Cloning Vector Research Articles

Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.

Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.

Functional characterization of Cinnamate 4-hydroxylase gene family in soybean (Glycine max).

Cinnamate 4-hydroxylase (C4H) is the first key cytochrome P450 monooxygenase (P450) enzyme in the phenylpropanoid pathway. It belongs to the CYP73 family of P450 superfamily, and catalyzes the conversion of trans-cinnamic acid to p-coumaric acid. Since p-coumaric acid serves as the precursor for the synthesis of a wide variety of metabolites involved in plant development and stress resistance, alteration in the expression of soybean C4H genes is expected to affect the downstream metabolite levels, and its ability to respond to stress. In this study, we identified four C4H genes in the soybean genome that are distributed into both class I and class II CYP73 family. GmC4H2, GmC4H14 and GmC4H20 displayed tissue- and developmental stage-specific gene expression patterns with their transcript accumulation at the highest level in root tissues. GmC4H10 appears to be a pseudogene as its transcript was not detected in any soybean tissues. Furthermore, protein homology modelling revealed substrate docking only for GmC4H2, GmC4H14 and GmC4H20. To demonstrate the function of GmC4Hs, we modified a cloning vector for the heterologous expression of P450s in yeast, and used it for microsomal protein production and enzyme assay. Our results confirmed that GmC4H2, GmC4H14 and GmC4H20 contain the ability to hydroxylate trans-cinnamic acid with varying efficiencies.

Phage N15-Based Vectors for Gene Cloning and Expression in Bacteria and Mammalian Cells.

Bacteriophage N15 is the first virus known to deliver linear prophage into Escherichia coli. During its lysogenic cycle, N15 protelomerase (TelN) resolves its telomerase occupancy site (tos) into hairpin telomeres. This protects the N15 prophage from bacterial exonuclease degradation, enabling it to stably replicate as a linear plasmid in E. coli. Interestingly, purely proteinaceous TelN can retain phage DNA linearization and hairpin formation without involving host- or phage-derived intermediates or cofactors in the heterologous environment. This unique feature has led to the advent of synthetic linear DNA vector systems derived from the TelN-tos module for the genetic engineering of bacterial and mammalian cells. This review will focus on the development and advantages of N15-based novel cloning and expression vectors in the bacterial and mammalian environments. To date, N15 is the most widely exploited molecular tool for the development of linear vector systems, especially the production of therapeutically useful miniDNA vectors without a bacterial backbone. Compared to typical circular plasmids, linear N15-based plasmids display remarkable cloning fidelity in propagating unstable repetitive DNA sequences and large genomic fragments. Additionally, TelN-linearized vectors with the relevant origin of replication can replicate extrachromosomally and retain transgenes functionality in bacterial and mammalian cells without compromising host cell viability. Currently, this DNA linearization system has shown robust results in the development of gene delivery vehicles, DNA vaccines and engineering mammalian cells against infectious diseases or cancers, highlighting its multifaceted importance in genetic studies and gene medicine.

Abstract 4710: Novel 3D cytotoxicity assay to assess the impact of chimeric antigen receptor (CAR) domain design on the tumor infiltration and cytotoxicity efficacy of CAR T-cell therapies for solid tumors

Abstract CAR T-cell therapy is a popular topic of discussion in and out of the scientific community. Already with multiple therapies FDA-approved for certain blood cancers, focus has rightly shifted toward FDA approval for solid tumor indications. Yet, advancing past clinical trials to FDA approval has yet to occur and has proved challenging. Of course, multiple factors are at play as to why, but we aim to use-in house expertise to elucidate one, namely CAR T-cell tumor infiltration and tissue migration and surveillance efficacy. Migration is a central parameter ignored in traditional 2D cytotoxicity assays, but there is no tumor cell killing by T cells if there is no T cell migration. We developed a novel first-of-its-kind organoid-based 3D cytotoxicity assay using multicompartment organoids and the most abundant extracellular matrix protein in human organs, collagen. We suspend solid tumor organoids in the center of CAR T-cell/collagen gel mixtures that are solidified then imaged in intervals in the span of two weeks by live-cell time-lapse reflection/fluorescence confocal microscopy, after which standard luciferase-based readouts of quantitative specific lysis is determined. Our assay allows high-resolution tracking of CAR T-cell 3D movements through collagen fibers surrounding solid tumor organoids to determine their random and directional migration as well as their surveillance and infiltration of solid tumor organoids. We will describe the differences between currently in clinical trial mesothelin-specific CAR T-cell therapies that differ in their scFv, hinge, transmembrane, and costimulatory domains; and comparing alongside the traditional 2D luciferase-based cytotoxicity assay, we will underline how 3D migration and infiltration around and into mesothelin-expressing ovarian cancer cell organoids allow the determination of CAR T-cell therapy efficacy of different CAR T clones in a lab’s arsenal for a given solid tumor through migration, infiltration, and subsequent cytotoxic capacity that is absent in traditional 2D cytotoxicity assays. CAR T-cell therapy vector design and cloning can thus be tuned for optimal migration and infiltration using our novel 3D cytotoxicity assay. Citation Format: Adrian Johnston, Zeqi Wan, Tina Chen, Yeongseo Lim, Cameron Lee, Wenxuan Du, Jude Philip, Denis Wirtz. Novel 3D cytotoxicity assay to assess the impact of chimeric antigen receptor (CAR) domain design on the tumor infiltration and cytotoxicity efficacy of CAR T-cell therapies for solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4710.

