Kinetic optimization of a protein-responsive aptamer beacon

Aptamers have been utilized as biosensors because they can be readily adapted to sensor platforms and signal transduction schemes through both rational design and selection. One highly generalizable scheme for the generation of the so-called aptamer beacons involves denaturing the aptamer with antisense oligonucleotides. For example, rational design methods have been utilized to adapt anti-thrombin aptamers to function as biosensors by hybridizing an antisense oligonucleotide containing a quencher to the aptamer containing a fluorescent label. In the presence of thrombin, the binding equilibrium is shifted, the antisense oligonucleotide dissociates, and the beacon lights up. By changing the affinity of the antisense oligonucleotide for the aptamer beacon, it has proven possible to change the extent of activation of the beacon. More importantly, modulating interactions between the antisense oligonucleotide and the aptamer strongly influences the kinetics of activation. Comparisons across multiple, designed aptamer beacons indicate that there is a strong inverse correlation between the thermodynamics of hybridization and the speed of activation, a finding that should prove to be generally useful in the design of future biosensors. By pre-organizing the thrombin-binding quadruplex within the aptamer the speed of response can be greatly increased. By integrating these various interactions, we were ultimately able to design aptamer beacons that were activated by threefold within 1 min of the addition of thrombin.

Nucleic acid pool preparation and characterization

Random sequence nucleic acid pools can be used in a variety of applications, including the selection of functional nucleic acids such as protein binding sites, aptamers, and ribozymes. while the design, synthesis, and purification of pools is relatively straightforward, keeping track of the size and complexity of a nucleic acid pool can sometimes task even an experienced researcher. The following protocol takes the reader through the steps necessary for the preparation of a pool of known complexity.

Viruses and other infections in stillbirth: what is the evidence and what should we be doing?

In Australia, as in other developed countries, approximately 40-50% of stillbirths are of unknown aetiology. Emerging evidence suggests stillbirths are often multifactorial. The absence of a known cause leads to uncertainty regarding the risk of recurrence, which can cause extreme anguish for parents that may manifest as guilt, anger or bewilderment. Further, clinical endeavours to prevent recurrences in future pregnancies are impaired by lack of a defined aetiology. Therefore, efforts to provide an aetiological diagnosis of stillbirth impact upon all aspects of care of the mother, and inform many parts of clinical decision making. Despite the magnitude of the problem, that is 7 stillbirths per 1000 births in Australia, diagnostic efforts to discover viral aetiologies are often minimal. Viruses and other difficult to culture organisms have been postulated as the aetiology of a number of obstetric and paediatric conditions of unknown cause, including stillbirth. Reasons forwarded for testing stillbirth cases for infectious agents are non-medical factors, including addressing all parents' need for diagnostic closure, identifying infectious agents as a sporadic cause of stillbirth to reassure parents and clinicians regarding risk for future pregnancies, and to reduce unnecessary testing. It is clear that viral agents including rubella, human cytomegalovirus (CMV), parvovirus B19, herpes simplex virus (HSV), lymphocytic choriomeningitis virus (LCMV), and varicella zoster virus (VZV) may cause intrauterine deaths. Evidence for many other agents is that minimal or asymptomatic infections also occur, so improved markers of adverse outcomes are needed. The role of other viruses and difficult-to-culture organisms in stillbirth is uncertain, and needs more research. However, testing stillborn babies for some viral agents remains a useful adjunct to histopathological and other examinations at autopsy. Modern molecular techniques such as multiplex PCR, allow searches for multiple agents. Now that such testing is available, it is important to assess the clinical usefulness of such testing.

Probabilistic modelling of European consumer exposure to cosmetic products

In this study, we describe the statistical analysis of the usage profile of the European population to seven cosmetic products. The aim of the study was to construct a reliable model of exposure of the European population from use of the selected products: body lotion, shampoo, deodorant spray, deodorant non-spray, facial moisturiser, lipstick and toothpaste. The first step in this process was to gather reliable data on consumer usage patterns of the products. These data were sourced from a combination of market information databases and a controlled product use study by the trade association Colipa. The market information study contained a large number of subjects, in total 44,100 households and 18,057 habitual users (males and females) of the studied products, in five European countries. The data sets were then combined to generate a realistic distribution of frequency of use of each product, combined with distribution of the amount of product used at each occasion using the CREMe software. A Monte Carlo method was used to combine the data sets. This resulted in a new model of European exposure to cosmetic products being constructed.

