TA Cloning Research Articles

Synthesis and molecular cloning of antimicrobial peptide chromogranin A N-46 gene using conventional PCR

BackgroundChromogranin A N-46 (CGA-N46) is an antimicrobial peptide (AMP) consisting of partial N terminus of human chromogranin A. ObjectiveSynthesis and molecular cloning the gene encoding CGA-N46. Materials and methodsThe coding sequence of CGA-N46 gene was synthesized using free bioinformatics tool (Gene2Oligo) that allows the development of in vitro gene synthesis. In this study two methods have been established, stepwise PCR and One Step Simplified Gene Synthesis (SGS) methods. The gene was obtained in stepwise PCR by three steps: 1st PCR to generate short DNA fragments using specific oligonucleotides, 2nd step was the overlap extension PCR (OE-PCR) to bond the short DNA fragments and the final step was the whole gene assembly using amplification primers. Nevertheless, the SGS method was achieved by only one step PCR with various concentrations of oligonucleotides (1000, 500, 250, 100, 50 and 25 nM) and amplification primers (400 nM). In order to achieve a DNA library for future studies, the obtained CGA-N46 gene was cloned into pCR-II TOPO TA cloning vector to create a recombinant vector which was preserved in Escherichia coli (E. coli) TOP10 bacterial stock using transformation process. ResultsThe stepwise PCR method generated a sharp band at expected MW (150 bp). In addition, the SGS method gave one faint band at 1 μM of oligonucleotides. Digestion and PCR analysis revealed that the CGA-N46 gene was successfully cloned in pCR-II TOPO TA cloning vector.

PGP-B2E, a Recombinant Compatible TA/TB-Ligation Vector for Rapid and Inexpensive Gene Cloning.

DNA cloning is the basic step for different fields of life science, and many efforts have been made to simplify this procedure. In this study, we report two general purpose plasmids (pGP), pGP-XB2E and pGP-B2E, for rapid and cost-effective construct of basic clones. The BciVI and XcmI cleavage sites are designed in pGP-XB2E to test plasmid linearization efficiency. The plasmid has better linearization efficiency by using BciVI which could almost completely digest 2μg plasmid in 10min with only one-tenth the recommended enzyme concentration. In order to further optimize the pGP-XB2E, a new plasmid, pGP-B2E, which removed XcmI cleavage site was designed. This vector is highly efficient for cloning PCR products up to 1812bp, and the number of colonies was about five times that of pGP-XB2E. In addition to TA cloning, blunt-end PCR products with T ended in the primer could be positively linked to the T-vector pGP-B2E without A-tailing treatment (TB cloning). Moreover, as an entry vector, pGP-B2E was also compatible for gateway recombination reaction without frameshift mutations. In general, this vector provides a universal, quick, and cost-efficient method for basic molecular cloning.

Apple polysaccharide could promote the growth of Bifidobacterium longum

It is widely accepted that regulating microbiome could improve human health. We previously observed apple polysaccharide (AP) reversed high-fat-induced microbial dysbiosis, but the mechanism remains to be elucidated.In this study, the function of AP in vitro was evaluated in Bifidobacterium longum (B. longum) and Lactobacillus rhamnosus (L. rhamnosus). The effects of AP on the composition of fecal bacteria of normal SD rats were investigated by qPCR, TA cloning and 16S sequencing. 0.125–2% AP showed no significant effect on the growth of B. longum and L. rhamnosus. DNA concentration of fecal bacteria cultured with 1% AP was significantly higher than that of control group. qPCR revealed that the number of Bifidobacterium and Lactobacillus in fecal flora incubated by 1% AP was significantly higher than that of control group. Three strains of escherichia coli (E. coli) in fecal bacteria were screened out and analyzed. AP can be utilized by one E. coli and the metabolic products of AP could enhance the proliferation of B. longum.These data suggest that AP could promote the growth of B. longum indirectly, and provide another basis to understand the health care function of apple.