First Report of the Association of Zygocactus virus X with Dragon Fruit (Hylocereus spp.) plants from Telangana, India.

Dragon fruit (Hylocereus spp.) a member of the family Cactaceae, is widely cultivated throughout the world, includingspan style="font-family:'Times New Roman'; letter-spacing:0.05pt; color:#333333"> India. During 2020-2021 crop growing season, mosaic symptoms were observed on the cladodes of dragon fruit plants (Purple Pink cultivar: 1-2% disease incidence) grown at a farmer's field of Telangana, India (Fig. S1 a). The symptomatic cladodes (n= 4), observed under leaf-dip electron microscopy (Zuchmaan and Zellnig, 2009) at Indian Agricultural Research Institute, New Delhi, revealed the presence of flexuous rod- shaped virus-like particles (Fig S1 b). Virus particles were of 580 x 13 nm size, corresponding to the genus Potexvirus. For further confirmation, the total RNA isolated from symptomatic cladodes using a NucleoSpin RNA Plant Mini kit (Macherey-Nagel). Subsequently, a reverse transcription polymerase chain reaction (RT-PCR) was performed using the PrimeScript 1st strand cDNA Synthesis Kit (Takara Bio). The cDNA was further amplified with the primers specific to coat protein (CP) gene of four different species of the genus Potexvirus known to infect members of Cactaceae family. Four sets of primers were used for detection, viz., Cactus virus X (CVX) (F, 5'-ATGTCTACTACTGGAGTCCA-3'; R, 5'-CTACTCAGGGCCTGGGAGAA-3'); Pitaya virus X (PiVX) (F, 5'-ATGGCTACTCAAACAGCACAA-3'; R, 5'-CTACTCTGGGGAGGGAAG-3'); Schlumbergera virus X (SchVX) (F, 5'-ATGTCGACCACTCCATCTTC-3'; R, 5'-TTATTCAGGGGATGGTAGTA-3') and Zygocactus virus X (ZyVX) (F, 5'-ATGTCTAACACTGCAGGAGT-3'; R, TCATTC GGGACCCGGTAGGA-3') (Duarte et al., 2008; Janssen et al., 2021; Parameswari et al., 2021), by following the PCR profile (Park et al., 2018). The species-specific primers of CVX, PiVX and SchVX did not amplify any amplicon, whereas the primers specific to ZyVX at nucleotide position 5841-6521 from complete CP gene have resulted in amplification of expected size (~680 base pairs) from all the samples. The gel-purified RT-PCR products were cloned into a pDrive cloning vector (Qiagen, Germany) and sequenced bi-directionally using Sanger sequencing. The resultant sequences (681 nt) of the CP gene showed 98% (nucleotide) and 100% (amino acid) sequence similarity with the CP gene sequence (Accession No: KY581590) of ZyVX. Hence, one representative sequence was deposited to the NCBI GenBank database as ZyVX-DPC isolate (Accession number- OK415019). The Neighbour Joining Phylogenetic Tree constructed using MEGA6 software (Tamura et al. 2013) showed grouping of Indian ZyVX-DPC isolate with the previously reported ZyVX isolates from Korea, Taiwan, China and Germany (Fig. S1c). These results confirmed the association of ZyVX with the symptomatic cladodes of dragon fruit plants collected from Telangana, India. Earlier studies revealed that ZyVX is a member of the genus Potexvirus known to infect dragon fruit plants from Brazil and China (Duarte et al., 2008). In India until now, anthracnose disease (Colletotrichum siamense) and CVX from Hylocereus spp. were reported (Abirami et al., 2019; Parameswari et al., 2021). To the best of our knowledge, this is the first report of ZyVX infection on dragon fruit in India. The draon fruit, being vegetatively propagated and with increasing cultivable area in India (Abirami et al, 2019), the present study gains significance. Further studies on mode of virus transmission, estimation of crop yield losses, host range studies and finding out source of resistance are essential.

