In spite of the enormous potential of CRISPR/Cas in basic and applied science, the levels of undesired genomic modifications cells still remain mostly unknown and controversial. Nowadays, the efficiency and specificity of the cuts generated by CRISPR/Cas is the main concern. However, there are also other potential drawbacks when DNA donors are used for gene repair or gene knock-ins. These GE strategies should take into account not only the specificity of the nucleases, but also the fidelity of the DNA donor to carry out their function. The current methods to quantify the fidelity of DNA donor are costly and lack sensitivity to detect illegitimate DNA donor integrations. In this work, we have engineered two reporter cell lines (K562_SEWAS84 and K562GWP) that efficiently quantify both the on-target and the illegitimate DNA donor integrations in a WAS-locus targeting setting. K562_SEWAS84 cells allow the detection of both HDR-and HITI-based donor integration, while K562GWP cells only report HDR-based GE. To the best of our knowledge, these are the first reporter systems that allow the use of gRNAs targeting a relevant locus to measure efficacy and specificity of DNA donor-based GE strategies. By using these models, we have found that the specificity of HDR is independent of the delivery method and that the insertion of the target sequence into the DNA donor enhances efficiency but do not affect specificity. Finally, we have also shown that the higher the number of the target sites is, the higher the specificity and efficacy of GE will be.

Common variable immunodeficiency (CVID) results in defective B cell differentiation and impaired antibody production and is the most common symptomatic primary immunodeficiency. Our aim was to evaluate the correlation among B cell subgroups, κ-deleting recombination excision circle (KREC) copy numbers, and clinical and immunological data of the patients with CVID, and evaluate the patients according to classifications currently available to define the role of KREC copy numbers in the diagnosis of CVID. KREC analysis was performed using a quantitative real-time polymerase chain reaction assay, and B cell subgroups were measured by flow cytometry. The median age of the patients (n = 30) was 25 (6-69) years. Parental consanguinity ratio was 33%. The median age at diagnosis was 15 (4-59), and follow-up period was 6 (1-37) years. CD19+ and CD4+ cell counts at the time of diagnosis were low in 66.7% and 46.7% of the patients, respectively. CD19+ cell counts were positively correlated with KREC copy numbers in patients and healthy controls. CD19+ cell counts and KREC copy numbers were significantly reduced in CVID patients compared to healthy controls as expected. KRECs are quantitative markers for B cell defects. We found low CD4+ cell numbers, recent thymic emigrants, and lymphopenia in some of the patients at diagnosis, which reminds the heterogeneity of CVID\'s etiology. In this study, a positive correlation was shown between CD19+ cell counts and KREC copy numbers. Low KREC copy numbers indicated B cell deficiency; however, high KREC copy numbers were not sufficient to rule out CVID.

Currently there is a lack in fundamental understanding of disease progression of most neurodegenerative diseases, and, therefore, treatments and preventative measures are limited. Consequently, there is a great need for adaptable, yet robust model systems to both investigate elementary disease mechanisms and discover effective therapeutics. We have generated a Tol2 Gateway-compatible toolbox to study neurodegenerative disorders in zebrafish, which includes promoters for astrocytes, microglia and motor neurons, multiple fluorophores, and compatibility for the introduction of genes of interest or disease-linked genes. This toolbox will advance the rapid and flexible generation of zebrafish models to discover the biology of the nervous system and the disease processes that lead to neurodegeneration.

Apoptosis is a physiological program of cell suicide conserved in invertebrates and vertebrates. Apoptosis is crucial to the normal development of organisms and in tissue homeostasis by promoting elimination of unwanted cells, including damaged or virus-infected cells. Due to the importance of programmed cell death for the survival of the organism, a tight regulation is exerted at various activation levels of the cell-death machinery. The utilization of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) to identify genes that inhibit the apoptotic process will be described using a transfection-based approach, illustrated by identification of the p49 gene.

Mast cells are the crucial effector cells for allergic reactions. They are activated through the aggregation of the high-affinity IgE receptor (FcεRI) with allergen and allergen-specific IgE. Tyrosine phosphorylation of FcεRI subunits and various signaling proteins is an initial triggering event, leading to the activation of several signaling pathways in mast cells. Much has been learned from analysis of mast cells derived from gene-targeted mice. Therefore, in this chapter we will first describe how to generate mast cells from mouse bone marrow cells and how to correct the genetic defect by retroviral transduction. Then we will describe how to assess early activation events by measuring several protein-tyrosine kinases (PTKs) and serine/threonine kinases (PS/TKs) such as Akt (protein kinase B), protein kinase C (PKC), and JNK. As signal transduction is highly dependent on protein-protein interactions, we will describe experimental details of co-immunoprecipitation methods that are used to confirm such interactions.

