scholarly journals Controlling uncertainty in aptamer selection

2016 ◽  
Vol 113 (43) ◽  
pp. 12076-12081 ◽  
Author(s):  
Fabian Spill ◽  
Zohar B. Weinstein ◽  
Atena Irani Shemirani ◽  
Nga Ho ◽  
Darash Desai ◽  
...  
Keyword(s):  
Population Distribution ◽  
Environmental Parameters ◽  
Binding Affinities ◽  
Affinity Ligands ◽  
Evolutionary Selection ◽  
High Affinity ◽  
Fitness Parameters ◽  
Exponential Enrichment ◽  
The Impact ◽  
Selection Of

The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these aptamers through evolutionary selection of high-affinity candidates from a highly diverse random pool. This randomness dictates an unknown population distribution of fitness parameters, encoded by the binding affinities, toward SELEX targets. Adding to this uncertainty, repeating SELEX under identical conditions may lead to variable outcomes. These uncertainties pose a challenge when tuning selection pressures to isolate high-affinity ligands. Here, we present a stochastic hybrid model that describes the evolutionary selection of aptamers to explore the impact of these unknowns. To our surprise, we find that even single copies of high-affinity ligands in a pool of billions can strongly influence population dynamics, yet their survival is highly dependent on chance. We perform Monte Carlo simulations to explore the impact of environmental parameters, such as the target concentration, on selection efficiency in SELEX and identify strategies to control these uncertainties to ultimately improve the outcome and speed of this time- and resource-intensive process.

scholarly journals Aptamer-iRNAs as Therapeutics for Cancer Treatment

2018 ◽  
Vol 11 (4) ◽  
pp. 108 ◽  
Author(s):  
Mario Soldevilla ◽  
Daniel Meraviglia-Crivelli de Caso ◽  
Ashwathi Menon ◽  
Fernando Pastor
Keyword(s):  
Cancer Therapy ◽  
Cancer Treatment ◽  
Antisense Oligonucleotides ◽  
Tertiary Structure ◽  
Potential Treatment ◽  
High Affinity ◽  
Different Types ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Aptamers are single-stranded oligonucleotides (ssDNA or ssRNA) that bind and recognize their targets with high affinity and specificity due to their complex tertiary structure. Aptamers are selected by a method called SELEX (Systematic Evolution of Ligands by EXponential enrichment). This method has allowed the selection of aptamers to different types of molecules. Since then, many aptamers have been described for the potential treatment of several diseases including cancer. It has been described over the last few years that aptamers represent a very useful tool as therapeutics, especially for cancer therapy. Aptamers, thanks to their intrinsic oligonucleotide nature, present inherent advantages over other molecules, such as cell-based products. Owing to their higher tissue penetrability, safer profile, and targeting capacity, aptamers are likely to become a novel platform for the delivery of many different types of therapeutic cargos. Here we focus the review on interfering RNAs (iRNAs) as aptamer-based targeting delivered agents. We have gathered the most reliable information on aptamers as targeting and carrier agents for the specific delivery of siRNAs, shRNA, microRNAs, and antisense oligonucleotides (ASOs) published in the last few years in the context of cancer therapy.

scholarly journals The Role of Sex and Gender in the Selection of Alzheimer Patients for Clinical Trial Pre-screening

2021 ◽  
Author(s):  
Maitee Rosende-Roca ◽  
Carla Abdelnour ◽  
Ester Esteban ◽  
Juan Pablo Tartari ◽  
EMILIO ALARCON ◽  
...  
Keyword(s):  
Elderly Women ◽  
Population Distribution ◽  
Neurodegenerative Disorder ◽  
Developed Countries ◽  
Assessment Tools ◽  
Sex And Gender ◽  
Screening Process ◽  
The Impact ◽  
Selection Of