IN SILICO B-CELL EPITOPE VACCINE DESIGN AND PHYLOGENETIC ANALYSIS OF EBOLA VIRUS ENVELOPE GLYCOPROTEIN

Ebola virus (EBOV) is a type of RNA virus from the family of Filoviridae. The 2014-2016 Ebola outbreak in African countries Guinea, Liberia and Sierra Leone has a total of 28,616 cases and 11,310 deaths. People suffering from Ebola disease reported to have symptoms such as fever, body aches, diarrhea and internal and external bleeding. Death from Ebola is mostly caused by multi-organ failure due to internal bleeding and fluid loss. Another Ebola outbreak has spiked this February 2021, suggesting low effectivity of the previous vaccines used. Zaire Ebola virus (EBOV) is known to be the species highly involved on the recent outbreak with a high mortality rate. This study is carried out to design B-cell epitope Ebola vaccine based on the conserved region of Zaire EBOV glycoprotein. Reverse vaccinology and immunoinformatic approaches are used in this study. Samples of Zaire EBOV glycoprotein sequences were retrieved from GenBank, NCBI. The 3D modelling was done by using SWISS-MODEL web server and PyMol software. Phylogenetic tree analysis was also done by using MEGA X. B-cell epitope prediction was done by BepiPred 2.0 and Emini Surface Accessibility using IEDB web server. Epitopes were selected based on its conservancy by comparing the sequences with the MEGA X alignment result. Antigenicity, allergenicity and toxicity properties of the peptides were predicted using VaxiJen 2.0, AllerTOP 2.0 and ToxinPred web servers. In silico cloning was done as the final step using pET-24a(+) expression vector. This study revealed that peptide “LEIKKPD”, “TGFGTNETEYLF”, “PYFGPAA”, “PYFGPA”, and “KLSSTNQL” are the best candidate of B-cell epitope vaccine. Phylogenetic tree and 3D modelling successfully showed the genetic and structural differences of Zaire EBOV GP originating from various countries. In silico cloning was also done using pET28a(+) expression vector to design clone vector map to be used for the next phase of vaccine development.

First report of mume virus A infecting Prunus salicina worldwide and Prunus mume in Korea.

Mume virus A (MuVA) of the genus Capillovirus in the family Betaflexiviridae was first isolated from a Japanese apricot tree (Prunus mume) exhibiting symptoms of diffuse chlorotic spots (Marais et al. 2018). MuVA infection has been reported in Japanese apricot trees in Japan as well as in peach (P. persica) and Japanese apricot trees in China (Marais et al. 2018; Zhang et al. 2021; Zheng et al. 2020). In the present study, the diversity of viruses and viroids infecting Chinese plum trees (P. salicina) was investigated using high-throughput sequencing (HTS). Ten flowers each from 50 trees without obvious symptoms related to virus and/or viroid infection were randomly collected from five orchards in Gimcheon, Korea, in April 2020. The samples from each Chinese plum tree were pooled, and the same amounts of 50 individual samples prepared in advance were pooled for the extraction of total RNA using the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Removal of ribosomal RNA and construction of cDNA library from the extracted total RNA were conducted using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina, San Diego, CA, USA). Paired-end RNA sequencing using Illumina NovaSeq 6000 System (paired-end reads of 101 bp and a total of 162,845,322 reads) and data analysis were performed at Macrogen (Daejeon, Korea). Adaptor and low-quality sequences of reads were removed using Trimmomatic program. Trimmed reads were assembled into contigs using Trinity program, and several databases including NCBI Nucleotide and Kyoto Encyclopedia of Genes and Genomes were used for functional annotation. HTS identified plum bark necrosis stem pitting-associated virus (PBNSPaV; four contigs ranging from 2081 to 3202 nucleotides) and hop stunt viroid (HSVd; one contig of 618 nucleotides). PBNSPaV and HSVd were also detected by RT-PCR (PBNSPaV det-F and PBNSPaV det-R for PBNSPaV [Al Rwahnih et al. 2007]; VP-19 and VP-20 for HSVd [Astruc et al. 1996]) and confirmed by Sanger sequencing of the amplified products. Interestingly, one contig derived from MuVA, which was not previously reported in Korea, was also detected. The contig was 7,618-nucleotide long (15,205 reads), and NCBI BLASTN search revealed 98.74% homology (100% query coverage) with the MuVA isolate pm14 (GenBank accession number MG783575). To design diagnostic primers for reverse transcription (RT)-polymerase chain reaction (PCR), the contig sequence and MuVA sequences available in NCBI GenBank (GenBank accession numbers MG783575 and MN412555) were aligned using CLC Main Workbench 6.9.1 (QIAGEN, Redwood, CA, USA). The following primer set (expected size of 1,143 bp) was prepared: MuVA-2F (5'-CAGCTTTGTGACTCYAACCC-3') and MuVA-2R (5'-AATGGCTTGAGGRCCTGCAG-3'). The primers target a partial region (nt position 1185 to 2327 on the basis of the reference genome sequence of MuVA, GenBank accession no. NC_040568) of the polyprotein gene (ORF1). Each of the 50 samples was tested for the presence of MuVA using the above-mentioned RT-PCR primers with SuPrimeScript RT-PCR Premix (GeNet Bio, Daejeon, Korea). MuVA was detected in three samples collected from the same orchard. The three amplicons were inserted into a T&A cloning vector (RBC Bioscience, Taipei, Taiwan) and sequenced at Macrogen. Three consensus sequences obtained by Sanger sequencing were registered in NCBI GenBank under accession numbers MW589492, MW589493, and MW589494. NCBI BLASTN search revealed that the Korean isolates of MuVA shared high homology with isolate pm14 [98.16%, 98.08%, and 98.16% (100% query coverage), respectively]. To confirm additional MuVA infections, leaf samples of Chinese plum trees were collected from orchards in Uiseong (70 trees) and Seongju (50 trees) as well as a Japanese apricot tree in Chuncheon, from April to July 2021. RT-PCR confirmed additional MuVA infections from Uiseong (one tree) and Seongju (one tree) as well as from the Japanese apricot tree in Chuncheon. NCBI BLASTN search of the three additional amplicons (GenBank accession numbers OM210030, OM210031, and OM210032) revealed high homology with isolate pm14 [98.25%, 98.08%, and 97.90% (100% query coverage)]. To the best of our knowledge, this is the first report of MuVA infecting P. mume in Korea and P. salicina worldwide. Further research is needed to investigate MuVA infections on various Prunus spp. including P. persica in Korea.

