The functional organization of the nopaline A. tumefaciens plasmid pTiC58

We have employed the P type plasmid RP4 and the transposons Tn1 and Tn7 to isolate insertion and deletion mutations in the nopaline Ti-plasmid pTiC58. Mutations that inactivate all known Ti phenotypes have been located on the physical map. Most importantly, we have positioned several regions involved in the determination of oncogenicity. They correspond to regions of homology between octopine and nopaline plasmids. One of these regions is part of the T-DNA, the Ti-plasmid DNA present in transformed plant cells. There are also segments of the T-DNA that are not essential for oncogenicity. One of these determines the biosynthesis of nopaline in tumors. The latter regions might allow insertion of foreign DNA that can then be introduced into plant cells.     

Metabolic and pathway engineering to influence native and altered erythromycin production through E. coli

The heterologous production of the complex antibiotic erythromycin through Escherichia coli provides a unique challenge in metabolic engineering. In addition to introducing the 19 foreign genes needed for heterologous biosynthesis, E. coli metabolism must be engineered to provide the propionyl-CoA and (2S)-methylmalonyl-CoA substrates required to allow erythromycin formation. In this work, three different pathways to propionyl-CoA were compared in the context of supporting E. coli erythromycin biosynthesis. The comparison revealed that alternative citramalate and threonine metabolic pathways (both starting from exogenous glycerol) were capable of supporting final compound formation equal to a proven pathway reliant upon exogenous propionate. Furthermore, two pathways to (2S)-methylmalonyl-CoA were compared in the production of a novel benzyl-erythromycin analog. A pathway dependent upon exogenous methylmalonate improved selectivity and facilitated antibiotic assessment of this new analog.     

Cloning and expression of a new bacteriophage (SHPh) DNA ligase isolated from sewage

During the last 50 years, major advances in molecular biology and biotechnology have been attributed to the discovery of enzymes that allow molecular cloning of important genes. One of these enzymes that has been widely acknowledged for its role in the development of biotechnology is the T4 DNA ligase. This enzyme joins the break in the DNA backbone structure by creating a phosphodiester bond between 5′ PO₄ and 3′ OH ends, in an ATP dependent multi-step reaction, thus allowing the ligation of related and foreign DNA sequences. Due to its role in modern DNA recombinant technology, there is a high demand on DNA ligase to allow the ligation of target DNA inserts into a chosen vector as part of DNA cloning technology. To closely look at ligase sequence diversity, a bacteriophage that infects DH5α (commercial lab strain of Escherichia coli) was isolated from sewage system in Hebron, Palestine. The DNA ligase gene of this phage was cloned and its sequence was compared to the NCBI database. The new bacteriophage ligase, named (South Hebron Phage, SHPh) DNA ligase, shows homology to T even bacteriophage DNA ligases posted in the NCBI database with 35 nucleotide differences, an indication of existed diversity among T even DNA ligation enzymes that can be used as markers in phage classification.     

Clearance of an immunosuppressive virus from the CNS coincides with immune reanimation and diversification

Background

The yellow fever virus, a member of the genus Flavivirus, is an arthropod-borne pathogen causing severe disease in humans. The attenuated yellow fever 17D virus strain has been used for human vaccination for 70 years and has several characteristics that are desirable for the development of new, live attenuated vaccines. We described here a methodology to construct a viable, and immunogenic recombinant yellow fever 17D virus expressing a green fluorescent protein variant (EGFP). This approach took into account the presence of functional motifs and amino acid sequence conservation flanking the E and NS1 intergenic region to duplicate and fuse them to the exogenous gene and thereby allow the correct processing of the viral polyprotein precursor.

Results

YF 17D EGFP recombinant virus was grew in Vero cells and reached a peak titer of approximately 6.45 ± 0.4 log10 PFU/mL at 96 hours post-infection. Immunoprecipitation and confocal laser scanning microscopy demonstrated the expression of the EGFP, which was retained in the endoplasmic reticulum and not secreted from infected cells. The association with the ER compartment did not interfere with YF assembly, since the recombinant virus was fully competent to replicate and exit the cell. This virus was genetically stable up to the tenth serial passage in Vero cells. The recombinant virus was capable to elicit a neutralizing antibody response to YF and antibodies to EGFP as evidenced by an ELISA test. The applicability of this cloning strategy to clone gene foreign sequences in other flavivirus genomes was demonstrated by the construction of a chimeric recombinant YF 17D/DEN4 virus.

