Antigen Gene Cloning and Expression of HIV-1 Toward an AIDS Vaccine Design Ⅰ.Amplification and Sequencing of HIV-1 Antigen Genes

Objective:To amplify antigen genes from patients with human immunodeficiency virus type 1 (HIV-1) in Guangdong Province for candidate AIDS vaccine design. Methods:Viral nucleic acid was isolated from 10 HIV-1 infected individuals' peripheral blood collected during 1995-2000 in Guangdong Province. The viral gag p24 gene and env gp120 gene were amplified by nested-PCR and sequenced. The homologies among HIV-1 isolates were compared with HIV-BLAST. Results: Among 10 HIV-1 isolates, nine are homologous to viruses of subtype B, and one is homologous to viruses of subtype E. Conclusion: Subtype B viruses of HIV-1 are predominantly present in Guangdong Province.

Cost-Effective Method of Gene Synthesis by Sequencing from Microchip-Derived Oligos for Droplet Cloning

Gene synthesis has provided important contributions in various fields including genomics and medicine. Current genes are 7 - 30 cents depending on the assembly and sequencing methods performed. Demand for gene synthesis has been increasing for the past few decades, yet available methods remain expensive. A solution to this problem involves microchip-derived oligonucleotides (oligos), an oligo pool with a substantial number of oligo fragments. Microchips have been proposed as a tool for gene synthesis, but this approach has been criticized for its high error rate during sequencing. This study tests a possible cost-effective method for gene synthesis utilizing fragment assembly and golden gate assembly, which can be employed for quicker manufacturing and efficient execution of genes in the near future. The droplet method was tested in two trials to determine the viability of the method through the accuracy of the oligos sequenced. A preliminary research experiment was performed to determine the efficacy of oligo lengths ranging from two to four overlapping oligos through Gibson assembly. Of the three oligo lengths tested, only two fragment oligos were correctly sequenced. Two fragment oligos were used for the second experiment, which determined the efficacy of the droplet method in reducing gene synthesis cost and speed. The first trial utilized a high-fidelity polymerase and resulted in 3% correctly sequenced oligos, so the second trial utilized a non-high-fidelity polymerase, resulting in 8% correctly sequenced oligos. After calculating, the cost of gene synthesis lowers down to 0.8 cents/base. The final calculated cost of 0.8 cents/base is significantly cheaper than other manufacturing costs of 7 - 30 cents/base. Reducing the cost of gene synthesis provides new insight into the cost-effectiveness of present technologies and protocols and has the potential to benefit the fields of bioengineering and gene therapy.

Cloning, sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies

The heavy chain variable region genes of 5 human polyreactive mAbs generated in our laboratory have been cloned and sequenced using polymerase chain reaction (PCR) technique. We found that 2 and 3 mAbs utilized genes of the VHIV and VHIII families, respectively. The former 2 VH segments were in germline configuration. A common VH segment, with the best similarity of 90.1 % to the published VHIII germline genes, was utilized by 2 different rearranged genes encoding the V regions of other 3 mAbs. This strongly suggests that the common VH segment is a unmutated copy of an unidentified germline VHIII gene. All these polyreactive mAbs displayed a large NDN region (VH-D-JH junction). The entire H chain V regions of these polyreactive mAbs are unusually basic. The analysis of the charge properties of these mAbs as well as those of other poly- and mono- reactive mAbs from literatures prompts us to propose that the charged amino acids with a particular distribution along the H chain V region,especially the binding sites (CDRs), may be an important structural feature involved in antibody polyreactivity.

Identification of a marine agarolytic bacterium Agarivorans albus QM38 and cloning and sequencing its beta-agarase genes

A total of 117 agar-decomposing cultures were isolated from coastal seawater around Qingdao, China. The phenotypic and agarolytic features of an agarolytic isolate, QM38, were investigated. The strain was gram negative, strictly aerobic, curved rod and polar flagellum. On the basis of several phenotypic characters, biochemical and morphological characters and phylogenetic analysis of the gene coding for the 16S rRNA, the strain was identified as Agarivorans albus strain QM38. This strain can liquefy the agar on the solid agar plate. An excellular agarase activity was determined in liquid culture. The enzyme exhibited maximal activity at 40 ℃, pH 7.6. Its activity was greatly affected by different concentrations of agarose. The highest activity 32 U/ml was achieved in the culture supernatant. The hydrolytic product was analyzed by fluorophore-assisted carbohydrate electrophoresis （FACE）. After complete hydrolysis of agarose, a series of agaro-oligosaccharides were produced. The main products of the enzymes were oligosaccharides in the degree of polymerization （DP） of 2, 4, 6 and 8. Three genes agaD01, agaD02 and agaD03, encodingβ-agarases, had been cloned from genomic DNA of Agarivorans albus strain QM38. The open reading frame of agaDOl, consisted of 2 988 bp, and shared 95.5%-98.9% identity to the β-agarase genes of some strains of Vibrio and Agarivorans. Gene agaD02 comprised 2 868 bp and encoded a 955- amino-acid protein. It showed 97.4% and 98.7~0 identity to the β-agarase genes of strain Vibrio sp. PO-303 and strain Vibrio sp. JT0107, respectively. Only partial sequence of agaD03 gene has been cloned. It showed 96.5% identity to β-agarase gene （agaB） of Pseudoalteromonas sp. CY24, and shared 96.8% identity to β-agarase-c gene of Vibrio sp. PO-303.

Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing

Objective:Autosomal recessive bestrophinopathy(ARB),a retinal degenerative disease,is characterized by central visual loss,yellowish multifocal diffuse subretinal deposits,and a dramatic decrease in the light peak on electrooculogram.The potential pathogenic mechanism involves mutations in the BEST1 gene,which encodes Ca2+-activated Cl−channels in the retinal pigment epithelium(RPE),resulting in degeneration of RPE and photoreceptor.In this study,the complete clinical characteristics of two Chinese ARB families were summarized.Methods:Pacific Biosciences(PacBio)single-molecule real-time(SMRT)sequencing was performed on the probands to screen for disease-causing gene mutations,and Sanger sequencing was applied to validate variants in the patients and their family members.Results:Two novel mutations,c.202T>C(chr11:61722628,p.Y68H)and c.867+97G>A,in the BEST1 gene were identified in the two Chinese ARB families.The novel missense mutation BEST1 c.202T>C(p.Y68H)resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1.Another novel variant,BEST1 c.867+97G>A(chr11:61725867),located in intron 7,might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators.Conclusion:Our findings represent the first use of third-generation sequencing(TGS)to identify novel BEST1 mutations in patients with ARB,indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes.The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.

To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant

Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.

Cloning and Sequencing of a Gene Encoding GOBP2 in the Antenna of Spodoptera exigua

A pair of degenerate primers was designed, based on the comparison of five insects' GOBP2 gene sequences reported previously. A specific band (about 400bp in length) was amplified from cDNA of Spodoptera exigua antenna and another specific band (about 2kb in length) was amplified from genomic DNA. The two segments were cloned into T-easy vector, respectively. Results of sequencing and structural analysis showed that the full-length of GOBP2Sexi ORF is 426bp, 141 amino acid residues were encoded. The predicted MW and pI are 16.07ku and 5.09 .respectively. There are six conservative Cys locus in the sequence, which is the typical characteristic of OBPs. GOBP2Sexi gene was inserted by two introns between amino acid residue 22 and 23 and between 82 and 83. The length of two introns is 160bp and 1403bp. Results of Northern blot showed that GOBP2 gene expressed specifically in the antenna of Spodoptera exigua, and the expression level is nearly equal in the antenna of male and female moths. The sequence was deposited in GenBank/EMBL and the accession number is AJ294809.

Cloning and Sequencing of a Gene Encoding Aminopeptidase N in the Midgut of Helicoverpa armigera(Hubner)

A cDNA encoding aminopeptidase N was cloned by degenerated PCR combined with RACE technique in this paper. The full-length of APN-Harm is 3 043 bp. Open reading frame is 2 856 bp in length, encoding 951 amino acid residues. Its predicted molecular weight and isoelectric point are 108. 3 kDa and 5.29, respectively. This deduced amino acid sequence shares some common structural features with aminopeptidase N from several moth species, including the consensus zinc-binding motif HEXXHX18E and the GAMEN motif common to gluzincin aminopeptidases. The first 20 amino acid residues at N-termini is hydrophobic transmembrane helix. The sequence of APN-Harm was deposited in GenBank and the accession number is AY181026.

Cloning and Sequencing of Kappa Light Chain Gene of a Mouse Monoclonal Antibody Directed Against Potato Virus Y

A cDNA library was constructed in λgt11 vectors, complementary to the mRNA isolated from a mouse hybridoma raised against potato virus Y(PVY). Thirty cDNA clones were selected from the cDNA library by in situ immunohybridization with goat anti-mouse kappa-chain-specific antibody conjugated to alkaline phosphatase, from which one clone, k6, having the largest insert was characterized by sequence analysis. The result shows that the immunoglobulin messenger RNA corresponding to k6 is 956 nucleotides in length excluding the poly(A) region, among which 31 bases code for the 5’ non-coding region, 57 for the leader sequence of the protein, 657 for the mature protein and 211 for the 3’ non-coding region. Comparison of deduced amino acid sequences of the protein and other kappa light chains shows that they share a 100% identity in their constant regions(CL) and 93.7% identity in their variable regions(VL). The kappa light chain encoded by k6 is considered to be specific to PVY since only one type of light chain is expressed in the hybridoma.