DNA binding, cleavage, catalytic, magnetic active; 2,2–bipyridyl based d-f hetero binuclear Gd(III), Cu(II) complexes and their Electrochemical, fluorescence studies

Several 2,2-bipyridyl-based d-f heterobinuclear [GdCuL1-5(bpy)2(NO3)2] complexes are present, where (Ligand 1) (9E)-N1-(2-Hydroxy-5-methylbenzylidene)–N2-((E)-2-(2-hydroxy-5-methyl benzylideneamino)ethyl)ethane-1,2-diamine. (Ligand 2) N1,N1-bis((E)-2-(2-hydroxy-5-methylbenzylideneamino)ethyl)ethane-1,2-diamine. (Ligand 3) (9E)-N1-(2-((E)-2-(2-hydroxy-5-methylbenzylideneamino)ethylamino)ethyl)–N2-(2-hydroxy-5-methylbenzylidene)ethane-1,2-diamine. (Ligand 4) (9E)-N1-(2-((E)-3-(2-hydroxy-5- methylbenzylideneamino) propylamino) ethyl)–N3-(2-hydroxy-5-methylbenzylidene)propane-1,3-diamine and (Ligand 5) (9E)-N-(2-hydroxy-5-methylbenzylidene)-3-(4-((E)-3-(2-hydroxy-5-methylbenzylideneamino)propyl)piperazin-1-yl)propan-1-amine. These compounds were described using spectroscopy and the elemental analysis method. Researches were conducted into the luminous, Genetic code, catalytic, magnetism, and breaking attributes of the [GdCuL1-5(bpy)2(NO3)2] complexes. In DMF with 0.1 M tetra-n-butylammonium perchlorate, the binuclear [GdCuL1-5(bpy)2(NO3)2] network complexes exhibit two one electron irreversible reduction events. VSM was used to calculate the complexes' magnetic susceptibility. There is ferromagnetic coupling in the [GdCuL1-5(bpy)2(NO3)2] complexes. The [GdCuL1-5(bpy)2(NO3)2] complexes' excited state lifetimes lengthen in the following order: [GdCuL5(bpy)2] [GdCuL1(bpy)2(NO3)2] [GdCuL3(bpy)2(NO3)2] [GdCuL4(bpy)2] and [GdCuL2(bpy)2(NO3)2]. The binuclear [GdCuL1-5(bpy)2(NO3)2] complexes' inceptive rate of progress for oxidizing 1,2-benzenediol to cyclohexa-3,5-diene-1,2-dione are longer chains with higher activity. Both the [GdCuL5(bpy)2(NO3)2] and [GdCuL4(bpy)2(NO3)2] complexes have strong DNA genetic code properties in the calf genus thymus. The complexes exhibit considerable singlet oxygen-mediated oxidative rift of circular recombinant plasmid pBR322 cloning vector in the existence of 2-sulfanylethanol.

