was no difference in 25(OH)D3 half-life (14.7 (3.5) days vs. 15.6 (2.5) days) between countries (P = 0.2). In multivariate analyses, 25(OH)D, 1,25(OH)2D, vitamin D binding protein and albumin-adjusted calcium (Caalb) explained 79% of variance in 25(OH)D3 half-life in Gambians, but no significant predictors were found in UK participants. For the countries combined, Caalb, PTH and plasma phosphate explained 39 % of half-life variability. 1,25(OH)2D, weight, PTH and country explained 81% of variability in 25(OH)D concentration; however, country alone explained 74%.

CONCLUSION

Factors known to affect 25(OH)D metabolism predict 25(OH)D3 half-life, but these differed between countries. Country predicted 25(OH)D, probably as a proxy measure for UVB exposure and vitamin D supply. This study supports the use of 25(OH)D half-life to investigate vitamin D metabolism.

25(OH)D2 half-life is shorter than 25(OH)D3 half-life and is influenced by DBP concentration and genotype

CONTEXT

There is uncertainty over the equivalence of vitamins D2 and D3 to maintain plasma 25-hydroxyvitamin D (25(OH)D).

OBJECTIVE

The objective of the study was to compare the plasma half-lives of 25(OH)D2 and 25(OH)D3 in two distinct populations with different dietary calcium intake and 25(OH)D status.

PARTICIPANTS

Healthy men (aged 24 and 39 y), resident in The Gambia (n = 18) or the United Kingdom (n = 18) participated in the study.

INTERVENTIONS

The intervention included an oral tracer dose of deuterated-25(OH)D2 and deuterated-25(OH)D3 (both 40 nmol). Blood samples were collected over 33 days.

MAIN OUTCOME MEASURES

25(OH)D2 and 25(OH)D3 plasma half-lives, concentrations of 25(OH)D, and vitamin D binding protein (DBP) and DBP genotypes were measured.

RESULTS

25(OH)D2 half-life [mean (SD)] [13.9 (2.6) d] was shorter than 25(OH)D3 half-life [15.1 (3.1) d; P = .001] for countries combined, and in Gambians [12.8 (2.3) d vs 14.7 (3.5) d; P < .001], but not in the United Kingdom [15.1 (2.4) d vs 15.6 (2.5) d; P = .3]. 25(OH)D concentration was 69 (13) and 29 (11) nmol/L (P < .0001), and the DBP concentration was 259 (33) and 269 (23) mg/L (P = .4) in The Gambia and United Kingdom, respectively. Half-lives were positively associated with plasma DBP concentration for countries combined [25(OH)D2 half-life: regression coefficient (SE) 0.03 (0.01) d per 1 mg/L DBP, P = .03; 25(OH)D3 half-life: 0.04 (0.02) d, P = .02] and in Gambians [25(OH)D2 half-life: 0.04 (0.01) d; P = .02; 25(OH)D3 half-life: 0.06 (0.02) d, P = .01] but not in UK participants. The DBP concentration × country interactions were not significant. DBP Gc1f/1f homozygotes had shorter 25(OH)D2 half-lives compared with other combined genotypes (P = .007) after correction for country.

CONCLUSIONS

25(OH)D2 half-life was shorter than 25(OH)D3 half-life, and half-lives were affected by DBP concentration and genotype. The stable isotope 25(OH)D half-life measurements provide a novel tool to investigate vitamin D metabolism and vitamin D expenditure and aid in the assessment of vitamin D requirements.

Kinetics and morphological instabilities of stressed solid-solid phase transformations

An atomistic model of the growth kinetics of stressed solid-solid phase transformations is presented. Solid phase epitaxial growth of (001) Si was used for comparison of new and prior models with experiments. The results indicate that the migration of crystal island ledges in the growth interface may involve coordinated atomic motion. The model accounts for morphological instabilities during stressed solid-solid phase transformations.

A stable isotope method for the simultaneous measurement of vitamin K1 (phylloquinone) kinetics and absorption

OBJECTIVES

To measure uptake and disposal kinetics and absolute absorption of vitamin K(1) using two stable isotope-labelled forms of vitamin K(1).