Cloning and sequencing genes related to preeclampsia

Objectives: To clone genes specifically expressed in the placenta of patients with preeclampsia. and to explain the mechanism in the etiopathology of preeclampsia. Methods: The placentae of preeclamptic and normotensive subjects with pregnancy were used as models, and the eDNA Library was constructed and 20 differentially expressed fragments were cloned after a new version of PCR-based subtractive hybridization. The false positive clones were identified by reverse dot blot analysis. With one of the obtained gene taken as the probe, the placentas of 10 normal pregnant women and 10 preeclamptic patients were studied by using dot hybridization methods. Results: Six false positive clones were identified by reverse dot blot, and the rest 14 clones were identified as preeclampsia-related genes. These clones were sequenced, and analyzed with BLAST analysis system. Eleven of 14 clones were genes already known, among which one belongs to necdin family; the rest 3 were identified as novel genes. These 3 genes were acknowledged by GenBank, with the accession numbers AF2322 16, AF2322 17, AF233648. The results of dot hybridization using necdin gene as probe were as follows: (1) There was this mRNA in the placental tissues of normal pregnancy as well as in that of preeclampsia. (2) The intensity of transcription of this mRNA in the placental tissues of preeclampsia increased significantly compared with that of the normal pregnancy (P＜0.05). Conclusions: This study for the first time reported this group of genes, especially necdin-expressing gene, which are related to the etiopathology of preeclampsia. In addition, the overtranscription of necdin gene has been found in preeclampsia. it is helpful in further studies of the etiology of preeclampsia.

CLONING AND SEQUENCING OF THE ALLOPHYCOCYANIN GENES FROM SPIRULINA MAXIMA (CYANOPHYTA)

The genes coding for the α-and β-subunit of allophycocyanin (apcA and apcB) fromthe cyanophyte Spirulina maxima were cloned and sequenced. The results revealed 44.4% of nucleotidesequence similarity and 30.4% of similarity of deduced amino acid sequence between them. The aminoacid sequence identities between S. maxima and S. platensis are 99 .4% for α subunit and 100% for βsubunit.

Cloning and Sequencing of S Gene of Novel Variant of Infectious Bronchitis Virus ZJ971 Isolates in China

A novel proventriculopathogic variant (isolate ZJ971) of infectious bronchitis virus (IBV) was identified from enlarged proeventriculus of the sick chickens in the study. The S gene cDNA segment with 3.6 kb in length was amplified by RT-PCR with special primers from the ZJ971 viral isolate of (IBV) and cloned into plasmid pBluescript SK( + ). The recombinants containing S gene of IBV-ZJ971 isolate were identified by digestion of restriction enzyme EcoRI, BamHI and PCR amplification. The cloned S gene from isolate IBV-7J971 was composed of 3492 bp in length encoding for a polypeptide of 1080 amino acids. Comparing the nucleotide of S gene of IBV isolate ZJ971 with that of reported IBV strains Beaudette, M41, Ark99 and CuT2, the homology was 97.3%, 97.5%, 88.6% and 85.6%, respectively; and the homology of the deduced amino acids of S protein of IBV isolate ZJ971 was 96%, 96.3%, 86.1% and 83.1% respectively; especially, the mutation of 3241st nucleotide of S gene of IBV isolate ZJ971 from G to T resulted in the translating termination of S protein at 3240th nucleotide site.

Gene Cloning and Bioinformatics Analysis of phoR Gene from Vibrio alginolyticus HY9901

PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using bioinformatics.Sequence analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid residues.The phylogenetic tree of PhoR revealed that it belongs to the same subclade as V.diabolicus.The SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).

CLONING AND SEQUENCING OF THE FERREDOXIN GENE OF BLUE-GREEN ALGA ANABAENA SIAMENSIS

The structure gene for ferredoxin, petFI, from Anabaena siamensis has been ampli-fied by polymerase chain reaction(PCR) and cloned into cloning vector pGEM-3zf(+). The nucleotidesequence of petFI has been determined with silver staining sequencing method. There is 96. 8% homologybetween coding region of petFI from A. siamensis and that of petFI from A. sp. 7120. Amino acid se-quences of seven strains of blue-green algae are compared.