Exploration of Gene Encoded Thermostable Enzymes by Using Random PCR from Natural Sample of Domas Crater

Thermophilic microorganisms can survive and live in extremely high-temperature habitats. This special trait made thermophilic microorganisms have heat-resistant proteins such as thermostable enzymes and have been used by the industry as biocatalysts. Some advantages of using thermostable enzymes in the industry are reducing operating costs, increasing the reaction rate, increasing productivity, and being environmentally friendly. This research aims to isolate the thermostable enzyme encoding gene and determine homology, differences in the sequence, and the closest relative of samples. The metagenomic approaches using random PCR techniques were used as a methodology in this research. The substances successfully obtained from random PCR of the metagenome samples were cloned in the cloning vector and then analyzed nucleotide sequence (sequencing). The highest protein homology in samples 23 and 24 are Short-chain Dehydrogenase Reductase (SDR) oxidoreductase [Caldivirga maquilingensis] of 58.58% and 58.02%, respectively. The 3-dehydroquinate dehydratease Type I [Metallosphaera] is the highest protein homology in sample 45, with a similarity of 79.88%. The phylogenetic tree analysis of sample 23 has the closest relationship with sample 24. Meanwhile, sample 45 has the closest relationship with 3-dehydroquinate dehydratase Type I from Metallospaera species. The three samples formed different branches with other amino acid sequences, showing that the three samples are new enzymes that are different from the previous ones.

A Versatile Toolset for Genetic Manipulation of the Wine Yeast Hanseniaspora uvarum.

Hanseniaspora uvarum is an ascomycetous yeast that frequently dominates the population in the first two days of wine fermentations. It contributes to the production of many beneficial as well as detrimental aroma compounds. While the genome sequence of the diploid type strain DSM 2768 has been largely elucidated, transformation by electroporation was only recently achieved. We here provide an elaborate toolset for the genetic manipulation of this yeast. A chromosomal replication origin was isolated and used for the construction of episomal, self-replicating cloning vectors. Moreover, homozygous auxotrophic deletion markers (Huura3, Huhis3, Huleu2, Huade2) have been obtained in the diploid genome as future recipients and a proof of principle for the application of PCR-based one-step gene deletion strategies. Besides a hygromycin resistance cassette, a kanamycin resistance gene was established as a dominant marker for selection on G418. Recyclable deletion cassettes flanked by loxP-sites and the corresponding Cre-recombinase expression vectors were tailored. Moreover, we report on a chemical transformation procedure with the use of freeze-competent cells. Together, these techniques and constructs pave the way for efficient and targeted manipulations of H. uvarum.

Production of Rhizopus oryzae lipase using optimized Yarrowia lipolytica expression system.

Yarrowia lipolytica is an alternative yeast for heterologous protein production. Based on auto-cloning vectors, a set of 18 chromogenic cloning vectors was developed, each containing one of the excisable auxotrophic selective markers URA3ex, LYS5ex and LEU2ex, and one of six different promoters: the constitutive pTEF, the phase dependent hybrid pHp4d, and the erythritol-inducible promoters from pEYK1 and pEYL1 derivatives. These vectors allowed to increase the speed of cloning of the gene of interest. In parallel, an improved new rProt recipient strain JMY8647 was developed by abolishing filamentation and introducing an auxotrophy for lysine (Lys-), providing an additional marker for genetic engineering. Using this cloning strategy, the optimal targeting sequence for Rhizopus oryzae ROL lipase secretion was determined. Among the eight targeting sequences, the SP6 signal sequence resulted in a 23% improvement in the lipase activity compared to that obtained with the wild-type ROL signal sequence. Higher specific lipase activities were obtained using hybrid erythritol-inducible promoters pHU8EYK and pEYL1-5AB, 1.9 and 2.2 times respectively, when compared with the constitutive pTEF promoter. Two copy strains produce a 3.3 fold increase in lipase activity over the pTEF monocopy strain (266.7 mU/mg versus 79.7 mU/mg).

Characterizing a standardized BioPart for PVQ-specific expression in C. elegans.

Synthetic biology relies on standardized biological parts (BioParts), and we aim to identify cell-specific promoters for every class of neuron in C. elegans . Here, we characterize a short BioPart (P nlp-17 , 300 bp) for PVQ-specific expression. P nlp-17 ::mScarlet showed bright, persistent, and specific expression in hermaphrodite and male PVQ neurons from multicopy arrays and single-copy insertions starting from the comma stage. We generated standardized P nlp-17 cloning vectors with gfp and mScarlet compatible with single-copy or array expression for PVQ-specific transgene expression or identification. To facilitate gene synthesis, we have incorporated P nlp-17 as a standard BioPart in our online transgene design tool (www.wormbuilder.org/transgenebuilder).

Bioinformatics and Functional Analysis of High Oleic Acid-Related Gene GmSAM22 in Soybean [Glycine max (L.) Merr.

