Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells.

Single-stranded DNA (ssDNA) templates along with Cas9 have been used for gene insertion but suffer from low efficiency. Here, we show that ssDNA with chemical modifications in 10-17% of internal bases (eDNA) is compatible with the homologous recombination machinery. Moreover, eDNA templates improve gene insertion by 2-3 fold compared to unmodified and end-modified ssDNA in airway basal stem cells (ABCs), hematopoietic stem and progenitor cells (HSPCs), T-cells and endothelial cells. Over 50% of alleles showed gene insertion in three clinically relevant loci (CFTR, HBB, and CCR5) in ABCs using eDNA and up to 70% of alleles showed gene insertion in the HBB locus in HSPCs. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. Knocking out TREX1 nuclease improved gene insertion using unmodified ssDNA but not eDNA suggesting that chemical modifications inhibit TREX1. This approach can be used for therapeutic applications and biological modeling.

Which intellectual activities are related to cognitive reserve? Introduction and testing a three-dimensional model.

BACKGROUND: A common belief among people and some researchers is that keeping yourself mentally active may decrease the risk of dementia. Over the past years, despite widespread efforts to identify proxies for protecting cognitive reserve against age-related changes, it is still not clear what type of intellectual activity would be beneficial for cognitive reserve. To fill this gap, we propose a three-dimensional model of intellectual activity. According to this conceptual model, intellectual activities could be distinguished based on their locations in a three-dimensions space, including; (1) Activation: active vs. passive, (2) Novelty: novel vs. familiar, and (3) Productivity: productive vs. receptive. We assumed that the activities that are categorized as more active, novel, and productive could be considered as a cognitive reserve proxy. METHODS: To test this hypothesis, a sample of 237 participants older than 50 years (Mage = 58.76 ± 6.66; 63.7% women) was recruited to take part in the study. Episodic, semantic and working memory were assessed with computerized battery tests (Sepidar) and a self-report questionnaire was used to assess intellectual activities. Activities were categorized in terms of; (1) passive, familiar, and receptive activities (radio/watching TV), (2) active, familiar, and receptive activities (solving crosswords), (3) active, novel, and receptive activities (reading), and (4) active, novel, and productive activities (writing). RESULTS: The results indicated that writing moderates the effect of age on episodic and semantic memory. Reading only moderates the effect of age on semantic memory, and radio/watching TV and solving crosswords do not play a role in moderation analysis. CONCLUSIONS: Our finding suggests that intellectual activities have different moderating effects on the relationships between age and memory performance. Individuals with high levels of participation in novel and productive activities over the life course are less likely to clinically demonstrate cognitive impairments. Our results support the potential benefit of the three-dimensional model to provide a better insight into the complex role of intellectual activities in cognitive reserve, particularly for older adults. Further research is needed to evaluate the efficacy and the benefits of the model.

STAMP-Based Digital CRISPR-Cas13a for Amplification-Free Quantification of HIV-1 Plasma Viral Loads.

Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 µL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 µL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.

Morphology around Nanopores Fabricated by Laser-Assisted Dielectric Breakdown and Its Impact on Ion and DNA Transport and Sensing.

Laser-assisted controlled dielectric breakdown (LaCBD) has emerged as an alternative to conventional CBD-based nanopore fabrication due to its localization capability, facilitated by the photothermal-induced thinning down in the hot spot. Here, we reported the potential impact of the laser on forming debris around the nanopore region in LaCBD. The debris was clearly observable by scanning electron microscopy (SEM) and photoluminescence (PL) spectroscopy. We found that debris formation is a unique phenomenon in LaCBD that is not observable in the conventional CBD approach. We also found that the LaCBD-induced debris is more evident when the laser power and voltage stress are higher. Moreover, the debris is asymmetrically distributed on the top and bottom sides of the membrane. We also found unexpected rectified ionic and molecular transport in those LaCBD nanopores with debris. Based on these observations, we developed and validated a model describing the debris formation kinetics in LaCBD by considering the generation, diffusion, drift, and gravity in viscous mediums. These findings indicate that while laser aids in nanopore localization, precautions should be taken due to the potential formation of debris and rectification of molecular transport. This study provides valuable insights into the kinetics of LaCBD and the characteristics of the LaCBD nanopore.

Digital CRISPR Systems for the Next Generation of Nucleic Acid Quantification.

Digital CRISPR (dCRISPR) assays are an emerging platform of molecular diagnostics. Digital platforms introduce absolute quantification and increased sensitivity to bulk CRISPR assays. With ultra-specific targeting, isothermal operation, and rapid detection, dCRISPR systems are well-prepared to lead the field of molecular diagnostics. Here we summarized the common Cas proteins used in CRISPR detection assays. The methods of digital detection and critical performance factors are examined. We formed three strategies to frame the landscape of dCRISPR systems: (1) amplification free, (2) in-partition amplification, and (3) two-stage amplification. We also compared the performance of all systems through the limit of detection (LOD), testing time, and figure of merit (FOM). This work summarizes the details of digital CRISPR platforms to guide future development. We envision that improvements to LOD and dynamic range will position dCRISPR as the leading platform for the next generation of molecular biosensing.

