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Results for “binary vectorization”

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PubMed1992

The nucleotide sequence of an infectious insect-transmissible clone of the geminivirus Panicum streak virus.

The infectious genome of a Kenyan isolate of Panicum streak virus (PSV) has been cloned and sequenced. Infection of host plants was done using an Agrobacterium binary vector containing a partial repeat of the genome. Progeny virus from resultant infections proved to be transmissible by the leafhopper Cicadulina mbila (Naude). Comparisons of the amino acid sequences of PSV DNA-encoded proteins with those of previously characterized geminiviruses infecting monocotyledonous plants, including maize streak virus, revealed high levels of identity. The evolutionary relationship between PSV and other geminiviruses infecting monocotyledons is discussed.

Amino Acid Sequence↗

PubMed2025

Construction and Segmental Reconstitution of Full-Length Infectious Clones of Milk Vetch Dwarf Virus.

The construction of infectious clones (ICs) is essential for studying viral replication, pathogenesis, and host interactions. Milk vetch dwarf virus (MDV), a nanovirus with a multipartite, single-stranded DNA genome, presents unique challenges for IC development due to its segmented genome organization. To enable functional analysis of its genome, we constructed full-length tandem-dimer-based ICs for all eight MDV genomic segments. Each segment was cloned into a binary vector and co-delivered into Nicotiana benthamiana, Nicotiana tabacum, Vicia faba, and Vigna unguiculata plants via Agrobacterium-mediated inoculation. Systemic infection was successfully reconstituted in all host plants, with PCR-based detection confirming the presence of all viral segments in the infected leaves of nearly all tested plants. Segmental accumulation in infected plants was quantified using qPCR, revealing non-equimolar distribution across hosts. This study establishes the first complete IC system for MDV, enabling reproducible infection, replication analysis, and quantitative segment profiling. It provides a foundational tool for future molecular investigations into MDV replication, host interactions, and viral movement, advancing our understanding of nanovirus biology and transmission dynamics.

Nicotiana↗

PubMed2025

Development of a plant-based vaccine against brucellosis: stable expression of Brucella abortus OMP25 in transgenic tobacco.

Brucellosis, caused by Brucella species, is a global threat to livestock farming, resulting in economic losses and socio-economic challenges, particularly in rural areas. Despite its impact, no licensed human vaccines are available. Animal vaccination remains the most cost-effective control method, but traditional vaccine production is expensive. Edible vaccines, using plants as bioreactors to produce immunogenic antigens, offer a low-cost alternative by eliminating complex purification processes. This study developed a transgenic plant by expressing the Brucella abortus outer membrane protein OMP25 in tobacco plants. OMP25, a conserved transmembrane protein with high immunogenicity, was cloned into a Gateway pDONR vector via a Boundary Pairing reaction and transferred to a binary destination vector via a Left-Right reaction. The destination vector was introduced into Agrobacterium tumefaciens and subsequently used for Agrobacterium-mediated transformation of tobacco plants. Transgenic plants were selected on media containing kanamycin, and the expression of the transgene was verified through the fluorescence of green fluorescent protein. Microcallus formation and shoot development on selective media confirmed kanamycin resistance and the successful integration of the transgene. After phenotypic selection, genomic DNA was extracted from transgenic plants and analyzed by PCR (Polymerase Chain Reaction) using primers specific to the OMP25 gene. Positive PCR results validated the successful integration of the OMP25 gene into the plant genome. Gene expression was further confirmed at the RNA level through real-time quantitative PCR (qRT-PCR) and at the protein level via Western blot analysis. Future studies will evaluate immune responses in animal models. This approach demonstrates the potential for low-cost, effective vaccines to combat brucellosis, addressing critical economic and public health challenges.

Plants, Genetically Modified↗

PubMed2024

Proteome-scale prediction of molecular mechanisms underlying dominant genetic diseases.