High yield, high quality, stable yield, adaptability to growth period, and modern mechanization are the basic requirements for crops in the 21st century. Soybean oleic acid is a natural unsaturated fatty acid with strong antioxidant properties and stability. Known as a safe fatty acid, it has the ability to successfully prevent cardiovascular and cerebrovascular disorders. Improving the fatty acid composition of soybean seeds, can not only speed up the breeding process of high-quality high-oil and high-oleic soybeans, but also have important significance in human health, and provide the possibility for the development of soybean oil as a new energy source. Hence, the aim of this study was to analyze the high oleic acid elated gene GmSAM22 in soybean. In this research the soybean oleic acid-related gene GmSAM22 was screened out by Genome-wide association analysis, a 662 bp fragment was acquired by specific PCR amplification, and the pMD18T cloning vector was linked by the use of a seamless cloning technique. Bioinformatics analysis of the signal peptide prediction, subcellular localization, protein hydrophobicity, transmembrane region analysis, a phosphorylation site, protein secondary and tertiary structure and protein interaction analysis of the protein encoded by the SAM22 gene was carried out. The plasmid of the gene editing vector is pBK041. The overexpression vector was transformed from pCAMBIA3301 as the base vector, and overexpression vector were designed. Positive plants were obtained by genetic transformation by the pollen tube channel method. Fluorescence quantitative PCR was performed on the T2 generation plants to detect the relative expression levels in different tissues. Southern Blot was used to detect the presence of hybridization signal. Screening genes BAR, 35S, and NOS in plants were identified by conventional PCR. 10 seeds with high and low oleic acid content were chosen for quantitative PCR identification, and finally, the concentration and morphology of soybean fatty acids were identified by near-far infrared spectroscopy. On 10 seeds with an upper and lower oleic acid content, a quantitative fluorescence analysis was done. In Southern blot hybridization, the SAM22 gene was integrated into the recipient soybean plant in hands of a sole copy. Fluorescence quantitative PCR appeared that the average relative expression of the SAM22 gene in roots, stems, leaves, and seeds was 1.70, 1.67, 3.83, and 4.41, respectively. Positive expression seeds had a 4.77% increase in oleic acid content. The level of oleic acid in the altered seeds was reduced by 4.13% when compared to CK, and it was discovered that the GmSAM22 gene could be a regulatory and secondary gene that promotes the conversion of stearic acid to oleic acid in soybean. There has not been a discussion of gene cloning or functional verification. The cloning and genetic transformation of the soybean SAM22 gene can effectively increase the content of oleic acid, which lays a foundation for the study of soybean with high oleic acid.

DamID-seq: A Genome-WideDNA Methylation Method that Captures Both Transient and Stable TF-DNA Interactions in Plant Cells.

Capturing the dynamic and transient interactions of a transcription factor (TF) with its genome-wide targets whose regulation leads to plants' adaptation to their changing environment is a major technical challenge. This is a widespread problem with biochemical methods such as chromatin immunoprecipitation-sequencing (ChIP-seq) which are biased towards capturing stable TF-target gene interactions. Herein, we describe how DNA adenine methyltransferase identification and sequencing (DamID-seq) can be used to capture both transient and stable TF-target interactions by DNA methylation. The DamID technique uses a TF protein fusedto a DNA adenine methyltransferase (Dam) from E. coli. When expressed in a plant cell, the Dam-TF fusion protein will methylate adenine (A) bases near the sites of TF-DNA interactions. In this way, DamID results in a permanent, stable DNA methylation mark on TF-targetgene promoters, even if the target gene is only transiently "touched" by the Dam-TF fusion protein. Herewe provide a step-by-step protocol to perform DamID-seq experiments in isolated plant cells for any Dam-TF fusion protein of interest. We also provide information that will enable researchers to analyze DamID-seq data to identify TF-binding sites in the genome. Our protocol includes instructions for vector cloning of the Dam-TF fusion proteins, plant cell protoplast transfections, DamID preps, library preparation, and sequencing data analysis. The protocol outlined in this chapter is performed in Arabidopsis thaliana, however, the DamID-seq workflow developed in this guide is broadly applicable to other plants and organisms.