Severe deficiencies of IGF-I, IGF-II, IGFBP-3, ALS and paradoxically high-normal bone mass in a child with insulin-resistance syndrome (Rabson-Mendenhall type)

Rabson-Mendenhall syndrome is a rare genetic disorder characterized by severe insulin resistance and hyperinsulinemia due to defects in signaling through the insulin receptor. Herein, we describe a new case of Rabson-Mendenhall syndrome in which investigations of the growth hormone (GH) - insulin-like growth factor (IGF) axis - reveal severe deficiencies in total and free insulin-like growth factor-I (IGF-I), IGF-II, IGF-binding protein-3 (IGFBP-3), and the acid labile subunit (ALS). Based on these findings, we anticipated significant bone deficits, as have been described in other clinical scenarios in which the IGF axis is significantly perturbed. Long-bone studies revealed no gross malformations. Paradoxically, DXA scanning revealed a total body bone density Z-score of +2.0 (0.8 gm/cm(2)), suggesting an overall high-normal BMD for age and a high BMD corrected for bone or height age. The mechanisms by which BMD is protected from severe deficiencies in the IGF-axis are unknown, yet may involve enhanced IGF sensitivity, increased local production of IGFs, and/or supra-physiological concentrations of insulin substituting for the actions of IGFs in bone.

European consumer exposure to cosmetic products, a framework for conducting population exposure assessments

Access to reliable exposure data is essential to evaluate the toxicological safety of ingredients in cosmetic products. This study was carried out by European cosmetic manufacturers acting within the trade association Colipa, with the aim to construct a probabilistic European population model of exposure. The study updates, in distribution form, the current exposure data on daily quantities of six cosmetic products. Data were collected using a combination of market information databases and a controlled product use study. In total 44,100 households and 18,057 individual consumers in five European countries provided data using their own products. All product use occasions were recorded, including those outside of home. The raw data were analysed using Monte Carlo simulation and a European Statistical Population Model of exposure was constructed. A significant finding was an inverse correlation between frequency of product use and quantity used per application for body lotion, facial moisturiser, toothpaste and shampoo. Thus it is not appropriate to calculate daily exposure to these products by multiplying the maximum frequency value by the maximum quantity per event value. The results largely confirm the exposure parameters currently used by the cosmetic industry. Design of this study could serve as a model for future assessments of population exposure to chemicals in products other than cosmetics.

Creatine supplementation, sleep deprivation, cortisol, melatonin and behavior

The effect of creatine supplementation and sleep deprivation, with intermittent moderate-intensity exercise, on cognitive and psychomotor performance, mood state, effort and salivary concentrations of cortisol and melatonin were examined. Subjects were divided into a creatine supplementation group and a placebo group. They took 5 g of creatine monohydrate or a placebo, dependent on their group, four times a day for 7 days immediately prior to the experiment. They undertook tests examining central executive functioning, short-term memory, choice reaction time, balance, mood state and effort at baseline and following 18-, 24- and 36-h sleep deprivation, with moderate intermittent exercise. Saliva samples were taken prior to each set of tests. A group x time analysis of covariance, with baseline performance the covariate, showed that the creatine group performed significantly (p < 0.05) better than the placebo group on the central executive task but only at 36 h. The creatine group demonstrated a significant (p < 0.01) linear improvement in performance of the central executive task throughout the experiment, while the placebo group showed no significant effects. There were no significant differences between the groups for any of the other variables. A significant (p < 0.001) main effect of time was found for the balance test with a linear improvement being registered. Cortisol concentrations on Day 1 were significantly (p < 0.01) higher than on Day 2. Mood significantly (p < 0.001) deteriorated up to 24 h with no change from 24 to 36 h. Effort at baseline was significantly (p < 0.01) lower than in the other conditions. It was concluded that, during sleep deprivation with moderate-intensity exercise, creatine supplementation only affects performance of complex central executive tasks.