Many dominant genetic disorders result from protein-altering mutations, acting primarily through dominant-negative (DN), gain-of-function (GOF), and loss-of-function (LOF) mechanisms. Deciphering the mechanisms by which dominant diseases exert their effects is often experimentally challenging and resource intensive, but is essential for developing appropriate therapeutic approaches. Diseases that arise via a LOF mechanism are more amenable to be treated by conventional gene therapy, whereas DN and GOF mechanisms may require gene editing or targeting by small molecules. Moreover, pathogenic missense mutations that act via DN and GOF mechanisms are more difficult to identify than those that act via LOF using nearly all currently available variant effect predictors. Here, we introduce a tripartite statistical model made up of support vector machine binary classifiers trained to predict whether human protein coding genes are likely to be associated with DN, GOF, or LOF molecular disease mechanisms. We test the utility of the predictions by examining biologically and clinically meaningful properties known to be associated with the mechanisms. Our results strongly support that the models are able to generalise on unseen data and offer insight into the functional attributes of proteins associated with different mechanisms. We hope that our predictions will serve as a springboard for researchers studying novel variants and those of uncertain clinical significance, guiding variant interpretation strategies and experimental characterisation. Predictions for the human UniProt reference proteome are available at https://osf.io/z4dcp/.

Humans↗

PubMed1991

The nucleotide sequence and genome structure of the geminivirus miscanthus streak virus.

A tandem dimer of miscanthus streak virus (MiSV) DNA was inserted into the T-DNA of the binary plasmid vector pBIN19 and agroinoculated into several monocotyledonous plants (monocots) using Agrobacterium tumefaciens or A. rhizogenes. Disease symptoms and geminate particles were produced in maize and Panicum milaceum plants, and MiSV-specific double-stranded and single-stranded DNAs were found in these plants. The nucleotide sequence of the infectious MiSV clone, consisting of 2672 nucleotides, was determined. Four open reading frames (ORFs) for proteins of Mr greater than 10K were identified, two (V0 and V2) in the virus (+) sense and two (C1 and C2) in the complementary (-) sense, although C2 did not have an ATG start codon. Unlike other geminiviruses infecting monocots, complementary-sense ORFs did not overlap. Potential splicing donor and acceptor sites were identified in the sequence of the border region between the C terminus of ORF C1 and the N terminus of ORF C2. Amino acid sequences predicted from three (V2, C1 and C2) of these ORFs showed significant homology with the corresponding ORFs of other geminiviruses infecting monocots. A fifth ORF (V1), which showed some homology with ORF V1 of other monocot-infecting geminiviruses despite having a coding capacity for a product of Mr 8.8K, was found just upstream of ORF V2 as observed in those geminiviruses. ORF V0 showed no significant homology with ORFs present in any other geminiviruses. A mutation of V0 indicated that the C-terminal 30% of this ORF was not necessary for infection in maize, but that sequences around the mutated LspI site might have some regulatory role.

Amino Acid Sequence↗

PubMed1991

Insect resistance of transgenic tobacco plants expressing delta-endotoxin gene of Bacillus thuringiensis.

The initiative B.thuringiensis delta-endotoxin (Bt toxin) gene clones TH12 and TH48 contain two different classes of homologous genes, the 5.3 kb class and 6.6 kb class, respectively. Bt toxin genes of both classes, modified at the 5'-end and truncated at the 3'-end, can still be expressed to produce the insecticidal, truncated toxin proteins in E. coli. The modified Bt toxin genes were inserted into the plant binary expression vector pBin 437 (a derivative plasmid of pBin 19) and were transferred into tobacco by Ti plasmid-mediated gene transfer system. Southern blot and DNA slot blot analysis indicate that the Bt toxin genes have been integrated into tobacco genome at a copy number of 1 to 5. Northern blot analysis of polyA+ RNAs from progeny of the transgenic plants revealed that Bt toxin genes of both 5.3 kb and 6.6 kb classes were expressed in transgenic plants, though the transcripts were degraded to RNAs of lower molecular weights. In insecticidal test, 5 plants from the progeny of 5.3 kb class gene-transformed SR1 tobacco plants and 3 plants from those of 6.6 kb class gene-transformed plants were found to be toxic to the testing larvea of H.assulta. In comparison with the control, mortality of the insects fed on transgenic plants reached 40-50% and the growth of the survived insects was remarkably inhibited. These results indicate that the modified Bt genes of the 5.3 kb and 6.6 kb classes were expressed in transgenic plants and could confer on the transgenic plants a new character of insect resistance.

Animals↗

PubMed1992

Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac.