1723. MK-3866, a metallo-β-lactamase inhibitor, is not subject to efflux in Pseudomonas aeruginosa

Abstract Background Metallo-beta (β)-lactamases (MBLs) are in the class B group of β-lactamases due to zinc ions in the active site that are required for enzymatic activity. MK-3866 is a small molecule MBL inhibitor (MBLi) that restores antibacterial activity against resistant MBL-expressing gram-negative bacteria. Efflux is an important mechanism of antibiotic resistance in Pseudomonas aeruginosa (Pa). Imipenem (IMI) is not subject to efflux and neither is relebactam (REL), a β-lactamase inhibitor (BLi) of class A and C β-lactamases that is approved in combination with IMI/cilastatin. An efflux assay was devised to characterize MBLis for potentiation of IMI or cefepime (FEP) in isogenic strain pairs of efflux wild-type and multiply efflux deleted (MED) strains of Pa. Our objective was to determine if MK-3866 and related analogs are subject to efflux in Pa. Methods Bacterial isolates were engineered to demonstrate the ability of MBLis to be effluxed by introducing IMI metallo-β-lactamase-1 (IMP-1) (by electroporation) or Verona integron-encoded metallo-β-lactamases (VIM-1, VIM-2) (utilizing the cloning vector pFlp2) into isogenic MED and wild-type (WT) Pa isolates. Susceptibility testing was performed with IMI or FEP at a fixed concentration equal to the Pa Clinical and Laboratory Standards Institute susceptibility breakpoint for each and including a fixed 4 µg/mL of REL to inhibit class A or C enzymes, referred to as the SLICE assay. The concentration of MK-3866 and analogues required to restore susceptibility to either antibiotic in WT and MED strains was assessed. Results MICs to the combination of MK-3866/REL/IMI or MK-3866/REL/FEP vary by ≤4-fold between the WT and MED strain of each isogenic strain pair (Table 1). In contrast, large differential MIC values (efflux ratios) can be seen for the MK-3866 analogues A and B, with more moderate efflux ratios observed for other analogues. The exact efflux ratio depended on the MBL studied and the antibiotic partner. Conclusion MK-3866 showed a low potential for efflux whether IMP-1, VIM-1, or VIM-2 was expressed, in contrast to analogues of MK-3866 which exhibited differentials from nominal to extreme (≥ 128-fold) between efflux WT versus MED isolates. Disclosures Katherine Young, M.S., Merck & Co., Inc.: Stocks/Bonds Asra Mirza, MS, Merck & Co., Inc.: Stocks/Bonds Carl Balibar, PhD, Merck & Co., Inc.: Stocks/Bonds Shuzhi Dong, PhD, Merck & Co., Inc.: Stocks/Bonds Frank Bennett, PhD, Merck & Co., Inc.: Stocks/Bonds Jinlong Jiang, PhD, Merck & Co., Inc.: Stocks/Bonds Haiqun Tang, PhD, Merck & Co., Inc.: Stocks/Bonds Claire Tudge, PhD, Merck & Co., Inc.: Stocks/Bonds Jack Scott, PhD, Merck & Co., Inc.: Stocks/Bonds Dexi Yang, PhD, Merck & Co., Inc.: Stocks/Bonds Alexander Pasternak, PhD, Merck & Co., Inc.: Stocks/Bonds.

Expression and purification of soluble recombinant β-lactamases using Escherichia coli as expression host and pET-28a as cloning vector

BackgroundDue to its high expression capability, recombination of Escherichia coli and pET vector has become the bioengineering preferred expression system. Because β-lactamases mediate bacterial antimicrobial resistance, these enzymes have a substantial clinical impact. Using the E. coli expression system, several kinds of β-lactamases have been produced. However, previous studies have been focused on characterizing target β-lactamases, and the effects of cultivation and induction conditions on the expression efficiency of target enzymes were not addressed.ResultsUsing pET-28a as the cloning vector and E. coli BL21(DE3) as the expression host, this study originally elucidated the effects of IPTG concentration, culture temperature, induction time, and restriction sites on recombinant β-lactamase expression. Moreover, the effects of the target protein length and the 6 × His-tag fusion position on enzyme purification were also explored, and consequently, this study yielded several important findings. (i) Only the signal peptide–detached recombinant β-lactamase could exist in a soluble form. (ii) Low-temperature induction was beneficial for soluble β-lactamase expression. (iii) The closer to the rbs the selected restriction site was, the more difficult it was to express soluble β-lactamase. (iv) The short-chain recombinant protein and the protein with His-tag fused at its C-terminus showed high affinity to the Ni2+ column.ConclusionsBased on our findings, researchers can easily design an effective program for the high production of soluble recombinant β-lactamases to facilitate other related studies.

Horizontal transfer of antibiotic resistance genes into microflora and blood cells in rats fed on GM-diet

BackgroundWith regard to the extensive production of genetically modified organisms, scientists focused on the safety of antibiotic resistance marker (ARM) genes present in GM-crops produced for the consumption of human or animal. We investigated the possible transfer of these genes to the microflora present in the gastrointestinal tract and blood cells of two groups of Male Wistar Albino rats fed on a transgenic diet containing the ARM genes nptII and aadA for 90 days. The conventional PCR was employed to screen for the presence of nptII and aadA genes in the experimental diets, and animals’ samples.ResultsThe occurrence of DNA transfer of nptII and aadA genes from GM-diet to blood and bacterial cells has been unambiguously demonstrated. Results were further confirmed by sequencing and blast analysis, indicating that both transferred segments shared significant alignment with number of Binary and Cloning Vectors with variable similarities. The frequency of transfer of DNA segments from the GM-diet into blood DNA was unexpectedly higher than its transfer to bacterial DNA which may be attributed to a number of factors.ConclusionsOur results unambiguously demonstrated the occurrence of DNA transfer of ARM genes (nptII and aadA) from GM plant diet to blood cells and enteric microflora in rats. Results may draw attentions to the importance of exploring the possible effects of transfer of ARM genes horizontally from GM products to consumers and to extend our attentions to the importance of a better understanding of the factors influencing HGT in the intestine of the GM-food consumers.