Targeted knockout of <italic>Kcna3</italic> and its function in Jurkat T cells using the CRISPR/Cas9 system

To explore the use of the CRISPR/Cas9 system to target Kv1.3 channel-encoding genes Kcna3 and elucidate the pathophysiological function mediated by Kv1.3 channels in Jurkat T cells. The first exon sgRNA of human Kcna3 in pX458-sgRNA recombinant vector was transferred into human Jurkat T cells via electroporation. T7EN1 digestion, Genomic PCR products and TA cloning sequencing, Western blot, and functional assays, such as electrophysiology, live-cell calcium imaging and ELISA were used to validate Kcna3 knockout effect in Jurkat T cells. The results of the sequencing analysis showed that the CRISPR/Cas9 recombinant plasmids pX458-sgRNA targeting Kcna3 were successfully constructed. The designed sgRNA2 can efficiently cleave genomic DNA. Kv1.3 protein expression could not be detected using Western blot analysis. Genomic PCR products and TA cloning sequencing showed the presence of Indel mutation. Whole-cell patch clamp experiments showed that Kv1.3 channel currents could not be recorded in Kcna3 knockout Jurkat T cells. Live-cell calcium imaging showed that the increase in free Ca2+ concentration in Kcna3 knockout Jurkat T cells was significantly lower than that in wild type Jurkat T cells. ELISA results showed that the IL-2 level of Kcna3 knockout Jurkat T cells was significantly decreased compared with that in wild-type Jurkat T cells ( P Kcna3 in Jurkat T cells using the CRISPR/Cas9 system strongly proved that Kv1.3 mediated the immune inflammatory response of Jurkat T cells, which provides a novel cell model for further study of the pathophysiological function of the Kv1.3 channel.

Rapid generation and selection of Cas9-engineering TRP53 R172P mice that do not have off-target effects

BackgroundGenetic mutations cause severe human diseases, and suitable animal models to study the regulatory mechanisms involved are required. The CRISPR/Cas9 system is a powerful, highly efficient and easily manipulated tool for genetic modifications. However, utilization of CRISPR/Cas9 to introduce point mutations and the exclusion of off-target effects in mice remain challenging. TP53-R175 is one of the most frequently mutated sites in human cancers, and it plays crucial roles in human diseases, including cancers and diabetes.ResultsHere, we generated TRP53-R172P mutant mice (C57BL/6 J, corresponding to TP53-R175P in humans) using a single microinjection of the CRISPR/Cas9 system. The optimal parameters comprised gRNA selection, donor designation (silent mutations within gRNA region), the concentration of CRISPR components and the cellular sites of injection. TRP53-R172P conversion was genetically and functionally confirmed. Combination of TA cloning and Sanger sequencing helped identify the correctly targeted mice as well as the off-target effects in the engineered mice, which provide us a strategy to select the on-target mice without off-target effects quickly and efficiently.ConclusionsA single injection of the this optimized CRISPR/Cas9 system can be applied to introduce particular mutations in the genome of mice without off-target effects to model various human diseases.

Genetic and chromosomal variation-caused inconsistencies in two parental tests

Two special cases were reported where inconsistency between children and the fathers were observed at FGA locus. Regular additional STR tests were performed and no more inconsistency was observed in the first case. Through the following TA cloning and sequencing, the first case turned to be a two-step mutation between child and father. In the second case, however, one more inconsistency was found in the additional test at D4S2366, which was on Chr. 4 as well. Then, seven randomly selected STR-loci on Chromosome 4 were analyzed, indicating a possible maternal uniparental disomy (UPD) in the child with normal phenotype. This study emphasizes gene or chromosomal variations may mislead parentage test, especially variations like UPD that are relatively unfamiliar to investigators. If all the inconsistent loci are on the same chromosome, investigators should take UPD into consideration, and further tests, like chromosomal-specific STR-typing, should be applied to prevent pseudo-exclusions.

ADRB2 Gene Knockout in Human Primary T Cells by Multiple sgRNAs Construced using CRISPR/Cas9 Technology