This report describes a series of transposon tagging vectors for dicotyledonous plants based on the maize transposable element Ac. This binary system includes the transposase (Ts) and the tagging element (Ds) on separate T-DNA vectors. Ts elements include versions in which transcription is driven either by the endogenous Ac promoter or by the cauliflower mosaic virus (CaMV) 35S promoter. Ds tagging element includes a gene conferring methotrexate (Mtx) resistance for selection and a supF gene to facilitate cloning of tagged sequences. The Ds element is flanked by a CaMV 35S promoter and the beta-glucuronidase (GUS) coding sequence so that GUS expression occurs upon excision of the element. We have transformed these Ts and Ds elements into tobacco and demonstrated that the Ts is functional with either promoter, and that the artificial Ds elements are capable of transposition. The amount of excision was found to depend upon both the individual Ts and Ds primary transformants used. Somatic excision of Ds was seen in up to 100% of progeny seedlings containing Ts and Ds. Germinal excision was detected in up to 48% of the progeny of plants containing both elements. Hence, this system can generate a sufficient number of events to be useful in gene tagging.

Base Sequence↗

PubMed1978

Learning processes in multilayer threshold nets.

An algorithm of learning in multilayer threshold nets without feedbacks is proposed. The net is built of threshold elements with binary inputs. During a learning process each input vector chi is accompanied by a teacher's decision omega (omega epsilon(1,...,M)). The pairs (chi[n], omega[n]) appear in successive steps independently according to some unknown stationary distribution p(chi, omega). The problem of learning of a threshold net has been decomposed to a series of problems of learning of the threshold elements. The proposed learning algorithm of the threshold elements has a perceptron-like form. It was proven that a decision rule of the threshold net stabilizes after a finite number of steps. For definite classes (p(chi,omega))K of distributions p(chi, omega), an optimal decision rule stabilizes after a finite number of steps. These classes (p(chi, omega))K also contain distributions describing learning processes with perturbations.

Feedback↗

PubMed1992

A new approach for three-dimensional reconstruction of arterial ultrasonography.

This report describes a computerized approach that allows the creation of realistic three-dimensional arterial images from two-dimensional contiguous slices derived from a conventional ultrasound scan. Furthermore, the study assesses the method's feasibility and accuracy by performing in vitro cadaver artery three-dimensional reconstructions. Images are digitized into a computer, with a resolution of 512 x 480 pixels, and a dynamic range of 8 bits/pixel (256 gray scale). After edge enhancement with convolution filters through the original binary data, the intraluminal and outer edges are traced and converted to a polygon vector within a defined three-dimensional space. Serial cuts, 2 mm apart, are then "stacked" into a three-dimensional model, with interpolation of polyhedra between slices. Sixteen normal and arteriosclerotic distal aortic and common iliac arteries were obtained from fresh cadavers. Three-dimensional reconstruction models were compared with gross examination of the original artery. Anatomically accurate reconstructions were obtained, all with detailed surface information. Data analyzed included diameter, area, residual lumen, and percent stenosis. Pearson's coefficients determined for the pairs of data indicated excellent correlation (greater than or equal to 0.90) between separate measurements. With use of the described technology it is feasible to perform arterial three-dimensional reconstructions on a personal computer, with detailed and accurate surface information. The three-dimensional reconstruction method used can reliably and consistently reproduce the anatomic specimens.

Arteries↗

PubMed1992

A T-DNA transfer stimulator sequence in the vicinity of the right border of pRi8196.

An 8 bp sequence repeated 6 times is present to the right of the mannopine type pRi8196 T-DNA right-border sequence. Experiments were designed to test whether these repeats have a role in T-DNA transfer. Several constructs in which different lengths of pRi8196 right-border region were linked to the cucumopine synthesis gene on an Agrobacterium-Escherichia coli shuttle vector were made. The recombinant plasmids were tested for their efficiency to act as a source of T-DNA in a binary system in which a wild-type Ri plasmid provided virulence and root-inducing functions. The T-DNA transfer efficiency of the constructs was assessed by computing the relative frequency of roots containing cucumopine. Depending on the Ri plasmid used as source of virulence functions, a high level of T-DNA transfer was observed only if 6 (pRi8196) or 5 (pRiA4) repeats were present. These results were confirmed by looking for single-stranded T-DNA molecules (T-strands) in bacteria induced for virulence. The repetition of the 8 bp unit was named 'T-DNA transfer stimulator sequence' (TSS).

