Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications

Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.

An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function

Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.

Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer

Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 103 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.

Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments

The SARS‐CoV‐2 virus and COVID‐19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random‐sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS‐CoV‐2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS‐CoV‐2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS‐CoV‐2. These include electrochemical and optical sensors, lateral flow devices, and aptamer‐linked immobilized sorbent assays.

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

Invited for the cover of this issue are John Brennan, Yingfu Li, and co‐workers at McMaster University. The image depicts MSA52 as a universal DNA aptamer that recognizes spike proteins of diverse SARS‐CoV‐2 variants of concern. Read the full text of the article at 10.1002/chem.202200078.

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS‐CoV‐2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one‐round SELEX experiments using five different trimeric spike proteins from variants, followed by high‐throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS‐CoV‐2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well‐suited for molecular recognition of rapidly evolving targets such as those found in SARS‐CoV‐2.

Functional Nucleic Acids Under Unusual Conditions

Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.

Cigarette smoking and cognitive function among older adults living in the community

Background. The present study aimed to examine the long-term impact of CS on Executive Function (EF) and memory among older adults living in the community. Methods. Clock Drawing Test (CDT) and Delayed Word Recall Test (DWRT) were used to examine EF and memory, respectively, using four waves of National Health and Aging Trend Study. The respondents were asked whether they have ever smoked, length of smoking, and age of start and quit smoking. Results. CS can have a long-term impact on both EF and memory. However, current smoking can increase the risk of EF impairment compared to former smokers. Lung disease and current smoking can have a synergic effect of impairment in EF. Conclusion. In the long-term, smoking can negatively affect cognitive. Lung diseases and smoking can synergize their impacts on EF. The impact of smoking on cognition varies across ethnic groups; hence, educational programs targeting minorities can reduce discrepancies.

Smoking Predicting Physical Activity in an Aging America

OBJECTIVES

Tobacco smoking and physical inactivity are among leading behavioral risk factors for ill health in older adults. This study considers how smoking is associated with physical activity.

DESIGN

Using a Life-Course model, data are analyzed regarding this relationship, controlling for, and interacted with, life-course and other factors. Daily smokers and sometimes smokers were hypothesized to engage in less leisure-time physical activity than those who never smoked, while those who stopped smoking were expected to do more than never smokers. Analyses were performed using SAS-Callable SUDAAN.

SETTING AND PARTICIPANTS

Secondary data from ten years of a national sample of adults aged 18 and over of the National Health Interview Survey, 2001-2010, are used (N = 264,945, missing data excluded, of 282,313 total cases).

MEASUREMENTS

Daily smokers, occasional smokers, and smoking quitters are compared to never smokers with regard to requisite physical activity (150 minutes per week of moderate, 100 of vigorous, and/or 50 of strengthening activity). Life-course measures include birth cohorts, age, and year of survey, as well as gender, race/ethnicity, and education.

RESULTS

Overall, hypotheses are supported regarding daily smokers and quitters; but the hypothesis is strongly rejected among sometimes smokers, who are much more likely to do requisite physical activity. Findings differ by age, sometimes smokers age 65 and over being less likely to do physical activity. Findings among all men are similar to the overall findings, while those among all women are similar to those for older respondents. Associations of smoking status with physical activity vary greatly by race/ethnicity.

CONCLUSIONS

Daily smokers may be most in need of both smoking cessation and leisure-time physical activity interventions. Smoking-cessation efforts may pay greater physical activity benefits among women and the aged, while smoking-reduction efforts may provide better outcomes among men. Smoking reduction efforts may pay more exercise benefits among African-Americans and Hispanics.

Evaluation of the New World Health Organization Case Definition of Severe Acute Respiratory Infection for Influenza Surveillance During the Peak Weeks of Two Influenza Seasons in Quebec, Canada

During the peak of the 2012-2013 and 2014-2015 influenza seasons in Quebec, Canada, the sensitivity of the new World Health Organization (WHO) case definition of severe acute respiratory infection (SARI) in <5-year-old children was 65% for polymerase chain reaction-confirmed influenza and 79% for other respiratory viruses (ORVs), whereas its specificity and positive predictive value were approximately 2- and 4-fold lower for influenza than ORVs (25% vs 40% and 18% vs 76%, respectively). The use of the WHO SARI definition for influenza surveillance in children should be interpreted with caution according to the specific surveillance goals.