Conclusion

This system is likely to be useful for a broader live attenuated YF 17D virus-based vaccine development for human diseases. Moreover, insertion of foreign genes into the flavivirus genome may also allow in vivo studies on flavivirus cell and tissue tropism as well as cellular processes related to flavivirus infection.     

Integrative Food-Grade Expression System Based on the Lactose Regulon of Lactobacillus casei

The lactose operon from Lactobacillus casei is regulated by very tight glucose repression and substrate induction mechanisms, which made it a tempting candidate system for the expression of foreign genes or metabolic engineering. An integrative vector was constructed, allowing stable gene insertion in the chromosomal lactose operon of L. casei. This vector was based on the nonreplicative plasmid pRV300 and contained two DNA fragments corresponding to the 3′ end of lacG and the complete lacF gene. Four unique restriction sites were created, as well as a ribosome binding site that would allow the cloning and expression of new genes between these two fragments. Then, integration of the cloned genes into the lactose operon of L. casei could be achieved via homologous recombination in a process that involved two selection steps, which yielded highly stable food-grade mutants. This procedure has been successfully used for the expression of the E. coli gusA gene and the L. lactis ilvBN genes in L. casei. Following the same expression pattern as that for the lactose genes, β-glucuronidase activity and diacetyl production were repressed by glucose and induced by lactose. This integrative vector represents a useful tool for strain improvement in L. casei that could be applied to engineering fermentation processes or used for expression of genes for clinical and veterinary uses.     

Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination.

Viewing the immune system as a molecular recognition device designed to identify “foreign shapes”, we estimate the probability that an immune system with N_Ab monospecific antibodies in its repertoire can recognize a random foreign antigen. Furthermore, we estimate the improvement in recognition if antibodies are multispecific rather than monospecific. From our probabilistic model we conclude: (1) clonal selection is feasible, i.e. with a finite number of antibodies an animal can recognize an effectively infinite number of antigens; (2) there should not be great differences in the specificities of antibody molecules among different species; (3) the region of a foreign molecule recognized by an antibody must be severely limited in extent; (4) the probability of recognizing a foreign molecule, P, increases with the antibody repertoire size N_Ab; however, below a certain value of N_Ab the immune system would be very ineffectual, while beyond some high value of N_Ab further increases in N_Ab yield diminishing small increases in P; (5) multispecificity is equivalent to a modest increase (probably less than 10) in the antibody repertoire size N_Ab, but this increase can substantially improve the probability of an immune system recognizing a foreign molecule.Besides recognizing foreign molecules, the immune system must distinguish them from self molecules. Using the mathematical theory of reliability we argue that multisite recognition is a more reliable method of distinguishing between molecules than single site recognition. This may have been an important evolutionary consideration in the selection of weak non-covalent interactions as the basis of antigen-antibody bonds.     

Nucleosomes affect local transformation efficiency

Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today''s recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.     

Stepping stones of life: natal dispersal in the group-living but noncooperative speckled warbler

In most cooperatively breeding birds the offspring of one sex, usually male, delays dispersal to remain on the natal territory and helps its parents to rear subsequent young. Thus delayed dispersal could be the first step in the evolution of cooperative breeding. We studied natal dispersal in a population of the group-living speckled warbler, Chthonicola sagittata, based on observations of a colour-banded population over 3 years. Unlike other group-living members of the Acanthizinae, all juvenile males in this population dispersed to settle on foreign territories as subordinates, which do not help rear the young. Speckled warblers showed all the life history traits that are thought to result in a saturated habitat and lead to delayed dispersal: they were sedentary, had high adult survival and had a male-biased sex ratio. However, they differed from other acanthizids in occurring at low density (0.18 birds/ha) on large breeding territories (6-12 ha), with a maximum of two males per territory. This may allow subordinates to live on foreign territories yet avoid aggression from dominants. A benefit of dispersal is that it provides an additional route to gaining a breeding vacancy. Dispersers can acquire vacancies on their new territory or on a neighbour's, but incest avoidance would be likely to constrain nondispersing males to neighbours' territories. A model of relative lifetime success showed that the survival benefits of natal philopatry are unlikely to outweigh this benefit of dispersal.     