SUBJECTS

Ten subjects (nine women and one man) aged between 22 and 31 years, with a mean (+/-standard deviation) body mass index of 22.5+/-2.4 kg/m(2). Subjects took capsules containing 3 microg of methyl-(13)C vitamin K(1), three times a day for six days to reach a steady state for plasma vitamin K(1) isotopic enrichment. On day seven, subjects were given an intravenous dose of Konakion MM to measure disposal kinetics and at the same time, a capsule containing 4 microg of ring-D(4) vitamin K(1) to measure absorption. Plasma vitamin K(1) concentration was measured by high-performance liquid chromatography and isotopic composition by gas chromatography mass spectrometry.

RESULTS

The disposal kinetics of the intravenous dose of vitamin K(1) were resolved into two exponentials with half-times of 0.22 (+/-0.14) and 2.66 (+/-1.69) h. Absorption of oral, deuterated vitamin K(1) was 13 (+/-9)%.

CONCLUSIONS

Two-compartmental kinetic parameters observed in this study are similar to those obtained previously using radioactive tracers, but there may be additional slow-turnover body pools acting as stores of vitamin K(1). The kinetic parameters determined from the intravenous dose allowed determination of the absolute absorption of vitamin K(1) from a bolus oral dose.

Use of CultureSwab Plus swabs with Amies gel agar for testing of naris specimens with the GeneOhm MRSA assay

The GeneOhm MRSA assay detects nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA). We compared the use of seeded swabs with liquid Stuart's medium and that of seeded swabs with Amies gel for the assay. Overall, the swabs with liquid Stuart's medium detected significantly greater numbers of MRSA than the swabs with Amies gel (P = 0.0003).

Hip arthroscopy in athletes

The limited data (n = 42) and diverse pathology within this study make statistical analysis difficult, although the observations are still meaningful. Diagnostic arthroscopy has defined elusive causes of disabling hip pain in an athletic population including occult labral and chondral damage and rupture of the ligamentum teres. Operative arthroscopy has been effective in reducing the symptoms associated with many of these forms of pathology. For more evident causes of hip pain, such as loose bodies or impinging osteophytes, arthroscopy offers an excellent alternative to traditional open techniques. This study has defined that many intraarticular disorders initially may go unrecognized. The benefit of earlier diagnosis seems intuitive and may minimize extraneous investigative studies, but there are a few caveats. First, various forms of extraarticular pathology (e.g., muscle strains) far outnumber intraarticular injuries and thus the temptation for an extensive intraarticular work up for every hip injury should be avoided. Second, as mentioned, does earlier diagnosis always mean early intervention? There is much that we may not fully understand regarding the natural history of many of these intraarticular disorders that we are only now learning to diagnose.

The conversion of air splints to provide buildup bolus in the treatment of extremities with skin involvement

An alternate method for bolusing superficial skin lesions of extremities during photon beam treatment was reviewed. Emergency first-aid air splints were filled with water and used as bolus in the treatment of a Kaposi's sarcoma of the leg. Large parallel-opposed 6-MV photon beams were employed. Sheets of bolus were placed under the air splint bolus to ensure coverage of the posterior skin surface. Computerized tomography was performed demonstrating conformity of the air splint bolus to the leg. A diode measurement verified adequate dose to the skin. The results confirm that by adding water to an emergency first-aid air splint to use as bolus was practical, reproducible, and aided in the accurate delivery of a homogenous dose to the skin surface of involved extremities.

Elbow arthroscopy for neglected osteochondritis dissecans of the capitellum

We reviewed results of elbow arthroscopy for neglected osteochondritis dissecans (OCD) of the capitellum. Of more than 140 patients having elbow arthroscopy at our institution, 10 patients (11 elbows) had OCD of the capitellum and fulfilled inclusion criteria. Criteria included symptoms of at least 2 years' duration, loss of motion for at least 6 months, or radiographic evidence of secondary degenerative changes. One patient was lost to follow-up. The remaining 9 (10 elbows) were male patients with a median age of 20 years (range, 15 to 58 years). Follow-up averaged 4.6 years (range, 2 to 8 years). Using a 100-point system, postoperative elbow scores averaged 92 (range, 55 to 100). All patients returned to preoperative activities, though only 8 of 10 believed that surgery resulted in improvement. Elbow arthroscopy for neglected OCD can result in functional improvement. However, results are not as good as those reported with earlier intervention.