Development of two salmonella-based oral vaccines against human respiratory syncytial virus

Human respiratory syncytial virus is the most common cause of bronchiolitis and other respiratory infections in infants and the elderly worldwide. We have developed two new oral vaccines using Salmonella typhi TY21a to carry and express the immunogenic epitopes of RSV fusion (F) and attachment (G) glycoproteins on its surface, separately. To evaluate the efficacy of the designed vaccines, BALB/c mice were orally immunized and then infected with RSV. Immune response analyses showed that cellmediated, mucosal and humoral immunity in the vaccinated mice were significantly enhanced compared to the control group. Both vaccines generated a balanced Th1/Th2 immune response which is crucial for efficiency of vaccines against RSV. Furthermore, histopathological examination proved that these vaccines were safe as they did not cause any Th2-associated adverse effects in the lungs of RSV-infected mice. The findings of this research suggest that Salmonella-F and Salmonella-G vaccine candidates may have strong potential to prevent RSV infection.

Apigenin modulates the expression levels of pro-inflammatory mediators to reduce the human insulin amyloid-induced oxidant damages in SK-N-MC cells

Amyloid depositions of proteins play crucial roles in a wide variety of degenerative disorders called amyloidosis. Although the exact mechanisms involved in amyloid-mediated cytotoxicity remain unknown, increased formation of reactive oxygen species (ROS) and nitrogen species and overproduction of pro-inflammatory cytokines are believed to play key roles in the process. In that regard, we investigated the effect of apigenin, a common dietary flavonoid with high antioxidant and anti-inflammatory properties on potential factors involved in cytotoxicity of human insulin amyloids. Pretreatment of SK-N-MC neuroblastoma cells with apigenin increased cell viability and reduced the apoptosis induced by insulin fibrils. In addition, apigenin attenuated insulin fibril-induced ROS production and lipid peroxidation. Our result also demonstrated that pretreatment of the fibril-affected cells with apigenin caused an increase in catalase activity and the intracellular glutathione content along with reduction in nitric oxide production and nuclear factor κB, tumor necrosis factor α, and interleukin 6 gene expression based on real-time polymerase chain reaction evaluation. In accordance with these results, apigenin could be a promising candidate in the design of natural-based drugs for treatment or prevention of amyloid-related disorders.

Challenges of implementing Iranian national laboratory standards

After four years of publishing the Iranian National Laboratory Standard and following a strategic plan to implement its requirements, it was decided to review the taken actions, evaluating the achievements and the failures, as well as analyzing the gaps and planning the interventional activities to resolve the problems. A thorough evaluation revealed that the progress of implementation process varies considerably in different provinces, as well as in laboratories in different public and private sectors. Diversity and heterogeneousity of laboratories throughout the country is one of unresolvable problems. Although we encounter shortage of resources in the country, improper allocation or distribution of resources and budgets make the problems more complicated. Inadequacy of academic training in laboratory sciences has resulted in necessity of holding comprehensive post-graduate training courses. Revising academic curriculum of laboratory sciences could be mostly helpful, moreover there should be organized, training courses with pre-determined practical topics. providing specific technical guidelines, to clarify the required technical details could temporarily fill the training gaps of laboratory staff. Inadequate number of competent auditors was one of the difficulties in universities. Another important challenge returns to laboratory equipment, developing the national controlling system to manage the laboratory equipment in terms of quality and accessibility has been planned in RHL. At last cultural problems and resistance to change are main obstacles that have reduced the pace of standardization, it needs to rationalize the necessity of establishing laboratory standards for all stakeholders.

First detected human bocavirus in a Malaysian child with pneumonia and pre-existing asthma: a case report

Human bocavirus (HBoV) is a newly discovered parvovirus associated with respiratory disease in children. There are many reports worldwide on the endemicity of this virus. Since it is relatively new, detection in clinical laboratories is not routinely performed. We describe the first detection of HBoV in Malaysia in a 13-month-old boy with pneumonia and underlying asthma. The infective agent was confirmed by molecular methods.