Base Sequence↗

PubMed1977

Profiling of odor components and their mixtures.

Observers evaluated five odors and their 26 mixtures (two, three, four, and five components) by magnitude estimation. Estimates revealed that in mixtures there is moderate suppression of perceived intensity; a vector model proposed by Berglund (Annals of the New York Academy of Sciences, 1974, 237, 35-51) provides a good prediction of the intensity of binary mixtures, but overpredicts the intensity of three, four, and five component mixtures. Hedonic tones of mixtures were difficult to predict from hedonic tones of components. Qualities of mixtures were difficult to predict from quality of components. Intermediacy, of quality and hedonic values, was often observed.

Adult↗

PubMed1979

Electron microscopical studies on the development of Babesia canis (Sporozoa) in the salivary glands of the vector tick Dermacentor reticulatus.

The formation of sporozoites of Babesia canis was studied by light- and electron microscopy in the salivary gland cells of adult female ticks from the 2nd day after attachment until 1 day after detachment. It was found that this process was initiated by the binary division of kinetes that had already entered or entered during the period examined. During division the kinetes (15 X 2.5 microns) lost their typical organelles, reduced their three-layered pellicle to a single membrane and became spherical. After nuclear division and a further time-lag cell division occurred, giving rise to two cells in which this process was repeated. After numerous binary divisions the parasites acquired more and more closely the shape of the later infectious, pyriform sporozoite. These sporozoites measured about 2.5 X 1.5 microns and also had a three-layered pellicle, with rhoptries and a few micronemes, but never contained "spherical bodies". The formation process needed about 2--3 days so that the transmission to the dog could be carried out while the tick engorges and this is probably the stimulation for the development. Finally the cytological features of this sporozoite formation were compared to those in the Theileria species studied by our group.

Animals↗

PubMed1977

Polydisperse particulate solids mixing and segregation: nonstationary Markov chains.

The feasibility of analyzing interparticulate translocations within agitated beds of polydisperse particulate solids in terms of Markov chains was investigated. A binary mixture of spherical particles subjected to vertical sine wave vibration is shown to behave in accordance with a nonstationary. Markov chain having singly stochastic transition matrixes. The transition probability elements of such matrixes, calculated from a knowledge of the initial and final occupancy vectors, agree with those estimated using tracer particles. With appropriate restrictions, the former method, based on the solution of simultaneous equations, permits a quantitative evaluation of particle mobilities throughout the bed.

Chemistry, Pharmaceutical↗

PubMedDate not supplied

[The susceptibility of mosquitoes for Plasmodium gallinaceum in the joint use of biologically active substances].

Making use of a model pair Aedes aegypti--Plasmodium gallinaceum, the authors assess the susceptibility of mosquito female survivors to malaria agent after treatment of larvae with various bioactive substances. Eight binary combinations of 6 preparations have been tried: dimilin and uvemon, insect development regulators; fundosol and copper sulfate, fungicides; phytobacteriomicin (PBM), a larvicidal antibiotic; bactoculicide, a bacterial agent. Combinations of PBM with compounds differing by their mechanisms of action were found to inhibit the specific effect of PBM on the vector, PBM specific effect consisting in depression of mosquito susceptibility to P. gallinaceum. PBM combinations with some agents may alter other parameters of the vector potential: combinations of copper sulfate or uvemon with low concentrations of PBM potentiated the larvicidal effect, and PBM mixtures with fungicides reduces the activity of female attacks.

Aedes↗

PubMed1979

Babesia microti: morphology, distribution and host relationship in Germany.

A short review has been given about recent studies on Babesia microti in natural animal host's near Munich (Southern Germany). An infected area has been studied in order to elucidate the outdoor relationship between the local strains and their preferred hosts, the European field vole Microtus agrestis. The seasonal variation of the parasites prevalence in voles shows a rise in the early summertime (71% of the catches infected). Roundish forms predominate in the erythrocytes. Multiplication never takes place by binary fission, but in "Maltese cross" form or budding-like. Normally the parasite is enveloped with a simple elementary membrane only, as shown by electron microscopy. The arthropod host is still not identified, infections of human beings not observed. This is the first finding and full description of B. microti in Germany.