To knockout ADRB2 gene rapidly and efficiently in human primary T cells by using CRISPR/Cas9 technology and multiple sgRNAs strategy. Six paired-sgRNAs, which were designed to target the 5' constitutive coding exons of ADRB2 gene, were cloned into pGL3-U6-sgRNA-PGK-Puro vector separately. The expre-ssion vectors containing the single sgRNAs were constructed and transiently co-transfected into HEK-293T cell line with Cas9 expression vector. The sgRNA-mediated cleavage efficiency was tested by T7EN I digestion assay. Concatenating four highly efficient paired sgRNAs were cloned into pGL3-U6-sgRNA-ccdB-EF1α-Puro expression vector. The reco-mbinant plasmid allows the cells to express 4 sgRNAs, which target different sites on the ADRB2 genomic locus. The cleavage efficiency and mutation model were tested by T7EN I digest assay and T-A cloning technique. Multiple sgRNAs plasmid and Cas9 plasmid was transiently transferred into human primary T cells by electroporation. Flow cytometry (FCM) was used to detect the knockout efficiency of β2 adrenergic receptor (β2-AR). The results of T7EN I digestion and TA cloning sequencing showed that the multiple sgRNAs strategy could obtain more abundant mutation types and higher gene editing efficiency than single sgRNA. In addition to the deletion and insertion of bases, large fragment DNA deletions and inversions could be observed. All of the random 10 TA clones for detection were genetically modified, thus the mutation efficiency was as high as 100%. FCM assay showed that 43.09% of the cells in the control T cells were β2-AR positive, but the proportion of β2-AR positive cells in the multiple sgRNAs electrotransformed T cells decreased to 25.61%. A method, which is simple and operable, for knocking out β2-AR in human primary T cells has been established preliminarily. The results are helpful for the further study of the role of β2-AR in human T cells.

Expression patterns of ectodysplasin and ectodysplasin receptor during early dental development in zebrafish

This study aims to study the expression patterns of ectodysplasin (EDA) and ectodysplasin receptor (EDAR) during the early development of zebrafish and provide a foundation for further research of the Eda signaling pathway in tooth development. Total RNA was extracted from zebrafish embryos at 48 hours postfertilization (hpf) and then reverse transcribed for cDNA library generation. The corresponding RNA polymerase was selected for the synthesis of the digoxin-labeled antisense mRNA probe of zebrafish pharyngeal tooth specific marker dlx2b and Eda signaling-associated genes eda and edar in vitro. The three sequences were ligated into a pGEMT vector with a TA cloning kit, and polymerase chain reaction (PCR) was applied to linearize the plasmid. The resultant PCR sequences were used as templates for synthesizing Dig-labeled mRNA probe dlx2b, eda, and edar. Zebrafish embryos were collected at 36, 48, 56, 60, 72, and 84 hpf, then whole mount in situ hybridization was performed for the detection of eda and edar expression patterns. Then, their expression patterns at 72 hpf were compared with the expression pattern of dlx2b. The mRNA antisense probes of dlx2b, eda, and edar were successfully obtained. The positive signals of eda and edar were observed in zebrafish pharyngeal tooth region at 48-72 hpf and thus conform to the signals of dlx2b in the positive regions. The ligand eda and edar, which are associated with the Eda signaling pathway, are strongly expressed only at the pharyngeal tooth region in zebrafish from tooth initiation to the morphogenesis stage. Thus, the Eda signaling pathway may be involved in the regulation of the early development of zebrafish pharyngeal teeth.

Abstract 5237: Development of a gene expression database of renal cell carcinoma cases by NGS-combined HiCEP to identify tumor markers

Abstract Objectives: High coverage expression profiling (HiCEP) is an AFLP-based comprehensive gene expression analysis technique invented in Japan. HiCEP has two unique characteristics. First, it can detect low amounts of mRNA with high sensitivity and reliability. Second, HiCEP enables highly quantitative and reproducible mRNA expression analyses. However, it requires complicated processes, including TA cloning of isolated transcripts, to obtain sequence information on detected peaks. We performed next-generation sequencing (NGS)-combined HiCEP and tried to establish a gene expression database of renal cell carcinoma (RCC) cases to identify effective tumor markers. Materials and methods: We collected cancerous and macroscopically non-cancerous regions from 83 RCC cases. Of these, six cases with clear cell RCC were analyzed by HiCEP. Total RNA was extracted from the cancerous and non-cancerous tissues of six clear cell RCC cases, and transcribed to cDNA. The cDNA was synthesized and subjected to digestion with the restriction enzymes MspI or MseI, followed by adapter ligation. Selective PCR by 256 kinds of primer pairs was used to amplify the HiCEP fragments, and products with fluorescently-labeled primer were then analyzed by capillary electrophoresis. HiCEP fragments were sequenced using a next-generation sequencer (ion PGM, Thermo Fisher Scientific). We compared the expression levels of HiCEP peaks in cancerous tissues with those in non-cancerous tissues. Results: We detected several HiCEP peaks in cancerous tissues that showed five times higher expression than in normal tissues. We determined the sequences of the HiCEP fragments by NGS, and developed the first ever cancerous tissue HiCEP fragment database. Conclusion: We successfully established an RCC gene expression database by NGS-combined HiCEP. We are now performing replication analyses and further analyses of blood samples from the same RCC cases to be able to identify diagnostic and prognostic markers of RCC. Citation Format: Makoto Kawaguchi, Hirotaka Matsuo, Ryoko Araki, Seiko Shimizu, Mikiya Takao, Akiyoshi Nakayama, Yosuke Kitamura, Masumi Abe, Keiichi Ito, Nariyoshi Shinomiya. Development of a gene expression database of renal cell carcinoma cases by NGS-combined HiCEP to identify tumor markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5237.