Hippocampal and motor regions contribute to memory benefits after enacted encoding: cross-sectional and longitudinal evidence.

The neurobiological underpinnings of action-related episodic memory and how enactment contributes to efficient memory encoding are not well understood. We examine whether individual differences in level (n = 338) and 5-year change (n = 248) in the ability to benefit from motor involvement during memory encoding are related to gray matter (GM) volume, white matter (WM) integrity, and dopamine-regulating genes in a population-based cohort (age range = 25-80 years). A latent profile analysis identified 2 groups with similar performance on verbal encoding but with marked differences in the ability to benefit from motor involvement during memory encoding. Impaired ability to benefit from enactment was paired with smaller HC, parahippocampal, and putamen volume along with lower WM microstructure in the fornix. Individuals with reduced ability to benefit from encoding enactment over 5 years were characterized by reduced HC and motor cortex GM volume along with reduced WM microstructure in several WM tracts. Moreover, the proportion of catechol-O-methyltransferase-Val-carriers differed significantly between classes identified from the latent-profile analysis. These results provide converging evidence that individuals with low or declining ability to benefit from motor involvement during memory encoding are characterized by low and reduced GM volume in regions critical for memory and motor functions along with altered WM microstructure.

Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison.

Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.

Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores.

The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.

Detection of SARS-CoV-2 with Solid-State CRISPR-Cas12a-Assisted Nanopores.

The outbreak of the SARS-CoV-2 caused the disease COVID-19 to spread globally. Specific and sensitive detection of SARS-CoV-2 facilitates early intervention and prevents the disease from spreading. Here, we present a solid-state CRISPR-Cas12a-assisted nanopore (SCAN) sensing strategy for the specific detection of SARS-CoV-2. We introduced a nanopore-sized counting method to measure the cleavage ratio of reporters, which is used as a criterion for positive/negative classification. A kinetic cleavage model was developed and validated to predict the reporter size distributions. The model revealed the trade-offs between sensitivity, turnaround time, and false-positive rate of the SARS-CoV-2 SCAN. With preamplification and a 30 min CRISPR Cas12a assay, we achieved excellent specificity against other common human coronaviruses and a limit of detection of 13.5 copies/µL (22.5 aM) of viral RNA at a confidence level of 95%. These results suggested that the SCAN could provide a rapid, sensitive, and specific analysis of SARS-CoV-2.

Nanofluidic charged-coupled devices for controlled DNA transport and separation.

Controlled molecular transport and separation is of significant importance in various applications. In this work, we presented a novel concept of nanofluidic molecular charge-coupled device (CCD) for controlled DNA transport and separation. By leveraging the unique field-effect coupling in nanofluidic systems, the nanofluidic molecular CCD aims to store charged biomolecules such as DNAs in discrete regions in nanochannels and transfer and separate these biomolecules as a charge packet in a bucket brigade fashion. We developed a quantitative model to capture the impact of nanochannel surface charge, gating voltage and frequency, molecule diffusivity, and gating electrode geometry on the transport and separation efficiency. We studied the synergistic effects of these factors to guide the device design and optimize the DNA transport and separation in a nanofluidic CCD. The findings in this study provided insight into the rational design and implementation of the nanofluidic molecular CCD.

CRISPR-based detection of SARS-CoV-2: A review from sample to result.

The current pandemic of the 2019 novel coronavirus (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concern. Rapid, affordable, and accurate diagnostics of SARS-CoV-2 is essential for early treatment and control of the disease spread. In the past few years, CRISPR technology has shown great potential for highly sensitive and specific molecular diagnostics. Amid the ongoing COVID-19 pandemic, there is an increasing interest in implementing CRISPR-based diagnostic principles to develop fast and precise methods for detecting SARS-CoV-2. In this work, we reviewed and summarized these CRISPR-based diagnostic systems as well as their characteristics and challenges. We also provided future perspectives of CRISPR-based sensing towards point-of-care molecular diagnosis applications.

Gene expression of angiogenesis and apoptotic factors in female BALB/c mice with breast cancer after eight weeks of aerobic training.