Animals↗

PubMed1991

Comparative study on Rickettsia-like organisms in the midgut epithelial cells of different Glossina species.

The midgut epithelium of Glossina morsitans centralis, G. austeni, G. pallidipes, G. palpalis palpalis, G. p. gambiensis, G. fuscipes fuscipes, G. tachinoides and G. brevipalpis from ILRAD-bred colonies was examined, by electron microscopy, for the presence and distribution of Rickettsia-like organisms (RLOs). RLOs were present in the midgut epithelial cells of all non-teneral tsetse. In G.m. centralis, G. pallidipes and, to a much lesser extent, G. brevipalpis, RLOs were numerous and were present in all the specimens examined. RLOs were present in fewer numbers in the epithelial cells of tenerals of these three tsetse species. In contrast, RLOs occurred in very much lower numbers within the midgut cells of nonteneral G. austeni, G. p. palpalis, G. p. gambiensis, G.f. fuscipes and G. tachinoides; were not seen in every specimen, and were rarely observed in the midgut cells of teneral testse. The RLOs were typical rod-shaped bacteria with an inner and outer membrane, which occurred free within the host cell cytoplasm and appeared to cause no obvious pathology. The micro-organisms divided by binary fission and at least two distinct morphological forms plus a range of intermediate forms were seen in the midgut cells. A comparison of the presence and numbers of RLOs within the midgut cells and the midgut infection rates of both Trypanosoma congolense and T. b. brucei, both between Glossina species and also within the same stock of tsetse, clearly indicates that the ability of trypanosomes to establish and develop to mature infections is unlikely to be correlated solely with the presence of RLOs within the tsetse midgut.

Animals↗

PubMed2025

Disease candidate genes prediction using positive labeled and unlabeled instances.

Identifying disease genes and understanding their performance is critical in producing drugs for genetic diseases. Nowadays, laboratory approaches are not only used for disease gene identification but also using computational approaches like machine learning are becoming considerable for this purpose. In machine learning methods, researchers can only use two data types (disease genes and unknown genes) to predict disease candidate genes. Notably, there is no source for the negative data set. The proposed method is a two-step process: The first step is the extraction of reliable negative genes from a set of unlabeled genes by one-class learning and a filter based on distance indicators from known disease genes; this step is performed separately for each disease. The second step is the learning of a binary model using causing genes of each disease as a positive learning set and the reliable negative genes extracted from that disease. Each gene in the unlabeled gene's production and ranking step is assigned a normalized score using two filters and a learned model. Consequently, disease genes are predicted and ranked. The proposed method evaluation of various six diseases and Cancer class indicates better results than other studies.

Humans↗

PubMed1991

Expression of v-src in embryonic neural retina alters cell adhesion, inhibits histogenesis, and prevents induction of glutamine synthetase.

Using Rous sarcoma virus as the vector, v-src or c-src genes were introduced into 6-day chicken embryo retina tissue in organ culture and their effects on retina development were investigated. Overexpression of c-src in many of the cells had no noticeable effect on retina development. In contrast, infection with v-src resulted in abnormal histogenesis and inhibition of differentiation. Although only a portion of the cells in infected tissue expressed the oncogene and displayed the transformation phenotype, the other cells were also hindered from becoming normally positioned and organized. Therefore, presence of oncogene-transformed cells within the tissue hindered organization and development of adjacent nontransformed cells. Failure of normal cell relationships impeded induction by cortisol of glutamine synthetase in Muller glia, which requires contact associations of the glia cells with neurons. The transformed cells tended to assemble into chaotic clusters, suggesting that their adhesiveness and contact affinities had become altered. This was confirmed by aggregation experiments with dissociated cells which showed that adhesiveness of transformed cells was greatly reduced and that they had lost the ability to cohere with nontransformed cells. In binary mixtures of transformed and nontransformed cells, the two sorted out into separate aggregates. Transformed cells formed loose clusters devoid of tissue architecture; aggregates of nontransformed cells became organized into retinotypic structures, and glutamine synthetase was inducible. Our findings suggest that the mechanisms of cell adhesion and cell affinities are a key target of v-src activity in infected cells and that modification of the cell surface may be a leading factor in other cellular changes characteristic of the v-src transformation phenotype.

Animals↗