CRISPR/Cas9 Ribonucleoprotein-mediated Precise Gene Editing by Tube Electroporation.

Gene editing nucleases, represented by CRISPR-associated protein 9 (Cas9), are becoming mainstream tools in biomedical research. Successful delivery of CRISPR/Cas9 elements into the target cells by transfection is a prerequisite for efficient gene editing. This protocol demonstrates that tube electroporation (TE) machine-mediated delivery of CRISPR/Cas9 ribonucleoprotein (RNP), along with single-stranded oligodeoxynucleotide (ssODN) donor templates to different types of mammalian cells, leads to robust precise gene editing events. First, TE was applied to deliver CRISPR/Cas9 RNP and ssODNs to induce disease-causing mutations in the interleukin 2 receptor subunit gamma (IL2RG) gene and sepiapterin reductase (SPR) gene in rabbit fibroblast cells. Precise mutation rates of 3.57%-20% were achieved as determined by bacterial TA cloning sequencing. The same strategy was then used in human iPSCs on several clinically relevant genes including epidermal growth factor receptor (EGFR), myosin binding protein C, cardiac (Mybpc3), and hemoglobin subunit beta (HBB). Consistently, highly precise mutation rates were achieved (11.65%-37.92%) as determined by deep sequencing (DeepSeq). The present work demonstrates that tube electroporation of CRISPR/Cas9 RNP represents an efficient transfection protocol for gene editing in mammalian cells.

Intron retention as an alternative splice variant of the cattle ANGPTL6 gene

Angiopoietin-like protein 6, which is encoded by ANGPTL6 gene (also known as angiopoietin growth factor, AGF), has been extensively characterized with regard to its proposed functions as angiogenesis and energy metabolism. The present results showed the occurrence of alternative splicing by intron retention (IR) event in the bovine ANGPTL6 gene (bANGPTL6). By means of RT-PCR, TA clone and sequencing, we have shown that the bANGPTL6 gene has a splice variant generated by the retention of its partial intron 3. The computational analysis of the bANGPTL6 genomic sequence showed that its intron 3 has a high percentage of GC (62.31%) and a length of 199 nt, characteristics that have been associated with an IR event. The IR event does not interfere with the coding region as the bANGPTL6 prepropeptide is entirely coded in the third exon. Additionally, both the intronless (namely, bANGPTL6α) and intron-retaining (namely, bANGPTL6β) ANGPTL6 transcripts are constitutively co-expressed in the bovine liver. Further, the relative expression level of different variants in liver was tested by both semi-RT-PCR and RT-qPCR methods. The results suggested bANGPTL6β are significantly higher than bANGPTL6α. Overall, our findings will be helpful for studies on the molecular mechanism of IR events and the functions of ANGPTL6 gene. Specially, bANGPTL6β gene probably contributes to a new target for treatment of obesity and obesity-related diseases.