BACKGROUND: Phase 1 evaluation of the VRC HIV DNA and rAd5 vaccines delivered intramuscularly (i.m.) supported proceeding to a Phase 2 b efficacy study. Here we report comparison of the i.m., subcutaneous (s.c.) and intradermal (i.d.) routes of administration.
METHODS: Sixty subjects were randomized to 6 schedules to evaluate the i.m., s.c. or i.d. route for prime injections. Three schedules included DNA primes (Wks 0,4,8) and 3 schedules included rAd5 prime (Wk0); all included rAd5 i.m. boost (Wk24). DNA vaccine dosage was 4 mg i.m. or s.c., but 0.4 mg i.d., while all rAd5 vaccinations were 1010 PU. All injections were administered by needle and syringe.
RESULTS: Overall, 27/30 subjects completed 3 DNA primes; 30/30 subjects completed rAd5 primes. Mild local pruritus (itchiness), superficial skin lesions and injection site nodules were associated with i.d. and s.c., but not i.m. injections. All routes induced T-cell and antibody immune responses after rAd5 boosting. Overall, >95% had Env antibody and >80% had Env T-cell responses.
CONCLUSIONS: The pattern of local reactogenicity following i.d. and s.c. injections differed from i.m. injections but all routes were well-tolerated. There was no evidence of an immunogenicity advantage following s.c. or i.d. delivery, supporting i.m. delivery as the preferred route of administration.
BACKGROUND: Clinicaltrials.gov NCT00321061.

BACKGROUND: DNA vaccine immunogenicity has been limited by inefficient delivery. Needle-free delivery of DNA using a CO2-powered Biojector® device was compared to delivery by needle and syringe and evaluated for safety and immunogenicity.
METHODS: Forty adults, 18-50 years, were randomly assigned to intramuscular (IM) vaccinations with DNA vaccine, VRC-HIVDNA016-00-VP, (weeks 0, 4, 8) by Biojector® 2000™ or needle and syringe (N/S) and boosted IM at week 24 with VRC-HIVADV014-00-VP (rAd5) with N/S at 10(10) or 10(11) particle units (PU). Equal numbers per assigned schedule had low (≤500) or high (>500) reciprocal titers of preexisting Ad5 neutralizing antibody.
RESULTS: 120 DNA and 39 rAd5 injections were given; 36 subjects completed follow-up research sample collections. IFN-γ ELISpot response rates were 17/19 (89%) for Biojector® and 13/17 (76%) for N/S delivery at Week 28 (4 weeks post rAd5 boost). The magnitude of ELISpot response was about 3-fold higher in Biojector® compared to N/S groups. Similar effects on response rates and magnitude were observed for CD8+, but not CD4+ T-cell responses by ICS. Env-specific antibody responses were about 10-fold higher in Biojector-primed subjects.
CONCLUSIONS: DNA vaccination by Biojector® was well-tolerated and compared to needle injection, primed for greater IFN-γ ELISpot, CD8+ T-cell, and antibody responses after rAd5 boosting.
BACKGROUND: ClinicalTrials.gov NCT00109629.

Gene therapy and vaccines are rapidly developing field in which recombinant nucleic acids are introduced in mammalian cells for enhancement, restoration, initiation or silencing biochemical function. Beside simplicity in manipulation and rapid manufacture process, plasmid DNA-based vaccines have inherent features that make them promising vaccine candidates in a variety of diseases. This present review focuses on the safety concern of the genetic elements of plasmid such as propagation and expression units as well as their host genome for the production of recombinant plasmid DNA. The highlighted issues will be beneficial in characterizing and manufacturing plasmid DNA for save clinical use. Manipulation of regulatory units of plasmid will have impact towards addressing the safety concerns raised in human vaccine applications. The gene revolution with plasmid DNA by alteration of their plasmid and production host genetics will be promising for safe delivery and obtaining efficient outcomes.

OBJECTIVE: To immunize the mice using the rAd/MDC-VP1 prime-pcDNA3/MDC-VP1 boost strategy and observe its immunological effect against Coxsackievirus B3(CVB3).
METHODS: BALB/c mice were randomly divided into four groups: PBS group, rAd/MDC-VP1 group, pcDNA3/MDC-VP1 group and rAd/MDC-VP1 prime-pcDNA3/MDC-VP1 boost group. Mice in each group were immunized intramuscularly. The titers of serum IgG and neutralizing antibody were tested by ELISA and trace neutralization assays respectively. The Lymphocytes proliferation activity and specific CTL cytotoxic activity were tested by CCK-8 assay. The mice in each group were challenged with lethal dose of CVB3, and the serum virus titer was assayed and the protection efficacy against Coxsackievirus infection was observed.
RESULTS: It was observed that the titers of CVB3 VP1 specific IgG and neutralizing antibody, non-specific lymphocytic proliferation activity and specific lymphocytic CTL cytotoxic activity of the rAd/MDC-VP1 prime-pcDNA3/MDC-VP1 boost group were much higher than those of the rest groups(P<0.05), what\'s more, after CVB3 challenged, the serum virus titer of this group was lower and the protection rate(41.67%) was higher (P<0.05).
CONCLUSIONS: Both the cellular and humoral immune responses in mice could be significantly enhanced by the rAd/MDC-VP1 prime-pcDNA3/MDC-VP1 boost strategy and the protection rate after challenged by lethal dose of virus could be increased.

In cystic fibrosis, genomic variants can result in defective processing of the CFTR precursor mRNA. Due to the complexity of the splicing process, the evaluation of their pathological effect is an important aspect both in the diagnostic field and in the study of basic regulatory mechanism. Efficient and correct splicing of CFTR relies on a complex process that includes recognition within the nascent transcripts of a series of different splicing regulatory elements that frequently overlap with the coding sequences. Identification of these elements is essential to determine the pathological impact of splicing-affecting genomic variants. In this chapter, to evaluate the effect of CFTR DNA variations on the pre-mRNA splicing process, different tools based on hybrid minigenes will be described.