The participation of mesenchymal stem cells in tumor stroma formation and their application as targeted-gene delivery vehicles

Recent evidence suggests that mesenchymal stem cells (MSC) selectively proliferate to tumors and contribute to the formation of tumor-associated stroma. The biological rationale for tumor recruitment of MSC remains unclear but may represent an effort of the host to blunt tumor cell growth and improve survival. There is mounting experimental evidence that normal stromal cells can revert malignant cell behavior, and separate studies have demonstrated that stromal cells can enhance tumor progression after acquisition of tumor-like genetic lesions. Together, these observations support the rationale for modifying normal MSC to deliver therapeutic proteins directly into the tumor microenvironment. Modified MSC can produce high concentrations of antitumor proteins directly within the Tumor mass, which have been shown to blunt tumor growth kinetics in experimental animal model systems. In this chapter we will address the biological properties of MSC within the tumor microenvironment and discuss the potential use of MSC and other bone marrow-derived cell populations as delivery vehicles for antitumor proteins.

Computational selection of nucleic acid biosensors via a slip structure model

Aptamers have been shown to undergo ligand-dependent conformational changes, and can be joined to ribozymes to create allosteric ribozymes (aptazymes). An anti-flavin (FMN) aptamer joined to the hammerhead ribozyme yielded an aptazyme that underwent small, FMN-dependent displacements in the helix that joined the aptamer and ribozyme. This 'slip structure' model in which alternative sets of base-pairs are formed in the absence and presence of ligand proved amenable to energetic and computational modeling. Initial successes in modeling the activities of known aptazymes led to the in silico selection of new ligand-dependent aptazymes from virtual pools that contained millions of members. Those aptazymes that were predicted to best fit the slip structure model were synthesized and assayed, and the best-designed aptazyme was activated 60-fold by FMN. The slip structure model proved to be generalizable, and could be applied with equal facility to computationally generate aptazymes that proved to be experimentally activated by other ligands (theophylline) or that contained other catalytic cores (hairpin ribozyme). Moreover, the slip structure model could be applied to the prediction of a ligand-dependent aptamer beacon biosensor in which the addition of the protein vascular endothelial growth factor (VegF) led to a 10-fold increase in fluorescent signal.

Correlates of placental infection with cytomegalovirus, parvovirus B19 or human herpes virus 7

Vertical transmission of viruses is an important cause of morbidity in the fetus and neonate. Placental viral infection indicates risk of vertical transmission, but not always transmission to, or disease of the fetus. Specimens from mothers and babies from three groups-two prospective and one retrospective cohort-were tested for pathogens of teratogenic potential using multiplex PCR. Placental infection was present in 13% of the 105 samples collected. Assessment of the prospective cohorts showed cytomegalovirus (CMV) detected in 4% of placentae from unselected women, parvovirus B19 in 1% and Ureaplasma parvum in 1% of placentae. In a retrospective cohort of women at high risk of transmitting congenital infection due to seroconversion during pregnancy, miscarriage or stillbirth, CMV was detected in 64% and human herpes virus type 7 in 9% of placentae. Of 14 PCR-positive placentae, two were associated with the birth of a living symptomatic infant, two with stillbirth, one with miscarriage, and two with elective terminations of pregnancy. Directed laboratory assessment of women at high risk of transmitting congenital infection, on the basis of clinical or laboratory markers, is important for accurate diagnosis of adverse outcomes of pregnancy. However, routine screening for viruses in the placentae from women with a low-risk serological profile for transmitting congenital infection is unlikely to result in significant numbers of additional diagnoses and is confounded by inadequacy of current diagnostic methods. The major pathogen detected in all cases of placental infection associated with fetal death was human CMV.