A substitution in the pre-S1 promoter region is associated with the viral regulation of hepatitis B virus

BackgroundMuch evidence has demonstrated the influence of Hepatitis B virus (HBV) mutations on the clinical course of HBV infection. As large (L) protein plays a crucial role for viral entry, we hypothesized that mutations in the pre-S1 promoter region might affect the expression of L protein and subsequently change the biological characters of virus.MethodsPatients infected with genotype C HBV were enrolled for analysis. HBV DNA sequences were inserted into a TA cloning vector and analyzed. To evaluate the effects of mutations in the pre-S1 promoter region, promoter activity and the expression of mRNA and L protein were analyzed using HepG2 cells.ResultsIn total, 35 patients were enrolled and 13 patients (37.1%) had a single base substitution in the pre-S1 promoter region; the most frequent substitution was a G-to-A substitution at the 2765th base (G2765A) in the Sp1 region. The HBV viral load showed a negative correlation with the substitution ratio of the Sp1 region or G2765A (r = − 0.493 and − 0.473, respectively). Among those with a viral load ≤5.0 log IU/ml, patients with the G2765A substitution showed a significantly lower HBV viral load than those with the wild-type sequence. HepG2 cells transfected with the G2765A substitution vector showed reduced luciferase activity of the pre-S1 promoter, as well as reduced expression of pre-S1 mRNA and L protein. Furthermore, the G2765A substitution greatly reduced the L protein expression level of vector-produced virus particles.ConclusionG2765A substitution in the pre-S1 promoter reduced the expression of L protein and resulted in a low viral load and less severe disease in chronic HBV infections.

High-Efficiency CRISPR/Cas9-Mediated Gene Editing in Honeybee (Apis mellifera) Embryos.

The honeybee (Apis mellifera) is an important insect pollinator of wild flowers and crops, playing critical roles in the global ecosystem. Additionally, the honeybee serves as an ideal social insect model. Therefore, functional studies on honeybee genes are of great interest. However, until now, effective gene manipulation methods have not been available in honeybees. Here, we reported an improved CRISPR/Cas9 gene-editing method by microinjecting sgRNA and Cas9 protein into the region of zygote formation within 2 hr after queen oviposition, which allows one-step generation of biallelic knockout mutants in honeybee with high efficiency. We first targeted the Mrjp1 gene. Two batches of honeybee embryos were collected and injected with Mrjp1 sgRNA and Cas9 protein at the ventral cephalic side and the dorsal posterior side of the embryos, respectively. The gene-editing rate at the ventral cephalic side was 93.3%, which was much higher than that (11.8%) of the dorsal-posterior-side injection. To validate the high efficiency of our honeybee gene-editing system, we targeted another gene, Pax6, and injected Pax6 sgRNA and Cas9 protein at the ventral cephalic side in the third batch. A 100% editing rate was obtained. Sanger sequencing of the TA clones showed that 73.3% (for Mrjp1) and 76.9% (for Pax6) of the edited current-generation embryos were biallelic knockout mutants. These results suggest that the CRISPR/Cas9 method we established permits one-step biallelic knockout of target genes in honeybee embryos, thereby demonstrating an efficient application to functional studies of honeybee genes. It also provides a useful reference to gene editing in other insects with elongated eggs.

A novel series of high-efficiency vectors for TA cloning and blunt-end cloning of PCR products

An efficient PCR cloning method is indispensable in modern molecular biology, as it can greatly improve the efficiency of DNA cloning processes. Here, I describe the development of three vectors for TA cloning and blunt-end cloning. Specifically, pCRT and pCRZeroT were designed to improve the efficiency of TA cloning. pCRZeroT can also be used with pCRZero to facilitate blunt-end cloning using the ccdB gene. Using pCRZero and pCRZeroT and applying the Golden Gate reaction, I developed a direct PCR cloning protocol with non-digested circular vectors and PCR products. This direct PCR cloning protocol yielded colony-formation rates and cloning efficiencies that are comparable with those obtained by conventional PCR cloning with pre-digested vectors and PCR products. The three plasmids I designed are available from Addgene (https://www.addgene.org/).