A host-vector system for heterologous gene expression in Streptococcus gordonii

We have developed a host-vector system for heterologous gene expression in Streptococcus gordonii (Sg) Challis (formerly Streptococcus sanguis), a commensal bacterium of the human oral cavity. The system is based on (i) integration of plasmid insertion vectors into the chromosome of specially engineered recipient hosts, and (ii) the use of the M6-protein-encoding gene (emm6) as a partner for construction of translational gene fusions. M6 is a streptococcal surface protein already proven useful as a fusion partner for the delivery of foreign antigens to the surface of Sg [Pozzi et al., Infect. Immun. 60 (1992) 1902–1907]. Insertion vectors carry a drug-resistance marker, different portions of emm6 and a multiple cloning site to allow construction of a variety of emm6-based fusions. Upon transformation of a recipient host with an insertion vector, 100% of transformants acquire both the drug-resistance marker and the capacity of displaying the M6 molecule on the cell surface. Chromosomal integration occurred at high frequency in recipient host GP1221. Transformation with 1 μg of insertion vector DNA yielded 8.1 x 10⁵ transformants per ml of competent cells     

Transformation of tomato using an Ri plasmid vector

An intermediate vector, pAMNeo10, was constructed containing the replication origin and carbenicillin-resistance gene of pBR322, an homology region to allow insertion into the T_L-DNA of pRiA4 in Agrobacterium A4T, and a chimaeric kanamycin-resistance gene (nop. neoΔ) for identification of T_L-DNA::pAMNeo10 transformed roots. Roots produced by inoculating stem explants of Lycopersicon esculentum, L. hirsutum × L. esculentum (KNVF Rootstock) and L. peruvianum with an exconjugant stain, A4T (pRiA4::pAMNeo10), were resistant to kanamycin at levels that completely inhibit the growth of transformed roots produced with wild-type A4T. When transformed by the exconjugant strain, roots of the three tomato hosts were resistant to different levels of kanamycin, and, in the case of L. peruvianum, regenerated plants were tolerant to much higher levels (10×) of kanamycin than the transformed roots from which they were derived. Kanamycin-resistant transformed roots expressed aminoglycoside phosphotransferase activity, and Southern blotting confirmed the presence of the intermediate vector sequence in transformed roots and in shoots of regenerated plants. T_R-DNA was shown to be present in most transformed roots and regenerated shoots by testing for agropine and mannopine. The application of Ri plasmid vectors to the study of foreign gene expression in plants is discussed.     

Coordinate expression and independent subcellular targeting of multiple proteins from a single transgene

A variety of conventional methods allow the expression of multiple foreign proteins in plants by transgene stacking or pyramiding. However, most of these approaches have significant drawbacks. We describe a novel alternative, using a single transgene to coordinate expression of multiple proteins that are encoded as a polyprotein capable of dissociating into component proteins on translation. We demonstrate that this polyprotein system is compatible with the need to target proteins to a variety of subcellular locations, either cotranslationally or posttranslationally. It can also be used to coordinate the expression of selectable marker genes and effect genes or to link genes that are difficult to assay to reporter genes that are easily monitored. The unique features of this polyprotein system are based on the novel activity of the 2A peptide of Foot-and-mouth disease virus (FMDV) that acts cotranslationally to effect a dissociation of the polyprotein while allowing translation to continue. This polyprotein system has many applications both as a research tool and for metabolic engineering and protein factory applications of plant biotechnology.     

Precision genome engineering in lactic acid bacteria

Innovative new genome engineering technologies for manipulating chromosomes have appeared in the last decade. One of these technologies, recombination mediated genetic engineering (recombineering) allows for precision DNA engineering of chromosomes and plasmids in Escherichia coli. Single-stranded DNA recombineering (SSDR) allows for the generation of subtle mutations without the need for selection and without leaving behind any foreign DNA. In this review we discuss the application of SSDR technology in lactic acid bacteria, with an emphasis on key factors that were critical to move this technology from E. coli into Lactobacillus reuteri and Lactococcus lactis. We also provide a blueprint for how to proceed if one is attempting to establish SSDR technology in a lactic acid bacterium. The emergence of CRISPR-Cas technology in genome engineering and its potential application to enhancing SSDR in lactic acid bacteria is discussed. The ability to perform precision genome engineering in medically and industrially important lactic acid bacteria will allow for the genetic improvement of strains without compromising safety.     