Abstract Background: Alzheimer disease (AD) is a progressive neurodegenerative disorder affecting the elderly with a prevalence of 7.1% in women and 3.3% in men aged 55 or older. Sex-related patterns have been reported in prognosis, biomarker status and risk factors. Despite this, the interaction of sex has received limited attention, with AD trials persistently recruiting lower numbers of women than the population distribution and a lack of information on the sex-disaggregated effects of anti-dementia therapies. This is the first study aiming to identify the role of sex in the selection for screening in AD clinical trials.Methods: This cross-sectional study provides a comprehensive analysis of screening eligibility according to a set of pre-selection criteria currently applied at Fundació ACE memory clinic for a more efficient trial screening process. A cohort of 6,667 women and 2,926 men diagnosed with AD dementia (55%) or mild cognitive impairment (45%) was analyzed. We also assessed the frequencies of men and women effectively screened for trial enrolment over a period of 10 years.Results: Women showed a significantly lower chance of being eligible for screening than men (OR=1.26; p<0.01). This imbalance was confirmed by a lower frequency of women screened for enrolment compared to the study population (63.0% vs 69.5%). Education was revealed as the key criterion contributing to this unbalance, with men showing over twice the chance of being screened compared with women (OR=2.25, p<0.01). Education-based differences were greater in earlier born patients, but the gap narrowed and achieved balance with increasing year of birth. Comorbidity was the most limiting criterion with sex differences in frequencies and significant discrimination against the selection of men (OR=0.86, p<0.01).Conclusions: The large number of low-educated elderly women with AD demands for a sex-focused approach in clinical research. New assessment tools insensitive to education level should be develop to enable a proportional representation of women. Although this gender education gap is mostly inexistent in developed countries, economic or cultural factors may lead to different scenarios in other regions. Overlooking the impact of sex may lead to a handicap in AD research with a direct adverse impact on women’s health.

scholarly journals Microhabitat selection of a Sicilian subterranean woodlouse and its implications for cave management

2021 ◽  
Vol 50 (1) ◽  
pp. 53-63
Author(s):  
Giuseppe Nicolosi ◽  
Stefano Mammola ◽  
Salvatore Costanzo ◽  
Giorgio Sabella ◽  
Rosolino Cirrincione ◽  
...  
Keyword(s):  
Environmental Parameters ◽  
High Sensitivity ◽  
Local Fauna ◽  
Terrestrial Invertebrates ◽  
The Public ◽  
Natural Reserve ◽  
Cave Management ◽  
Abundance And Distribution ◽  
The Impact ◽  
Selection Of

Human activities in subterranean environments can affect different ecosystem components, including the resident fauna. Subterranean terrestrial invertebrates are particularly sensitive to environmental change, especially microclimatic variations. For instance, microclimate modifications caused by the visitors may directly affect local fauna in caves opened to the public. However, since numerous factors act synergistically in modulating the distribution and abundance of subterranean species, it remains challenging to differentiate the impact of human intervention from that of other factors. Therefore, evidence of the impact of tourism on cave invertebrate fauna remains scarce. Over a year and with approximately two visits a month, we investigated the effects of the presence of visitors on the subterranean endemic woodlouse Armadillidium lagrecai in the strict natural reserve of Monello Cave (Sicily, Italy). We found that natural microclimatic fluctuations, and not direct human disturbance, were the main factors driving the distribution of A. lagrecai. Specifically, A. lagrecai select for more climatically stable areas of the cave, where the temperature was constantly warm and the relative humidity close to saturation. We also observed a significant temporal effect, with a greater abundance of A. lagrecai in summer and a gradual decrease during the winter months. The number of visitors in the Monello Cave had no effect on the abundance and distribution of A. lagrecai. However, considering the high sensitivity of the species to microclimatic variations, it seems likely that a significant increase in the number of visitors to the cave could indirectly affect this species by altering local microclimate. Constant monitoring of the environmental parameters within the cave is therefore recommended.

scholarly journals High-affinity RNA ligands to basic fibroblast growth factor inhibit receptor binding

1993 ◽  
Vol 90 (23) ◽  
pp. 11227-11231 ◽  
Author(s):  
D Jellinek ◽  
C K Lynott ◽  
D B Rifkin ◽  
N Janjić
Keyword(s):  
Growth Factor ◽  
Fibroblast Growth Factor ◽  
Basic Fibroblast Growth Factor ◽  
High Specificity ◽  
Fibroblast Growth ◽  
Affinity Ligands ◽  
Surface Receptors ◽  
High Affinity ◽  
Rna Ligands ◽  
Exponential Enrichment

We have isolated RNA ligands with low-nanomolar affinity and high specificity to basic fibroblast growth factor from a pool of 10(14) molecules containing 30 randomized positions by the systematic evolution of ligands by exponential enrichment (SELEX) procedure. High-affinity ligands could be classified into two families based on sequence and secondary structure similarities. Representative RNA ligands from the two families compete with one another as well as with heparin for binding to the protein. Furthermore, we show that these ligands inhibit the first step in the signaling pathway of basic fibroblast growth factor: binding of the growth factor to its cell-surface receptors. These findings emphasize the general usefulness of SELEX as a tool for discovering potent, specific oligonucleotide antagonists of target proteins.