Cloning, Expression and Purification of DegQ Protease, a Bacterial Analog to Pregnancy Related Serine Protease (HtrA3)

The High Temperature Requirement A (HtrA) family of enzymes are a diverse group of serine proteases, present in both prokarya and eukarya, and are generally responsible for the degradation of misfolded proteins. The dysregulation of HtrA3 in human somatic cells gives rise to various forms of cancer and preeclampsia. DegQ is a bacterial analog to HtrA3 found in the periplasm of E. coli and has the properties of an HtrA protease: it is a serine endopeptidase that works to protect the cell during high temperature by degrading specific damaged proteins. Currently, the interactions that dictate which specific substrates DegQ degrades are unknown. Insights into this interaction could lay the foundation for studying the interactions of the human HtrA3 protease. Previously, four N‐terminal truncated versions of DegQ were identified in prokarya, indicating an N‐terminal signaling sequence. Substrate cleavage in each of these variants has not been characterized, therefore, the goal of this study is to select for the active version to further characterize. Initial experiments utilized molecular cloning, protein expression and purification to obtain each variant. Affinity tags, such as the histidine‐tag, has greatly simplified the purification of recombinant proteins. However, the presence of such tags can interfere with a protein's biological function. To circumvent this problem, experiments were designed to obtain the protein without the use of a tag. To this end, four PCR forward primers were designed for the appropriate coding region using E. coli as template genomic DNA, each with an NdeI site engineered at the 5′ end. The reverse primer for each was the same, and designed with a stop codon followed by a SacI site at the 3′ end. The PCR product was then ligated into a linearized dephosphorylated pGEM vector using TA cloning. Orientation of the gene was determined through the use of restriction enzyme cuts. This vector and the pET24b expression vector were digested with NdeI and the gene was ligated into the pET24b vector. Orientation was again tested using SacI sites, and analyzed by gel electrophoresis. Based upon the theoretical mass distribution of the cleaved oligonucleotides from the gel electrophoresis, plasmids with positive results were purified for verification through sanger sequencing. Each pET24b‐DegQ vector was individually transformed into BL21(DE3) E. coli cells, grown in LB broth and expressed with 0.1 mM IPTG for 4 hours at room temperature. Protein was purified using a DEAE‐sephacel column, followed by an ammonium sulfate precipitation, and further purification on a G‐75‐sephadex size exclusion gel filtration column. Ultimately the proteases were purified to homogeneity without the use of an affinity tag for comparison of proteolytic activity.Support or Funding InformationMWSU Department of Chemistry MWSU Department of Biology MWSU PORTAL grantThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

DNA barcoding detects floral origin of Indian honey samples.

The unique medicinal and nutritional properties of honey are determined by its chemical composition. To evaluate the quality of honey, it is essential to study the surrounding vegetation where honeybees forage. In this study we used conventional melissopalynological and DNA barcoding techniques to determine the floral source of honey samples collected from different districts of the state of Mizoram, India. Pollen grains were isolated and genomic DNA was extracted from the honey samples. PCR amplification was carried out using universal barcode candidates ITS2 and rbcL to identify the plant species. Furthermore, TA cloning was carried out to screen the PCR amplicon libraries to identify the presence of multiple plant species. Results from both the melissopalynological and DNA barcoding analyses identified almost exactly the same 22 species, suggesting that both methods are suitable for analysis. However, DNA barcoding is easier and widely practiced. Hence, it can be concluded that DNA barcoding is a useful tool in determining the medicinal and commercial value of honey.

Construction of eukaryotic expression vector for human platelet CD36 gene 220C>T and 429+4insg variants and analysis of their expressions in HEK293T cells

To construct eukaryotic expression vectors for human platelet CD36 gene 220 C>T and 429+4insg variants and analyze their expressions in HEK293T cells. RNA was isolated from human platelets and reversely transcribed into cDNA. Sequences of 220C>T and 429+4insg variants were derived by PCR amplification. The target sequence was ligated into a pcDNA3.1/V5-His-TOPO vector by TA cloning, which was transformed into TOP10 E. coli. Positive plasmids were screened by blue-white selection. After sequencing, plasmid DNA carrying 220C>T or 429+4insg variant was used to transfect HEK293T cells with the help of effectene. Expression of CD36 protein was then analyzed by flow cytometry and Western blotting. An eukaryotic expression vector pcDNA3.1/V5-His-CD36 (220C>T/429+4insg) was constructed by TA cloning. After transfected into HEK293T cells, the 220C>T and 429+4insg variants resulted in CD36 deficiency in HEK cells, which was confirmed by flow cytometry and Western blotting. The 220C>T and 429+4insg variants can cause CD36 deficiency in human platelets. This system may be used for assessing the effect of 220C>T, 429+4insg, and other variants on the expression of CD36.