Cloning and Sequencing of cSZ1 Gene of Eimeria acervulina Changchun Strain

[ Objective] To analyze Eimetria acervulina cSZl gene sequence and thus to find a candidate antigen for vaccine development.[ Method] According to the cSZl gene sequence of Eimeria acervulina published in GenBank, a pair of specific primers was designed. Then, the cSZl gene of Eirneda acervulina Changchun strain was amplified by reverse-transcription polymerase chain reaction （RT-PCR） and sequenced. [ Result] Compared with the published cSZ1 gene sequence, five nucleotide mutation sites appeared in the cSZ1 gene of Eirneda acervulina Changchun strain. They had a nucleotide sequence similarity of 99.47%, and their encoding region had a nucleotide sequence similarity of 99.61%. Among these mutation sites, two appeared in cSZl gene ORF, and A185G mutation led to substitution of valine by isoleucine. [Conclusion] Protein encoded by cSZ1 gene can be used as a candidate antigen for vaccine development.

Cloning, Sequencing, and Characterization of Porcine Sterol Regulatory Element Binding Proteins-1c Gene

Primers were designed according to the known sequences of Sterol Regulatory Element Binding Proteins-1c (SREBP-1c) genes of human, rat and pig. RT-PCR was then used to amplify porcine SREBP-1c gene with total RNA of spleen tissue. A 760 bp segment of cDNA was cloned and sequenced. Homogeneous comparison showed that the sequence of porcine SREBP-1c had 99.9% and 99.1% homogeneity with the two known partial mRNA sequences of porcine SREBP-1c gene. The complete cDNA was obtained mainly based on the known partial sequences, which has 3 830 bp, encoding 1 151 amino acids with a calculated molecular weight of 121 479 Da. It is the first time that we get complete encode sequence of porcine SREBP-1c gene. The complete cDNA sequence has high homogeneity with SREBP-1c gene of other species. A characteristic structure of HLH (Helix-Loop-Helix) and four transmembrane segments were found in the amino acids. The sequence had been submitted to GenBank (Accession No.NM_-214157).

Cloning and sequencing of core gene cDNA of Chinese hepatitis C virus

A hepatitis C virus(HCV)cDNA fragment,534bp in length and designated asQ534,was obtained by PCR amplification with self-designed primers.Q534 was cloned in-to Hinc Ⅱ site of pUC18 and the recombinant plasmid pQ534 was then selected from thebacterial transformants.The sequence analysis indicated that Q534 was a cDNA fragmentof HCV core gene,and located in HCV genome from positions 320 to 853 incorrespondence with Chiron’s prototype sequence.The homologies between Q534 and theprototype at the levels of nucleotides and amino acids were 90.0% and 97.6%,respectively.The homologies of Q534 with Japanese HCV-J and HCV-BK strains were 96.6% and97.0% at the nucleotide level,and 98.2% and 98.8% at the amino acid level.In terms ofthe sequence,this Chinese HCV isolate should belong to HCV group Ⅱ.

Cloning and Sequencing of the Pokeweed Antiviral Protein Gene and Its Expression in E. coli

The total RNA was isolated from pokeweed (Phytolacca americana) leaves using the method of guanidine isothiocyanite and used as a template to amplify the deleted mutant pokeweed antiviral protein (PAP) gene by RT-PCR and then the gene was cloned into the pGEMR-T vector. The sequencing results showed that the PAP gene consisted of 711nt, which was 99.6% identical to the PAP gene reported by Lin et al (1991). The IPTG-inducible expression vector containing the PAP gene was constructed and transferred into the E. coli strain BL21 (DE3)-plysS. A specific protein was produced after induction with 0.4m mol/L IPTG and its molecular weight was 26ku. The results of the double diffusion on the agar plate and the western blotting test showed that the protein produced in E. coli was highly identical with the PAP extracted by a Frenchman from French pokeweed leaves. These revealed that PAP gene was actually achieved and exactly expressed in E. coli.

The Cloning and Sequencing of Read-through Protein Gene from BYDV-GAV Virus

The cDNA of BYDV-GAV read-through protein(RTP)gene was amplified from the extracted RNA of BYDV-GAV by using the polymerase chain reaction(PCR),and cloned into pGEM-7zf(+).Its complete nucleotide sequence was determined by dideoxynucleotide chain-termination method.The BYDV-GAV RTP gene consists of 1377nt.Its sequences were most similar to that of the RTP gene of BYDV-MAV with identities of 87.4%and 87.1%at the nucleotide and amino acid levels,respectively.