HER2 comparison with novel 3-gene marker sets for risk prediction of distant recurrence of breast carcinoma

20009

Background: The risk of distant recurrence in patients with invasive breast carcinoma (BrCa) is predicted imperfectly by currently used factors (e.g. nuclear grade, hormone receptor status), complicating adjuvant therapy decisions. In an effort to discover biomarkers for recurrence, we retrospectively analyzed BrCa recurrence and tumor gene amplification. Multi-gene marker sets were evaluated for predictive significance and accuracy. Because studies of HER2 as a suitable biomarker report positive and negative results, we compared our marker sets with HER2. Methods: 229 of 723 BrCa patients met inclusion criteria: invasive ductal carcinoma, no isolated local recurrence, minimum 4 years follow-up, and archived specimens adequate for fluorescent in situ hybridization (FISH) assay. Study endpoint was recurrence, or non-recurrence throughout follow-up. FISH was performed on formalin-fixed paraffin sections with probes for previously identified genomic regions. Signals were counted with a Metasystems workstation, and used in a “Prognostic Index” (PI) to categorize recurrence risk. One-sided Fisher’s exact test was used to assess increased incidence of distant recurrence in relation to PI and HER2, and increased incidence of HER2 amplification in relation to PI. Results: Two separate 3-gene marker sets were obtained that predict clinical outcome for hormone receptor + (HR+) and hormone receptor − (HR−) tumors. In HR+ samples a PI based upon regions surrounding CYP24, PDCP6IP, and BIRC5 was the best predictor of recurrence, while for HR- specimens the PI was based on the NR1D1, SMARCE1, and BIRC5 regions. The PIs are significantly associated with recurrence of HR+ and HR− tumors (OR = 9.52, 95% CI > 2.12, p = 0.0024; and OR = 12.3, 95% CI > 1.45, p = 0.0188, respectively). However, tumor HER2 amplification was not prognostic for recurrence (OR = 1.76, 95% CI > 0.77, p = 0.1395). Furthermore, there was no significant association of PI with HER2 status (OR = 1.56, CI > 0.57, p = 0.862). Conclusions: Prognostic Indices based on copy numbers of two 3-gene marker sets significantly predict clinical outcome of stage I-III invasive ductal carcinoma. HER2 amplification, included in our previous whole genome survey but not present in our final marker sets, had no prognostic value.

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A blinded, randomized, multicenter study of an intravenous Staphylococcus aureus immune globulin

OBJECTIVES

Very low birth weight (VLBW) infants are vulnerable to nosocomial infections and subsequent morbidity; including infections caused by Staphylococcus aureus: 85% of nosocomial S. aureus infections are caused by capsular polysaccharide (CPS) types 5 and 8. Altastaph is a polyclonal investigational human immunoglobulin G (IgG) with high levels of opsonizing S. aureus CPS types 5 and 8 IgG.

METHODS

A Phase 2 clinical trial to assess the safety and kinetics of Altastaph in VLBW infants. Neonates in this multicenter study were randomized to receive two identical 20 ml/kg i.v. infusions of either 0.45% NaCl placebo or 1000 mg Altastaph/kg. Each infant was followed for 28 days after the second infusion or until discharge. Serum S. aureus CPS types 5 and 8 IgG levels were measured preinfusion and at various times after each infusion.

RESULTS

Of 206 neonates, 158 received both infusions. Adverse events were similar in the two treatment groups. Six subjects (3% in each group) discontinued owing to an adverse event. Geometric mean anti-type 5 IgG levels were 402 and 642 mcg/ml 1 day following infusion of the first (day 0) and Second (day 14) doses, respectively, in neonates < or =1000 g and slightly higher in neonates 1001 to 1500 g. Trough levels before second infusion were 188 mcg/ml. Type 8 IgG levels were similar. Geometric mean IgG levels among placebo recipients were consistently <2 and <5 mcg/ml for types 5 and 8 in both weight groups. Three episodes of S. aureus bacteremia occurred in each arm.

CONCLUSIONS

Infusion of Altastaph in VLBW neonates resulted in high levels of specific S. aureus types 5 and 8 CPS IgG. The administration of this anti-staphylococcal hyperimmune globulin was well tolerated in this population.

Thrombolysis for intraventricular hemorrhage after endovascular aneurysmal coiling

OBJECTIVE AND IMPORTANCE

Current applications of lytic therapy for intraventricular hemorrhage (IVH) rely on exclusion of vascular abnormalities as etiology. Its use in patients with recently coiled aneurysms remains far from considered safe. We report a patient with subarachnoid hemorrhage (SAH) and massive IVH from aneurysmal rupture, which was safely treated with intraventricular recombinant tissue plasminogen activator (rt-PA) after endovascular coiling. We also review two other similar cases reported in the literature.