Sequencing of a large off-ladder allele at Penta E locus

To identify a rare large off ladder (OL) allele at the Penta E locus. Chelex-100 was used to extract DNAs from the blood samples. The PCR fragments were purified, extracted, and subjected to TA cloning and sequencing. An OL allele was identified by the PowerPlex™ 21 at the Penta E locus, which was postulated as allele 26 based on assigned size. The OL allele was verified as a novel fragment containing 26 full AAAGA repeats. OL alleles and microvariants should be verified by direct sequencing. Typing of OL alleles has significance for both daily work and forensic genetics.

Development of an efficient in vivo cell-based assay system for monitoring hepatitis C virus genotype 4a NS3/4A protease activity.

Hepatitis C virus (HCV) represents a serious worldwide healthcare problem. No protective vaccines against HCV have been developed yet due to the fact that HCV is rapidly mutable, allowing the virus to escape from the neutralizing antibodies. Understanding of HCV was initially hampered by the inability to achieve viral replication in cell culture. Given its essential roles in viral polyprotein processing and immune evasion, HCV NS3/4A protease is a prime target for antiviral chemotherapy. We aimed to establish in vivo cell-based assay system for monitoring the activity of NS3/4A protease from HCV genotype 4a, the predominant genotype in Egypt, and the Middle East. Furthermore, the developed system was used to evaluate the inhibitory potency of a series of computer-designed chemically-synthesized compounds against NS3/4A protease from HCV genotype 4a. Native as well as mutant cleavage sites to NS3/4A protease were cloned in frame into β-galactosidase gene of TA cloning vector. The target specificity of HCV NS3/4A was evaluated by coexpression of β-galactosidase containing the protease cleavage site with NS3/4A protease construct in bacterial cells. The activity of β-galactosidase was colorimetrically estimated in the cell lysate using orthonitro phenyl β-D-galactopyanoside (ONPG) as a substrate. We successfully developed an efficient cell-based system based on the blue/white selection of bacterial cells that are able to express functional/nonfunctional β-galactosidase enzyme.

Diagnosis of Spinal Muscular Atrophy: A Simple Method for Quantifying the Relative Amount of Survival Motor Neuron Gene 1/2 Using Sanger DNA Sequencing.

Background:Spinal muscular atrophy (SMA) is caused by homozygous deletion or compound heterozygous mutation of survival motor neuron gene 1 (SMN1), which is the key to diagnose SMA. The study was to establish and evaluate a new diagnostic method for SMA.Methods:A total of 1494 children suspected with SMA were enrolled in this study. Traditional strategy, including multiplexed ligation-dependent probe amplification (MLPA) and TA cloning, was used in 1364 suspected SMA children from 2003 to 2014, and the 130 suspected SMA children were tested by a new strategy from 2015 to 2016, who were also verified by MLPA combined with TA cloning. The SMN1 and SMN2 were simultaneously amplified by polymerase chain reaction using the same primers. Mutation Surveyor software was used to detect and quantify the SMN1 variants by calculating allelic proportions in Sanger sequencing. Finally, turnaround time and cost of these two strategies were compared.Results:Among 1364 suspected SMA children, 576 children had SMN1 homozygous deletion and 27 children had SMN1 compound heterozygous mutation. Among the 130 cases, 59 had SMN1 homozygous deletion and 8 had heterozygous deletion: the SMN1-specific peak proportion on exon 7 was 34.6 ± 1.0% and 25.5 ± 0.5%, representing SMN1:SMN2 to be 1:2 and 1:3, respectively. Moreover, five variations, including p.Ser8Lysfs *23 (in two cases), p.Leu228*, p.Pro218Hisfs *26, p.Ser143Phefs*5, and p.Tyr276His, were detected in 6/8 cases with heterozygous deletion, the mutant allele proportion was 31.9%, 23.9%, 37.6%, 32.8%, 24.5%, and 23.6%, which was similar to that of the SMN1-specific site on exon 7, suggesting that those subtle mutations were located in SMN1. All these results were consistent with MLPA and TA cloning. The turnaround times of two strategies were 7.5 h and 266.5 h, respectively. Cost of a new strategy was only 28.5% of the traditional strategy.Conclusion:Sanger sequencing combined with Mutation Surveyor analysis has potential application in SMA diagnosis.