Cyclin B1 Is an Independent Prognostic Proliferation Marker with a High Reproducibility in a Population-Based Lymph Node Negative Breast Cancer Cohort

Purpose: A large proportion of women with lymph node negative breast cancer treated with chemotherapy do not benefit from such treatment. Proliferation markers can recognize patients at high risk for recurrence. However, no proliferation marker is generally accepted for clinical use. We investigated the independent prognostic importance of cyclin B1 in node negative breast cancer and included a study of the reproducibility.Study Design: In a population-based, case-control study, 190 women who died from breast cancer were defined as cases and 190 women alive at the time for the corresponding case's death as controls. Inclusion criteria were tumor size ≤ 50 mm, no lymph node metastases, and no adjuvant chemotherapy. Tumor tissue was immunostained for cyclin B1. Two investigators evaluated the staining independently by counting approximately 100, 200, 500, and 1000 cells.Results: Cyclin B1 was statistically significantly associated to breast cancer death, in both uni- and multivariate analyses (adjusted for tumor size, age, and endocrine therapy), with odds ratios 2-3 for both investigators. The reproducibility between the two investigators was good to very good, regardless of the number of counted cells (kappa values between 0.74 and 0.82).Conclusions: Cyclin B1 is a prognostic factor for breast cancer death in a population-based and node negative patient cohort and can identify high-risk node negative patients with a good to very good reproducibility.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6051.

The effect of increasing blood flow rate on dialysis adequacy in hemodialysis patients

Inadequacy of dialysis is one of the determinants of morbidity and mortality in patients undergoing dialysis. The aim of this study was to assess the effect of increasing blood flow rate during hemodialysis (HD) on the adequacy of dialysis. In this study, 42 patients on maintenance HD were assessed. Body weight and blood urea nitrogen (BUN) levels before and after HD sessions were recorded on all the study patients. Volume of ultrafiltration, the duration of dialysis, percentage of filter clearance and flow rate of the dialysate were collected and documented in a checklist. Both Kt/V and urea reduction ratio (URR) were determined at two different blood pump speeds, i.e. 200 and 250 mL/min. During HD, hemodynamic status and vital signs of patients were monitored and controlled. After collecting the necessary data, efficiency of dialysis was calculated using the standard formula. Descriptive and analytical statistics was carried out to analyze the data. Using blood flow rate of 200 mL/min, 16.7% of patients had Kt/V higher than 1.3 and URR higher than 65. On the other hand, with flow rate of 250 mL/min, 26.2% of patients had Kt/V higher than 1.3 and 35.7% of subjects had URR higher than 65. Paired t-test with 95% confidence showed a significant difference in dialysis efficiency between two groups. Our data further confirm that increasing the blood flow rate by 25% is effective in increasing dialysis adequacy in HD patients.

Respiratory System Model for Quasistatic Pulmonary Pressure-Volume (P-V) Curve: Generalized P-V Curve Analyses

A normalized P-V curve is proposed for quantitative comparisons of quasistatic P-V curves from different sources, including data from different investigators, airway pressure-volume curves versus transpulmonary pressure-volume curves, normal versus injured respiratory system, and animal tests versus clinical data. Similarities and differences among five different data groups we analyzed are shown to be quantified through the nondimensional pressure range of an individual data set, combined with the magnitudes of two nondimensional parameters of the inflation limb, derived from a respiratory system model previously reported.

Respiratory System Model for Quasistatic Pulmonary Pressure-Volume (P-V) Curve: Inflation-Deflation Loop Analyses

A respiratory system model (RSM) is developed for the deflation process of a quasistatic pressure-volume (P-V) curve, following the model for the inflation process reported earlier. In the RSM of both the inflation and the deflation limb, a respiratory system consists of a large population of basic alveolar elements, each consisting of a piston-spring-cylinder subsystem. A normal distribution of the basic elements is derived from Boltzmann statistical model with the alveolar closing (opening) pressure as the distribution parameter for the deflation (inflation) process. An error minimization by the method of least squares applied to existing P-V loop data from two different data sources confirms that a simultaneous inflation-deflation analysis is required for an accurate determination of RSM parameters. Commonly used terms such as lower inflection point, upper inflection point, and compliance are examined based on the P-V equations, on the distribution function, as well as on the geometric and physical properties of the basic alveolar element.