Prospective analysis of hip arthroscopy with 2-year follow-up

PURPOSE

Numerous indications, but little outcome data, have been reported for hip arthroscopy. The purpose of this prospective study is to report the 2-year results of hip arthroscopy performed on a consecutive series of patients for a variety of disorders.

TYPE OF STUDY

Case series.

MATERIALS AND METHODS

There were 38 procedures performed on 35 patients who have achieved 2-year follow-up. All patients were assessed with a modified Harris hip score (pain and function) preoperatively and postoperatively at 1, 3, 6, 12, and 24 months or until a subsequent procedure was performed. Variables studied included age, sex, diagnosis, duration of symptoms, onset of symptoms, center-edge angle, Workers' Compensation, and pending litigation.

RESULTS

Follow-up was obtained on all patients. The median score improved from 57 to 85 points. This included 10 cases (9 patients) who underwent a subsequent procedure at an average of 10 months (6 total hip arthroplasty, 1 core decompression, 3 second arthroscopy) with an index score of 54 compared with 52 at the time of the second procedure. The median improvement for the following diagnoses was: loose body (34), labral lesion (27), synovitis (26), chondral injury (18), arthritis (14), and avascular necrosis (-11). Of the variables studied, the most statistically significant finding was that older men with longer duration of symptoms did worse. Two complications occurred in 1 patient: partial neuropraxia of the lateral femoral cutaneous nerve and focal myositis ossificans along the anterior portal tract.

CONCLUSIONS

Hip arthroscopy can be performed for a variety of conditions (except end-stage avascular necrosis) with reasonable expectations of success and an acceptable complication rate. This is the first report to quantitate the results of hip arthroscopy for a heterogeneous population.

Brain-computer interfaces based on the steady-state visual-evoked response

The Air Force Research Laboratory has implemented and evaluated two brain-computer interfaces (BCI's) that translate the steady-state visual evoked response into a control signal for operating a physical device or computer program. In one approach, operators self-regulate the brain response; the other approach uses multiple evoked responses.

Iron-superoxide dismutase expression in transgenic alfalfa increases winter survival without a detectable increase in photosynthetic oxidative stress tolerance

To determine whether overexpression of Fe-superoxide (SOD) dismutase would increase superoxide-scavenging capacity and thereby improve the winter survival of transgenic alfalfa (Medicago sativa L.) plants, two genotypes were transformed with the vector pEXSOD10, which contains a cDNA for Arabidopsis Fe-SOD with a chloroplast transit peptide and cauliflower mosaic virus 35S promoter. A novel Fe-SOD was detected by native PAGE in both greenhouse- and field-grown transgenic plants, but activity varied among independent transgenic plants. The increased Fe-SOD activity was associated with increased winter survival over 2 years in field trials, but not with oxidative stress tolerance as measured by resistance of leaves to methyl viologen, a superoxide generator. Total shoot dry matter production over 2 harvest years was not associated with Fe-SOD activity. There was no detectable difference in the pattern of primary freezing injury, as shown by vital staining, nor was there additional accumulation of carbohydrates in field-acclimated roots of the transgenic alfalfa plants. We did not detect any difference in growth of one transgenic plant with high Fe-SOD activity compared with a non-transgenic control. Therefore, the improvement in winter survival did not appear to be a consequence of improved oxidative stress tolerance associated with photosynthesis, nor was it a consequence of a change in primary freezing injury. We suggest that Fe-SOD overexpression reduced secondary injury symptoms and thereby enhanced recovery from stresses experienced during winter.