Foreign protein production using plant cell and organ cultures: Advantages and limitations

Plants and plant tissue cultures are used as host systems for expression of foreign proteins including antibodies, vaccines and other therapeutic agents. Recombinant or stably transformed plants and plant cell cultures have been applied for foreign protein production for about 20 years. Because the product concentration achieved exerts a major influence on process economics, considerable efforts have been made by commercial and academic research groups to improve foreign protein expression levels. However, post-synthesis product losses due to protease activity within plant tissues and/or extracellular protein adsorption in plant cell cultures can negate the benefits of molecular or genetic enhancement of protein expression. Transient expression of foreign proteins using plant viral vectors is also a practical approach for producing foreign proteins in plants. Adaptation of this technology is required to allow infection and propagation of engineered viruses in plant tissue cultures for transient protein expression in vitro.     

Intestinal parasitic infection among foreign housemaids in northwestern Saudi Arabia: A cross-sectional study

Owing to Saudi Arabia's high-income economy many Saudi families hire foreign housemaids. However, since the housemaids are potential carriers of intestinal parasites, hiring them increases the risk of transmission to the Saudi community. In this context, this study aimed to evaluate the prevalence of intestinal parasitic infections in foreign housemaids in northwestern Saudi Arabia. Using direct wet mount and concentration by flotation, the stool samples of 169 housemaids were examined, and eleven parasite species, six helminths and five protozoans, were detected. The overall prevalence of intestinal parasitic infection was 20.11% (34/169). Twelve cases were infected with one intestinal helminth, 12 were infected with one intestinal protozoan, and 10 had polyparasitism. The most common intestinal parasites were Cryptosporidium spp. (n = 10), hookworms (n = 7), and T. Trichiura (n = 7). The findings highlight that intestinal parasites present an important public health concern for foreign housemaids in Saudi Arabia. More vigilance is thus required, and periodic follow-up should be exercised throughout foreign housemaids' stay in the country.     

Structural modifications of outer membrane vesicles to refine them as vaccine delivery vehicles

In an effort to devise a safer and more effective vaccine delivery system, outer membrane vesicles (OMVs) were engineered to have properties of intrinsically low endotoxicity sufficient for the delivery of foreign antigens. Our strategy involved mutational inactivation of the MsbB (LpxM) lipid A acyltransferase to generate OMVs of reduced endotoxicity from Escherichia coli (E. coli) O157:H7. The chromosomal tagging of a foreign FLAG epitope within an OmpA-fused protein was exploited to localize the FLAG epitope in the OMVs produced by the E. coli mutant having the defined msbB and the ompA::FLAG mutations. It was confirmed that the desired fusion protein (OmpA::FLAG) was expressed and destined to the outer membrane (OM) of the E. coli mutant from which the OMVs carrying OmpA::FLAG are released during growth. A luminal localization of the FLAG epitope within the OMVs was inferred from its differential immunoprecipitation and resistance to proteolytic degradation. Thus, by using genetic engineering-based approaches, the native OMVs were modified to have both intrinsically low endotoxicity and a foreign epitope tag to establish a platform technology for development of multifunctional vaccine delivery vehicles.     

Introduction of the foreign transposon Tn4560 in Streptomyces coelicolor leads to genetic instability near the native insertion sequence IS1649

We report an altered pattern of genetic instability for Streptomyces coelicolor when the bacterium harbored a foreign transposon, Tn4560. Deletions, amplifications, and circularizations of the linear 8.7-Mb chromosome occurred more frequently at sites adjacent to native insertion elements, notably IS1649. In contrast, deletions, amplifications, and circularizations of a wild-type strain happened at heterogeneous sites within the chromosome. In 50 strains examined, structural changes removed or duplicated hundreds of contiguous S. coelicolor genes, altering up to 33% of the chromosome. S. coelicolor shows a bias toward one type of genetic instability during this particular assault from the environment, the invasion of foreign DNA.     

New cloning vectors using benomyl resistance as a dominant marker for selection inNeurospora crassa and in other filamentous fungi

We describe five new plasmid vectors derived from pBR322 that carry theNeurospora crassa β-tubulin gene conferring resistance to benomyl. The benomyl resistance gene has been modified to eliminate an internalEcoRI site to facilitate the cloning ofEcoRI restriction fragments. These plasmids allow rapid subcloning of fragments from one replicon to another without insert fragment purification due to the presence of different drug resistance markers (resistance to kanamycin, tetracycline, or chloramphenicol) carried on the plasmids. These vectors will allow rapid transformation ofN. crassa and other filamentous fungi to allow phenotypic characterization of subcloned fragments.