CLINICAL PRESENTATION

A 61-year-old man presented with a ruptured anterior communicating artery aneurysm causing SAH and IVH (Hunt & Hess grade IV, Fisher grade III with IVH). During coiling of the aneurysm, extravasation of contrast was noted on fluoroscopy. Follow-up head computed tomography (CT) scan showed casted ventricles. Once in the intensive care unit, the patient progressed to coma, which did not improve with external ventricular drainage alone.

INTERVENTION

After endovascular coiling of the aneurysm, intraventricular rt-PA was administered. Isovolemic injections of 2 mg rt-PA every 12 hours were performed for a total of four doses. No clinical or radiological evidence of worsening SAH/IVH was documented. At the time of discharge, the patient was awake but requiring assistance with activities of daily living.

CONCLUSION

We report the safe administration of intraventricular rt-PA after endovascular coiling of a ruptured cerebral aneurysm. Two other similar cases were found in the literature and are reviewed. Hindrance of aneurysmal cavity thrombosis by early administration of rt-PA (increasing the risk of rerupture) remains a widespread concern. The lack of such instances should therefore be acknowledged. We propose that inclusion of such patients in trials assessing safety/efficacy of thrombolytic therapy in the treatment of patients with intracranial hemorrhage should be carefully considered.

Diagnosis of and screening for cytomegalovirus infection in pregnant women

No single diagnostic test for cytomegalovirus (CMV) infection is currently available for pregnant women at all stages of gestation. Improved accuracy in estimating the timing of primary infections can be used to identify women at higher risk of giving birth to congenitally infected infants. A diagnostic algorithm utilizing immunoglobulin G (IgG), IgM, and IgG avidity was used to prospectively screen serum from 600 pregnant women enrolled from two groups: < or =20 weeks gestation (n = 396) or >20 weeks gestation (n = 204). PCR testing of urine and/or blood was performed on all seropositive women (n = 341). The majority (56.8%) of women were CMV IgG seropositive, with 5.5% being also CMV IgM positive. In the IgM-positive women, 1.2% had a low-avidity IgG, indicating a primary CMV infection and a high risk of intrauterine transmission. Two infants with asymptomatic CMV infection were born of mothers who had seroconverted in the second trimester of pregnancy. Baseline, age-stratified CMV serostatus was established from 1,018 blood donors. Baseline seropositivity from a blood donor population increased with age from 34.9% seroprevalence at less than 20 years of age to 72% seroprevalence at 50 years of age. Women at high risk of intrauterine transmission of CMV were identified at all stages of gestation. Women infected with CMV during late gestation may be more likely to transmit the virus, so failure to detect seroconversions in late gestation may result in failure to detect infected neonates.

Characterization of a Pressurized C5−C16 Hydrocarbon Gas Calibration Standard for Air Analysis

A compressed gas standard containing parts-per-billion (ppb) amounts of the volatile hydrocarbons methylpentadiene (isoprene, 540 ppb) and isooctane (259 ppb) and a series of less volatile C12-C16 n-alkanes (n-dodecane, 349 ppb; n-tridecane, 340 ppb; n-tetradecane, 202 ppb; n-pentadecane, 271 ppb; and n-hexadecane, 308 ppb) was prepared by a one-step (no further gas dilution) microgravimetric method. The gravimetric mixing ratios were confirmed by referencing to a capillary diffusion method. The cylinder was heated to 75 degrees C to minimize condensation losses of analytes to the cylinder walls. Mixing ratios were monitored over a 2.5-year period. Some initial analyte losses (approximately 3 to 20%) were observed for the heavier C14-C16 n-alkanes. Subsequently, analyte loss rates were found to be in the range of <1.0% per year for n-dodecane to n-hexadecane. The developed guidelines for preparation, storage, and retrieval of these semivolatile analytes enable the use of compressed gas standards for calibration and method development purposes in the environmental gas-phase analysis of these and related compounds.