The effects of signal salience and caffeine on performance, workload, and stress in an abbreviated vigilance task

In 2 experiments, a 12-min computerized vigilance task was demonstrated to reproduce the vigilance decrement, high workload (NASA-TLX), and stressful character (Dundee Stress State Questionnaire) of vigilance tasks lasting 30 min or more. In Experiment 1, the abbreviated task was also shown to duplicate the signal salience effect, a major finding associated with long-duration vigilance tasks. Moreover, Experiment 2 showed that performance on the abbreviated task can be enhanced by caffeine - a drug that benefits long-duration tasks. This enhancement effect was limited to performance, however, suggesting that caffeine influences factors that control signal detection but not those that control task-induced stress. The results parallel those obtained with long-duration tasks and support a resource-depletion model of the vigilance decrement. The abbreviated task might be useful in situations in which long-duration tasks are precluded (e.g., performance assessment batteries, neuropsychological testing, and brain imaging).

Winter survival of transgenic alfalfa overexpressing superoxide dismutase

To test the hypothesis that enhanced tolerance of oxidative stress would improve winter survival, two clones of alfalfa (Medicago sativa) were transformed with a Mn-superoxide dismutase (Mn-SOD) targeted to the mitochondria or to the chloroplast. Although Mn-SOD activity increased in most primary transgenic plants, both cytosolic and chloroplastic forms of Cu/Zn-SOD had lower activity in the chloroplast SOD transgenic plants than in the nontransgenic plants. In a field trial at Elora, Ontario, Canada, the survival and yield of 33 primary transgenic and control plants were compared. After one winter most transgenic plants had higher survival rates than control plants, with some at 100%. Similarly, some independent transgenic plants had twice the herbage yield of the control plants. Prescreening the transgenic plants for SOD activity, vigor, or freezing tolerance in the greenhouse was not effective in identifying individual transgenic plants with improved field performance. Freezing injury to leaf blades and fibrous roots, measured by electrolyte leakage from greenhouse-grown acclimated plants, indicated that the most tolerant were only 1 degrees C more freezing-tolerant than alfalfa clone N4. There were no differences among transgenic and control plants for tetrazolium staining of field-grown plants at any freezing temperature. Therefore, although many of the transgenic plants had higher winter survival rates and herbage yield, there was no apparent difference in primary freezing injury, and therefore, the trait is not associated with a change in the primary site of freezing injury.

Winter survival of transgenic alfalfa overexpressing superoxide dismutase

To test the hypothesis that enhanced tolerance of oxidative stress would improve winter survival, two clones of alfalfa (Medicago sativa) were transformed with a Mn-superoxide dismutase (Mn-SOD) targeted to the mitochondria or to the chloroplast. Although Mn-SOD activity increased in most primary transgenic plants, both cytosolic and chloroplastic forms of Cu/Zn-SOD had lower activity in the chloroplast SOD transgenic plants than in the nontransgenic plants. In a field trial at Elora, Ontario, Canada, the survival and yield of 33 primary transgenic and control plants were compared. After one winter most transgenic plants had higher survival rates than control plants, with some at 100%. Similarly, some independent transgenic plants had twice the herbage yield of the control plants. Prescreening the transgenic plants for SOD activity, vigor, or freezing tolerance in the greenhouse was not effective in identifying individual transgenic plants with improved field performance. Freezing injury to leaf blades and fibrous roots, measured by electrolyte leakage from greenhouse-grown acclimated plants, indicated that the most tolerant were only 1 degrees C more freezing-tolerant than alfalfa clone N4. There were no differences among transgenic and control plants for tetrazolium staining of field-grown plants at any freezing temperature. Therefore, although many of the transgenic plants had higher winter survival rates and herbage yield, there was no apparent difference in primary freezing injury, and therefore, the trait is not associated with a change in the primary site of freezing injury.

Flatulence in pet dogs

AIM

The purpose of this study was to obtain information on aspects of dogs' lifestyle and diet that may be related to flatulence, whether the dogs were flatulent or not and if the owners were concerned about flatulence of their pet.

METHODS

The owners of 110 pet dogs were randomly selected from the Massey University clinic tiles and asked to complete a questionnaire relating to their dog's flatulence, lifestyle and diet.