OBJECTIVES: Breast cancer is the most common cancer in women, caused by a disorder in the angiogenesis and apoptosis process. Exercise can affect the process of angiogenesis and apoptosis in the tumor tissue. Thus, the aim of the present study was to investigate the changes in angiogenesis and apoptotic factors in mice with breast cancer after 8 weeks of exercise training. MATERIALS AND METHODS: Sixteen females BALB/c mice (age: 3-5 weeks and weight: 17.1 ± 0.1 g) with breast cancer were randomly divided into two groups of aerobic training and control. The aerobic training included 8 weeks and 5 sessions per week of running with an intensity of 14-20 m.min-1. HIF-1α, VEGF, miR-21 and cytochrome C, Apaf-1, caspase-9, and caspase-3 gene expressions were examined by real-time PCR. Repeated measures ANOVA, Bonferroni's post hoc test, and independent samples t-test were used to analyze the data (P<0.05). RESULTS: The results showed that aerobic training reduced the growth of tumor volume and significantly reduced miR-21 gene expression. Aerobic training also significantly increased the gene expression of HIF-1α, cytochrome C, Apaf-1, caspase-9, and caspase-3, while changes in VEGF gene expression were not statistically significant. CONCLUSION: It appears that aerobic exercise training reduces tumor size and ameliorates breast cancer by reducing miR-21 gene expression, suppressing the apoptosis process, and reducing angiogenesis.

Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN).

Nucleic acid detection methods are crucial for many fields such as pathogen detection and genotyping. Solid-state nanopore sensors represent a promising platform for nucleic acid detection due to its unique single molecule sensitivity and label-free electronic sensing. Here, we demonstrated the use of the glass nanopore for highly sensitive quantification of single-stranded circular DNAs (reporters), which could be degraded under the trans-cleavage activity of the target-specific CRISPR-Cas12a. We developed and optimized the Cas12a assay for HIV-1 analysis. We validated the concept of the solid-state CRISPR-Cas12a-assisted nanopores (SCAN) to specifically detect the HIV-1 DNAs. We showed that the glass nanopore sensor is effective in monitoring the cleavage activity of the target DNA-activated Cas12a. We developed a model to predict the total experimental time needed for making a statistically confident positive/negative call in a qualitative test. The SCAN concept combines the much-needed specificity and sensitivity into a single platform, and we anticipate that the SCAN would provide a compact, rapid, and low-cost method for nucleic acid detection at the point of care.

The Role of Forced and Voluntary Training on Accumulation of Neural Cell Adhesion Molecule and Polysialic Acid in Muscle of Mice with Experimental Autoimmune Encephalomyelitis.

It has been suggested that depletion of adhesion molecules is one of the factors associated with or possibly responsible for multiple sclerosis (MS) progression. The aim of this study was to investigate the effect of forced and voluntary training before and after induction of experimental autoimmune encephalomyelitis (EAE) on accumulation of neural cell adhesion molecule (NCAM) and polysialic acid (PSA) in neuromuscular junction denervation in plantaris and soleus muscles in C57BL/6 female mice. A total of 40 female C57BL/6 mice, 10-week-old, were randomly divided into four groups, including induced control groups without EAE induction, induced EAE without training, and forced and voluntary training groups. Myelin oligodendrocyte glycoprotein peptide 35-55 (300 µg in saline; MOG 35-55; KJ Ross-Petersen ApS, Denmark) was injected subcutaneously at the base of the tail of each mouse. Clinical assessment of EAE was performed daily using a 15-point scoring system following immunization. Training groups performed the swimming program for 30 min/day, 5 times/week, for 4 weeks. Mice had access to a treadmill for one hour per day, 5times/week, for 4 weeks in individual cage. The mice were scarified, and the plantaris and soleus muscles were then isolated for investigation of proteins expression using IHC. An analysis of the preventive exercise (before) and recovery exercise (after) of the EAE was performed. Images of the stained sections were taken using a fluorescent microscope. Quantitative image analysis was performed using ImageJ software package. The obtained data from the mean percentage expression of PSA and NCAM in pre- and post-soleus and plantaris muscles showed that the highest and lowest expression levels of PSA and NCAM belonged to control and swim EAE (SE) groups, respectively. The low expression levels of PSA and NCAM were detected in rat with MS without intervention. In conclusion, the relationship between increasing levels of NCAM and PSA protein expression and voluntary and compulsory activity were detectable both in pre and post-soleus and plantaris. However, voluntary activity resulted in more expression levels of NCAM and PSA than that of compulsory. In conclusion, since it has been suggested that depletion of NCAM is one of the factors associated with or possibly responsible for MS progression, these findings show exercise MS progression may be reduced by increasing expression of exercise-related adhesion molecule such as NCAM and PSA (a glycan modification of the NCAM).

Microfluidic deformability-activated sorting of single particles.