Methods for Restricting Maximum Exposure Rate in Computerized Adaptative Testing

Methodology ◽  
2007 ◽  
Vol 3 (1) ◽  
pp. 14-23 ◽  
Author(s):  
Juan Ramon Barrada ◽  
Julio Olea ◽  
Vicente Ponsoda
Keyword(s):  
Measurement Accuracy ◽  
Computerized Adaptive Testing ◽  
Computation Time ◽  
Adaptive Testing ◽  
Exposure Rate ◽  
Control Parameters ◽  
The Impact ◽  
Two Alternatives ◽  
Selection Of ◽  
Maximum Exposure

Abstract. The Sympson-Hetter (1985) method provides a means of controlling maximum exposure rate of items in Computerized Adaptive Testing. Through a series of simulations, control parameters are set that mark the probability of administration of an item on being selected. This method presents two main problems: it requires a long computation time for calculating the parameters and the maximum exposure rate is slightly above the fixed limit. Van der Linden (2003) presented two alternatives which appear to solve both of the problems. The impact of these methods in the measurement accuracy has not been tested yet. We show how these methods over-restrict the exposure of some highly discriminating items and, thus, the accuracy is decreased. It also shown that, when the desired maximum exposure rate is near the minimum possible value, these methods offer an empirical maximum exposure rate clearly above the goal. A new method, based on the initial estimation of the probability of administration and the probability of selection of the items with the restricted method ( Revuelta & Ponsoda, 1998 ), is presented in this paper. It can be used with the Sympson-Hetter method and with the two van der Linden's methods. This option, when used with Sympson-Hetter, speeds the convergence of the control parameters without decreasing the accuracy.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

FEATURES OF ORGANOPHOSPHATES IMMOBILIZATION VIA STREPTAVIDIN-BIOTIN SYSTEM FOR EXPERIMENTS ON SELECTION OF APTAMERS

2020 ◽  
pp. 12-20
Author(s):  
D. A. Belinskaya ◽  
Yu. V. Chelusnova ◽  
V. V. Abzianidze ◽  
N. V. Goncharov
Keyword(s):  
Polyethylene Glycol ◽  
Organophosphorus Compounds ◽  
Binding Energies ◽  
Rna Aptamers ◽  
Main Method ◽  
Modeling Methods ◽  
Molecular Dynamics Methods ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Poisoning with organophosphorus compounds occupy one of the leading places in exotoxicosis. At the first stage, the detoxification of organophosphates can be provided with the help of DNA or RNA aptamers that bind the poison in the bloodstream. Currently, the main method of searching for aptamers is the experimental method of systematic evolution of ligands by exponential enrichment (SELEX). In the process of aptamer selection, the target molecule must be immobilized via the streptavidin-biotin complex. Since the poison molecule is small in size, to increase its availability for binding to aptamer, it is necessary to use a spacer between organophosphorus compounds and biotin. The aim of this work was to optimize the selection of aptamers for organophosphorus compounds by increasing the availability of a poison molecule immobilized via the streptavidin-biotin complex on the example of paraoxon. For this purpose, three spacers between organophosphorus compounds and biotin were tested using molecular modeling methods: three links of polyethylene glycol (3-PEG), four links of polyethylene glycol (4-PEG) and aminohexyl. The conformation of the biotinylated paraoxon complex with streptavidin and the interaction of paraoxon with the binding fragment of the aptamer were modeled using molecular docking and molecular dynamics methods. The ability of biotinylated paraoxon to bind to the aptamer has been evaluated by analyzing the surface area of the paraoxon available to the solvent, as well as by calculating the free binding energies. It has been shown that only in the case of aminohexyl immobilized paraoxon can contact the aptamer. At the final stage, the synthesis of paraoxon bound to biotin via aminohexyl was carried out.

Impact of removing ESBL designation from culture reports on the selection of antibiotics for the treatment of infections associated with ESBL-producing organisms

2020 ◽  
Vol 41 (5) ◽  
pp. 604-607 ◽  
Author(s):  
Mark D. Lesher ◽  
Cory M. Hale ◽  
Dona S. S. Wijetunge ◽  
Matt R. England ◽  
Debra S. Myers ◽  
...  
Keyword(s):  
Antimicrobial Stewardship ◽  
Antibiotic Prescribing ◽  
The Impact ◽  
Inhibitor Combination ◽  
Lactamase Inhibitor ◽  
Selection Of

AbstractWe characterized the impact of removal of the ESBL designation from microbiology reports on inpatient antibiotic prescribing. Definitive prescribing of carbapenems decreased from 48.4% to 16.1% (P = .01) and β-lactam–β-lactamase inhibitor combination increased from 19.4% to 61.3% (P = .002). Our findings confirm the importance of collaboration between microbiology and antimicrobial stewardship programs.

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