RESULTS

Flatulence was detected by 47 owners and occurred more often in less active inside dogs than those exercised more often. No individual food or dietary association was identified. Nineteen of the 47 owners of flatulent dogs would alter their dog's diet if that change would reduce flatulence.

CONCLUSION

Flatulence occurs in pet dogs and most owners accept flatulence and were unconcerned about its consequence.

In Situ Studies of the Interaction of Dislocations with Point Defects during Annealing of Ion Implanted Si/SiGe/Si (001) Heterostructures

: Strained layer heterostructures provide ideal systems with which to study the dynamics of dislocation motion via in situ transmission electron microscopy, as the geometry, strain state, and kinetics can be characterized and directly controlled. We discuss how these structures are used to study dislocation-point defect interactions, emphasizing the experimental requirements necessary for quantification of dislocation motion. Following ion implantation, different concentrations and types of point defects are introduced within the SiGe epilayer depending on the implantation species, energy, and current density. By annealing samples in situ in the transmission electron microscope (TEM) following implantation, we can directly observe dislocation motion and quantify the effect of dislocation-point defect interactions on dislocation velocities. We find that dislocation motion is impeded if the implantation dose peak lies within the epilayer, as dislocations pin at point defect atmospheres. Shallow BF2 implantation into the sample capping layer results in more complicated behavior. For low current density implants, dislocation velocities may be dramatically increased; at higher current densities the magnitude of this increase is significantly smaller. Implantation of different ions separately implicates fluorine as the species responsible for the observed increases in dislocation velocities, presumably due to an electrical effect on the rate of dislocation kink nucleation.

Subcellular localization of avian sarcoma virus and human immunodeficiency virus type 1 integrases

The composition and subcellular trafficking of subviral preintegration complexes are reported to vary among the different retroviruses. The process by which the avian sarcoma virus (ASV) preintegration complex gains access to target chromatin remains unknown. Here we report that ASV integrase (IN) expressed as a fusion to beta-galactosidase accumulates in the nuclei of transfected COS-1 cells. In contrast, human immunodeficiency type 1 (HIV-1) IN-beta-galactosidase fusions expressed similarly are predominantly cytoplasmic. To identify the region of ASV IN that specifies nuclear localization, various subdomains of the protein were expressed as beta-galactosidase fusions and their subcellular locations were assessed cytochemically and by indirect immunofluorescence. These analyses showed that the ASV IN protein possesses a functional nuclear localization signal that spans amino acids 206 to 235 and displays limited homology with known nuclear transport signals.

Prescribing practice and cost of antibacterial prophylaxis for surgery at a US Veteran Affairs hospital

This study retrospectively compared the actual drug-related cost of antibacterial prophylaxis for specific operative procedures with the theoretical costs based on recommendations published in Medical Letter on Drugs and Therapeutics, the Surgical Infection Society, and those of the chiefs of each surgical subspecialty at our institution. We identified all patients who received in intravenous bacterial for prophylaxis before a clean or clean-contaminated operation between 1st January and 30th September 1993, using the medical centre's computerised information system. The information included comprehensive surgical case histories, and pharmacy and microbiology records. Only those operations in which recommendations for surgical prophylaxis were present in all 3 guidelines were included. The outcome measures were antibacterial-related costs (drug acquisition and administration costs), the number of antibacterial doses dispensed, and choice of antibacterial agents. During the study period, 3,322 operations were performed, 2,993 of which were excluded. Thus, 329 patients undergoing operations in 6 subspecialties were included in the analysis. The actual mean cost per patient significantly exceeded the projected costs using Medical Letter Consultants' and Surgical Infection Society guidelines for all 6 subspecialties [mean excess cost per patient: $US49.04 and $US34.95, respectively (1994 values)] and institutional guidelines for 4 of the 6 subspecialties (mean excess cost per patient: $US24.36). The actual mean number of doses per patient significantly exceeded those projected using Medical Letter Consultants' and Surgical Infection Society guidelines for all 6 subspecialties (mean excess number of doses per patient: 6.0 and 4.0, respectively) and institutional guidelines for 4 of the 6 subspecialties (mean excess number of doses per patient: 2.9). The choice of antibacterial was appropriate in approximately 90% of cases. We conclude that the practice of antibacterial prophylaxis for specific operative procedures performed by 6 subspecialties is not in accordance with institutional or published guidelines, and the excess cost is primarily a result of prolonged duration of antibacterial prophylaxis.