Mechanical properties have emerged as a significant label-free marker for characterizing deformable particles such as cells. Here, we demonstrated the first single-particle-resolved, cytometry-like deformability-activated sorting in the continuous flow on a microfluidic chip. Compared with existing deformability-based sorting techniques, the microfluidic device presented in this work measures the deformability and immediately sorts the particles one-by-one in real time. It integrates the transit-time-based deformability measurement and active hydrodynamic sorting onto a single chip. We identified the critical factors that affect the sorting dynamics by modeling and experimental approaches. We found that the device throughput is determined by the summation of the sensing, buffering, and sorting time. A total time of ~100 ms is used for analyzing and sorting a single particle, leading to a throughput of 600 particles/min. We synthesized poly(ethylene glycol) diacrylate (PEGDA) hydrogel beads as the deformability model for device validation and performance evaluation. A deformability-activated sorting purity of 88% and an average efficiency of 73% were achieved. We anticipate that the ability to actively measure and sort individual particles one-by-one in a continuous flow would find applications in cell-mechanotyping studies such as correlational studies of the cell mechanical phenotype and molecular mechanism.

Preliminary Reliability and Validity of the Iranian Computerized Version of Memory Tasks of the Betula Study.

INTRODUCTION: This study aimed to evaluate the reliability and validity of an Iranian computerized memory battery modeled after the Betula study. METHODS: This study aimed to evaluate the reliability and validity of an Iranian computerized memory battery modeled after the Betula study ( Nilsson et al., 1997). The researchers developed this battery as an assessment tool in the Sepidar prospective cohort study. One hundred and ninety-nine participants aged 19-83 years were tested extensively on different aspects of memory. Exploratory factor analysis of the data demonstrated factors similar to those reported by the Betula study. RESULTS: The authors succeeded to converge the cross-sectional findings of the study and the data from longitudinal studies of memory aging by correcting possible cohort effects. Investigating age differences in episodic and semantic memory factor scores corrected by education and socioeconomic status revealed no significant difference between younger and older adults before ages 53 to 60, though linear age-related declines existed thereafter. CONCLUSION: The results support the reliability and construct validity of this computerized battery for memory assessment in Iranian adults.

The effects of different proxies of cognitive reserve on episodic memory performance: aging study in Iran.

OBJECTIVE: The main aim of the present study is to investigate the association between different measures of cognitive reserve including bilingualism, mental activities, type of education (continuous versus distributed), age, educational level, and episodic memory in a healthy aging sample. METHODS: Four hundred and fifteen participants aged between 50 and 83 years participated in this cross-sectional study and were assessed with the Psychology Experimental Building Language Test battery tapping episodic memory. Demographic variables were collected from a questionnaire designed by the research team. RESULTS: Compared to participants with continuous type of education, those with distributed type performed better in tests of episodic memory, while no differences were found between bilingual and monolingual participants. We additionally found that age negatively predicts episodic memory, whereas playing mind teasers and educational level have positive relationships with episodic memory. CONCLUSIONS: Our results indicate that higher cognitive reserve, as measured by distributed educational training, higher level of education, and doing regular mental activities, is associated with better performance on episodic memory tasks in older adults. These results were discussed in connection with successful aging and protection against memory decline with aging.

Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing.

Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.

Quantitative Analysis of Factors Affecting the Event Rate in Glass Nanopore Sensors.

While the solid-state nanopore sensors have shown exceptional promise with their single-molecule sensitivity and label-free operations, one of the most significant challenges in the nanopore sensor is the limited analyte translocation event rate that leads to prolonged sensor response time. This issue is more pronounced when the analyte concentration is below the nanomolar (nM) range, owing to the diffusion-limited mass transport. In this work, we systematically studied the experimental factors beyond the intrinsic analyte concentration and electrophoretic mobility that affect the event rate in glass nanopore sensors. We developed a quantitative model to capture the impact of nanopore surface charge density, ionic strength, nanopore geometry, and translocation direction on the event rate. The synergistic effects of these factors on the event rates were investigated with the aim to find the optimized experimental conditions for operating the glass nanopore sensor from the response time standpoint. The findings in the study would provide useful and practical insight to enhance the device response time and achieve a lower detection limit for various glass nanopore-sensing experiments.

Calibration-Free Nanopore Digital Counting of Single Molecules.

Nanopore sensor conceptually represents an ideal single molecule counting device due to its unique partitioning-free, label-free electronic sensing. Existing theories and experiments have shown that sample concentration is proportional to the molecule translocation rate. However, a detailed nanopore geometry and size characterization or a calibration curve of concentration standards are often required for quantifying the unknown sample. In this work, we proposed and validated a calibration-free nanopore single molecule digital counting method for isolated molecule quantification. With the background ions as the in situ references, the molecule translocation rates can be normalized to the ion translocation rates (i.e., baseline current). This in situ reference alleviates the requirement for knowing the nanopore geometry and size or generating a calibration curve. In recognition of this effect, we developed a quantitative model for nanopore quantification without the need for prior knowledge of experimental conditions such as nanopore geometry, size, and applied voltage. This model was experimentally validated for different nanopores and DNA molecules with different sizes. We anticipate this calibration-free digital counting approach would provide a new avenue for nanopore-based molecule sensing.