Tomato and Jute Mallow are Two New Hosts of Papaya Bunchy Top Phytoplasma, a 16SrXII-O Subgroup Strain in Nigeria.

Nigerian papaya bunchy top (NGPBT) phytoplasma was first identified in diseased papaya plants growing in Ibadan, Oyo State, Nigeria (Kazeem et al. 2021). The NGPBT phytoplasma is a 'Candidatus Phytoplasma convolvuli'-related strain and represents a subgroup lineage, 16SrXII-O (the accession number of the reference strain is MW530522, Kazeem et al. 2021). The present communication reports that NGPBT phytoplasma can also infect tomato (Solanum lycopersicum) and jute mallow (Corchorus olitorius). Since May 2020, tomato and jute mallow grwn in Ibadan have been observed to develop yellowing, little leaf, and stunting symptoms (Fig. 1). Because the symptomatic plants occurred in the region approximately 1 km adjacent to where the NGPBT disease was reported, and the symptoms of infected plants resembled those of phytoplasma infection, molecular diagnostic assays for phytoplasma detection were deployed. Total DNAs were extracted from symptomatic plants, including four tomato plants and three jute mallows, as well as from asymptomatic two tomato and two jute mallow plants. The DNA samples were subjected to semi-nested PCR using phytoplasma 16S rRNA gene-specific primers P1A and P7A, followed by P1A and 16S-SR (Lee et al. 2004). An amplicon of 1.5 kb was obtained from each of the symptomatic plants, while no amplicon resulted from DNA samples of asymptomatic plants or negative controls without DNA templates (water and PCR reagents only). PCR products were cloned into the TOPO TA cloning vector (Invitrogen, Carlsbad, CA, USA), and three clones were chosen for each sample for Sanger sequencing (Psomagen Inc., Rockville, MD, USA). The nearly full-length 16S rRNA gene sequences (1.53kb) derived from tomato (OP123558) and jute mallow (OP123559) samples were identical. Based on the iPhyClassifier phytoplasma classification web tool (Zhao et al. 2009) and the BLAST search against the NCBI nucleotide database, these phytoplasma strains showed 100% sequence identity in 16S rRNA gene with the NGPBT phytoplasma (16SrXII-O, MW530522). Moreover, two additional genetic loci including ribosomal protein genes rplV-rpsC, and rplO-secY-adk were also amplified by nested PCR or semi-nested PCR with specific primers rpStolF/rpStolR followed by rpStolF2/rpStolR (Martini et al. 2007), and SecYF1a (Xll)/MapR-703-a, followed by SecYF2a (Xll)/MapR-703-a (Lee et al. 2010). Gene fragments of rplV-rpsC (1238bp) and rplO-secY-adk (2064bp) were amplified from DNAs of diseased papaya, tomato, and jute mallow plants. The obtained sequences were deposited into GenBank, respectively: rplV-rpsC (OP123560, OP123562, and OP123563) and rplO-secY-adk (OP123565, OP123567, and OP123568). Multilocus sequence analysis (MLSA) indicated that the sequences of phytoplasmas amplified from three different plant hosts were also identical in rp, secY, and adk genes. The MLSA results demonstrate that tomato and jute mallow are two new hosts of NGPBT phytoplasmas. This also marks the first time that phytoplasma diseases are associated with tomato and jute mallow in Nigeria, as prior to this study, phytoplasma diseases were only reported in coconut palm and papaya in the country (Osagie et al. 2016; Kazeem et al. 2021). Results from the present study suggest that insect vector(s) for the transmission of the NGPBT phytoplasma are present in the region. Since both tomato and jute mallow are important vegetable crops in Nigeria, timely dissemination of emerging disease information is needed to alert growers and extension personnel in the region. In addition, ongoing incidence, and prevalence surveys of NGPBT disease indicate that more infected papaya and tomato plants have been observed in the region than in previous years. A better understanding of the NGPBT phytoplasma disease epidemiology will help devise strategies to control the diseases associated with the NGPBT phytoplasma.

Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs.

Isolation and characterization of full-length genes encoding the anti-human CD45 antibody from the hybridoma cell line 16E8-F2

Though the hybridoma technology has been widely applied in the production of monoclonal antibodies, it has existed some disadvantages including low yield and genetic instability. Therefore, an alternative approach should be taken into account. Recently, recombinant monoclonal antibody technology has emerged as the best choice to cure hybridoma related drawbacks. However, recombinant antibodies require known genes for their generation. The purpose of this study is to collect the full-length genes encoding the anti-human CD45 antibody derived from the hybridoma cell line 16E8-F2. In this research, we designed specific primer pairs to amplify the light and heavy chain genes of the antibody through the PCR method. Afterward, the genes were separately cloned into a cloning vector called pJET1.2/blunt. The generated recombinant pJET1.2 vectors will serve as the main material source to manufacture the recombinant monoclonal antibody recognizing human CD45 protein tomorrow.