Monoclonal antibodies against Rous sarcoma virus integrase protein exert differential effects on integrase function in vitro

We have prepared and characterized several monoclonal antibodies (MAbs) against the Rous sarcoma virus integrase protein (IN) with the aim of employing these specific reagents as tools for biochemical and biophysical studies. The interaction of IN with the purified MAbs and their Fab fragment derivatives was demonstrated by Western blot (immunoblot), enzyme-linked immunosorbent assay, and size exclusion chromatography. A series of truncated IN proteins was used to determine regions in the protein important for recognition by the antibodies. The MAbs described here recognize epitopes that lie within the catalytic core region of IN (amino acids 50 to 207) and are likely to be conformational. A detailed functional analysis was carried out by investigating the effects of Fab fragments as well as of intact MAbs on the activities of IN in vitro. These studies revealed differential effects which fall into three categories. (i) One of the antibodies completely neutralized the processing as well as the joining activity and also reduced the DNA binding capacity as determined by a nitrocellulose filter binding assay. On the other hand, this MAb did not abolish the cleavage-ligation reaction on a disintegration substrate and the nonspecific cleavage of DNA by IN. The cleavage pattern generated by the IN-MAb complex on various DNA substrates closely resembled that produced by mutant IN proteins which show a deficiency in multimerization. Preincubation of IN with substrate protected the enzyme from inhibition by this antibody. (ii) Two other antibodies showed a general inhibition of all IN activities tested. (iii) In contrast, a fourth MAb stimulated the in vitro joining activity of IN. Size exclusion chromatography demonstrated that IN-Fab complexes from representatives of the three categories of MAbs exhibit different stoichiometric compositions that suggest possible explanations for their contrasting effects and may provide clues to the relationship between the structure and function of IN.

Rapid solution assays for retroviral integration reactions and their use in kinetic analyses of wild-type and mutant Rous sarcoma virus integrases

A rapid method for quantitating products of the oligodeoxynucleotide processing reaction in vitro has been developed to facilitate enzymatic studies of the retroviral integrases. Unlike earlier procedures, this assay does not depend on polyacrylamide gel electrphoresis but separates products by batch adsorption to PEI-cellulose. A joining assay has also been modified, to facilitate measurement of the two distinct steps in the integration reaction under parallel conditions. Since these methods allow quantitation of numerous samples in a short period of time, they are especially useful for investigation of kinetic parameters and to measure the effects of possible inhibitors of integrase. These assay systems were used to examine the enzymatic activity of wild-type Rous sarcoma virus integrase and selected mutant proteins with substitutions of single conserved amino acids. In contrast to previous studies, reactions were performed under conditions of substrate excess, and rates, rather than yields of product generated after a given period of incubation, were determined. The results showed that substitutions of several highly conserved residues in what is most likely an evolutionarily conserved catalytic domain of the integrases resulted in a 4- to 10-fold decrease in the apparent rate of processing relative to wild type, under optimized standard conditions. Changing an invariant acidic residue reduced the rate by approximately 60-fold. When joining activity was determined, the relative effects of the substitutions tested generally paralleled the results with processing. However, with both wild-type and mutant integrase proteins, the linear phase of the joining reaction was preceded by what appears to be an exponential "burst" phase.

The effects of gamma irradiation versus white cell reduction on the mixed lymphocyte reaction

The risk of transfusion-associated graft-versus-host disease (TA-GVHD) is related to the number of viable T cells transfused. Whether white cell (WBC)-reduced blood components would carry a decreased risk of TA-GVHD was considered, and the allogeneic mixed lymphocyte reaction was used as an in vitro model for TA-GVHD. An exponential decline in the mixed lymphocyte reaction was found to occur, as a result of either an arithmetic increase in the dose of gamma irradiation given to responding cells or a logarithmic decrease in the number of unirradiated responding cells. Irradiation of responding cells with 600 cGy or a 0.6 log10 reduction in the number of responding cells produced a 95-percent decline in the mixed lymphocyte reaction. Although these studies do not validate the use of WBC reduction as a substitute for gamma irradiation for the prevention of TA-GVHD, they suggest that the relative risk of TA-GVHD resulting from the use of standard cellular components versus WBC-reduced components merits further investigation.