A Mechanistic Model for Quasistatic Pulmonary Pressure-Volume Curves for Inflation

A mechanistic model of the respiratory system is proposed to understand differences in quasistatic pressure-volume (p-V) curves of the inflation process in terms of the alveolar recruitment and the elastic distension of the wall tissues. In the model, a total respiratory system consists of a large number of elements, each of which is a subsystem of a cylindrical chamber fitted with a piston attached to a spring. The alveolar recruitment is simulated by allowing a distribution of the critical pressure at which an element opens; while the wall distension is represented by the piston displacement. Relations are derived between parameters in the error-function p-V model equation and properties of the mechanistic model. The parameters of the model-based p-V equation are determined for clinical data sets of patients with acute respiratory distress syndrome.

Kinetic spectrophotometric determination of thiocyanate based on its inhibitory effect on the oxidation of methyl red by bromate

A kinetic spectrophotometric method for measuring thiocyanate is described. The proposed method is based on the inhibitory effect of thiocyanate on the oxidation of Methyl Red by bromate in the presence of nitrite, which was monitored at 520 nm. The variables affecting the rate of the reaction were investigated and the optimum conditions were established. Thiocyanate can be measured in the range of 0.05-1.1 microg ml(-1) with a detection limit of 0.025 microg ml(-1). This method has been used to determine trace thiocyanate in urine and tap water samples.

Control of hippocampal morphogenesis and neuronal differentiation by the LIM homeobox gene Lhx5

The mammalian hippocampus contains the neural circuitry that is crucial for cognitive functions such as learning and memory. The development of such circuitry is dependent on the generation and correct placement of the appropriate number and types of neurons. Mice lacking function of the LIM homeobox gene Lhx5 showed a defect in hippocampus development. Hippocampal neural precursor cells were specified and proliferated, but many of them failed to either exit the cell cycle or to differentiate and migrate properly. Lhx5 is therefore essential for the regulation of precursor cell proliferation and the control of neuronal differentiation and migration during hippocampal development.

Serum prolactin concentrations are elevated after syncope

The distinction between syncope and epileptic seizures is a common clinical diagnostic problem. Elevated serum prolactin (PRL) concentrations are used to help differentiate epileptic from nonepileptic attacks such as pseudoseizures. Reports of PRL concentrations following syncope have been variable. To determine whether PRL rises after syncope, we measured serum PRL concentrations during a 45-minute passive 60-degree head-up tilt in 21 patients with a history of near-fainting or syncope. Head-up tilt triggered hypotension (mean arterial pressure 51 mm Hg, 95% CI = 45-57) with syncope in 11 patients. PRL concentrations were elevated ( > 19 ng/mL) and reached a maximum within the first 30 minutes after tilt-induced syncope in nine patients (PRL supine: 11 ng/mL, 95% CI = 7-15, vs. PRL after syncope: 52 ng/mL, 95% CI = 36-67; a greater than fourfold rise), while they remained unchanged in 10 patients who had a normal response to head-up tilt (PRL supine: 6 ng/mL, 95% CI = 5-8, vs. maximum PRL while upright: 8 ng/mL, 95% CI = 6-10). The findings indicate that elevated PRL concentrations are present after hypotensive syncope and are of little use in differentiating such syncope from epileptic seizures.

Heterologous enzyme function in Escherichia coli and the selection of genes encoding the catalytic RNA subunit of RNase P

The gene for the catalytic RNA subunit of RNase P has been isolated from several Enterobacteriaceae by complementation of an Escherichia coli strain that is temperature-sensitive for RNase P activity. The selection procedure relies on the ability of the heterologous gene products to function enzymatically in E. coli. This procedure obviates the need for positive results in DNA blot hybridization experiments or for the purification of holoenzyme to identify the RNA component of RNase P and its corresponding gene from organisms other than E. coli. Comparisons of the variations in sequences provide the basis for a refined two-dimensional model of the secondary structure of M1 RNA.