Retroviral integrase functions as a multimer and can turn over catalytically

A number of studies have demonstrated that the retroviral protein integrase (IN) alone is sufficient to carry out two discrete steps required for retroviral integration: the endonucleolytic processing of viral DNA ends and the cleavage and joining of host DNA to the processed viral DNA termini. Little is known about the biochemical and biophysical mechanisms involved in these reactions. Here, we employ in vitro assays of Rous sarcoma virus IN to demonstrate for the first time that IN is capable of multiple turnover in both the processing and joining reactions. The turnover number calculated for the processing reaction is 0.26 cleavages/min/mol of IN. Our steady state kinetic studies indicate that both the processing and joining activities require a multimeric form of IN. Ultracentrifugation analyses reveal a substrate-independent reversible equilibrium among the monomeric, dimeric, and tetrameric forms of this protein. From these results we conclude that the minimal functional unit for both the processing and joining of each viral DNA end is an IN dimer.

Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases

Our comparison of deduced amino acid sequences for retroviral/retrotransposon integrase (IN) proteins of several organisms, including Drosophila melanogaster and Schizosaccharomyces pombe, reveals strong conservation of a constellation of amino acids characterized by two invariant aspartate (D) residues and a glutamate (E) residue, which we refer to as the D,D(35)E region. The same constellation is found in the transposases of a number of bacterial insertion sequences. The conservation of this region suggests that the component residues are involved in DNA recognition, cutting, and joining, since these properties are shared among these proteins of divergent origin. We introduced amino acid substitutions in invariant residues and selected conserved and nonconserved residues throughout the D,D(35)E region of Rous sarcoma virus IN and in human immunodeficiency virus IN and assessed their effect upon the activities of the purified, mutant proteins in vitro. Changes of the invariant and conserved residues typically produce similar impairment of both viral long terminal repeat (LTR) oligonucleotide cleavage referred to as the processing reaction and the subsequent joining of the processed LTR-based oligonucleotides to DNA targets. The severity of the defects depended upon the site and the nature of the amino acid substitution(s). All substitutions of the invariant acidic D and E residues in both Rous sarcoma virus and human immunodeficiency virus IN dramatically reduced LTR oligonucleotide processing and joining to a few percent or less of wild type, suggesting that they are essential components of the active site for both reactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification and characterization of intragenic sequences which repress human immunodeficiency virus structural gene expression

Examination of the life cycle of the human immunodeficiency virus (HIV) has shown that multiple levels of regulation exist, including some which require the virus-encoded Rev protein. In the absence of Rev, mRNAs encoding the structural proteins remain untranslated, a phenomenon which appears, in part, to be caused by nuclear entrapment of these RNA species. To examine the basis for repression of structural gene mRNA expression, a heterologous assay system was utilized to determine whether regions present within gag and pol contain elements capable of suppressing gene expression when present in cis. Both genes were found to contain cis-acting repressor sequences (CRS) that block gene expression when present within the 3' untranslated portion of a heterologous gene transcript. The element within pol was found to have the strongest repressive effect. While Rev alone was unable to reverse the repression observed with the pol sequence, addition of the env Rev-responsive element (RRE) in cis and Rev in trans did cause reversal of inhibition. Deletion mutagenesis defined a 260-bp element within the 3' portion of pol that contains a potent CRS which functions when present in the sense orientation. The corresponding region in HIV-2 pol was found to contain a functionally similar CRS element. To examine the mechanism of repression, the effects of the CRS elements on both the abundance and subcellular distribution of the mRNAs were examined. Neither was dramatically altered when examined in the context of a heterologous reporter (chloramphenicol acetyltransferase) mRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

A technique for the preparation of cross-sectional TEM samples of ZnSe/GaAs heterostructures which eliminates process-induced defects

Cross-sectional transmission electron microscopy (TEM) sample preparation of ZnSe/GaAs epitaxial films is investigated. Conventional argon ion milling is shown to produce a high density (approximately 5-8 x 10(11)/cm2) of small (diameter approximately 60-80 A) extended defects (stacking faults, microtwins, double positioning twins, etc.). In addition, transmission electron diffraction results indicate a thin ZnO layer can also occasionally form upon ion milling or electron-beam irradiation although the exact conditions for ZnO formation are not well understood. Conventional TEM (amplitude contrast) and high-resolution TEM (phase contrast) imaging in combination with transmission electron diffraction studies were performed to determine the optimum method of removing the ion milling related damage and ZnO layers during sample preparation. HF/HCl, NaOH/H2O, H2SO4/H2O2/H2O and Br2/CH3OH etching mixtures as well as low voltage argon or iodine ion milling were studied. A low energy (2 keV) iodine or argon ion milling step was shown to remove the ZnO layer and reduced the density of the extended defects associated with Ar+ ion milling, but was unsuccessful in removing all of the defects. Auger electron spectroscopy results indicate residual iodine was either left on the surface or implanted beneath the surface during iodine ion milling. Etching the XTEM samples in HF/HCl was shown to be effective in removing the ZnO layer but had little or no effect on the ion milling induced defects. Etching the samples in a 0.5% Br2/CH3OH solution resulted in complete elimination of the ion milling induced extended defects including the residual defects associated with iodine ion milling. In addition the Br2/CH3OH etch produced the best surface morphology. Thus a brief (1-2 seconds) Br2/CH3OH etch after conventional preparation (argon ion milling) of cross-sectional ZnSe/GaAs TEM samples appears to be an inexpensive and superior alternative to iodine ion milling.

Loss of pathogenicity of spleen focus-forming virus after pseudotyping with Akv

Friend virus complex (FV), which comprises replication-competent Friend murine leukemia virus (FMuLV) plus replication-defective spleen focus-forming virus (SFFV), induces a multistage erythroleukemia. We have examined the role of replication-competent helper virus in the early and late stages of FV disease by replacing FMuLV, the native helper, with Akv, the endogenous ecotropic MuLV of AKR mice. SFFVP/FRE, an established fibroblast line nonproductively infected with the polycythemic strain of SFFV, was superinfected with FMuLV or with Akv. Although supernatants from these cells showed similar titers in the XC plaque assay, supernatants from Akv-infected SFFVP/FRE cells showed 100- to 5,000-fold less activity than did those from FMuLV-infected cells with respect to spleen focus induction in vivo. Since virions isolated from these two supernatants contained similar ratios of SFFV to helper virus genomic RNA, it did not appear that the difference was due to a relative inability of Akv to package SFFV. Although FMuLV- and Akv-rescued SFFV are equally infectious in a mouse fibroblast cell line (NIH 3T3), FMuLV-rescued SFFV was far more efficient in inducing erythroid bursts in cultured primary bone marrow cells. Adding Akv to preparations of FMuLV-rescued SFFV did not significantly interfere with burst induction. Helper-free SFFV induced 50- to 500-fold more spleen foci when coinjected with FMuLV than it did with Akv. Helper virus also affected mortality rates that reflect the late stage of the disease. When FMuLV- or Akv-rescued SFFV was injected into NIH Swiss mice at dosage levels adjusted to give equal numbers of spleen foci, all mice receiving FMuLV-rescued SFFV developed splenomegaly and died, whereas no mice receiving Akv-rescued SFFV died or developed detectable splenomegaly. When FMuLV was coinjected with Akv-rescued SFFV, the mortality rate rose from 0 to 100%. Injection of helper-free SFFV alone did not induce mortality, but coinjection of helper-free SFFV with FMuLV resulted in 100% mortality. Thus, the helper virus used to rescue SFFV plays at least a quantitatively important role in the early stage of FV disease and a crucial role in the late stage of the disease in vivo.