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At least 397 records · Page 22Linked to original sources

PubMed2005

Molecular characterization of integrons in non-typhoid Salmonella serovars isolated in Japan: description of an unusual class 2 integron.

OBJECTIVES: To characterize class 1 and class 2 integrons among non-typhoid Salmonella enterica serovars in Japan, and also to monitor the spread of the multidrug-resistant S. enterica serovar Typhimurium DT104. METHODS: A total of 105 Salmonella isolates were included in this study. The broth microdilution method was used to determine the MIC values of a range of antibiotics for these isolates. PCR and DNA sequencing were used for screening and characterization of class 1 and class 2 integrons. RESULTS: PCR sequencing analysis revealed the presence of seven profiles of class 1 integrons in addition to a new type of class 2 integron. The identified gene cassettes within class 1 integrons were as follows; aadA1, aadA2 and aadA5, which confer resistance to streptomycin and spectinomycin; aadB, which confers resistance to gentamicin, kanamycin and tobramycin; dfrA1 and dfrA17, which confer resistance to trimethoprim; bla(PSE-1), which confers resistance to ampicillin; catB3, which confers resistance to chloramphenicol; and sat1, which confers resistance to streptothricin. Two strains of the multidrug-resistant S. Typhimurium DT104 were characterized in this study. DNA sequencing of class 2 integrons identified one with an unusual array of gene cassettes, sat, sat1 and aadA1. CONCLUSIONS: In this study, we characterized the antibiotic resistance gene cassettes within class 1 integrons in different isolates of non-typhoid Salmonella serovars, and we also identified a new type of class 2 integron.

Base Sequence↗

PubMed2006

Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins.

Investigations of opsin evolution outside of vertebrate systems have long been focused on insect visual pigments, whereas other groups have received little attention. Furthermore, few studies have explicitly investigated the selective influences across all the currently characterized arthropod opsins. In this study, we contribute to the knowledge of crustacean opsins by sequencing 1 opsin gene each from 6 previously uncharacterized crustacean species (Euphausia superba, Homarus gammarus, Archaeomysis grebnitzkii, Holmesimysis costata, Mysis diluviana, and Neomysis americana). Visual pigment spectral absorbances were measured using microspectrophotometry for species not previously characterized (A. grebnitzkii=496 nm, H. costata=512 nm, M. diluviana=501 nm, and N. americana=520 nm). These novel crustacean opsin sequences were included in a phylogenetic analysis with previously characterized arthropod opsin sequences to determine the evolutionary placement relative to the well-established insect spectral clades (long-/middle-/short-wavelength sensitive). Phylogenetic analyses indicate these novel crustacean opsins form a monophyletic clade with previously characterized crayfish opsin sequences and form a sister group to insect middle-/long-wavelength-sensitive opsins. The reconstructed opsin phylogeny and the corresponding spectral data for each sequence were used to investigate selective influences within arthropod, and mainly "pancrustacean," opsin evolution using standard dN/dS ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a historical (i.e., phylogenetic) context. Although the conservative dN/dS methods did not detect any selection, 4 amino acid properties (coil tendencies, compressibility, power to be at the middle of an alpha-helix, and refractive index) were found to be influenced by destabilizing positive selection. Ten amino acid sites relating to these properties were found to face the binding pocket, within 4 A of the chromophore and thus have the potential to affect spectral tuning.

Animals↗

PubMed1991

A micro method involving micro high-performance liquid chromatography-mass spectrometry for the structural characterization of neutral glycosphingolipids and monosialogangliosides.

A micro method involving high-performance liquid chromatography-fast atom bombardment mass spectrometry (HPLC/FAB/MS) has been developed for the sensitive structural characterization of neutral glycosphingolipids and monosialogangliosides. The method involves a micro silica gel column (0.3 mm i.d. x 100 mm) and a micro HPLC apparatus working at a flow rate of 6 microliters/min. All injected materials can be structurally characterized by mass spectrometry without the splitting or wasting of materials, which was not possible with our previous method [M. Suzuki et al. (1990) J. Biochem. 108, 92-98]. A mixture containing 160 ng each of five neutral glycosphingolipids (GlcCer, LacCer, Gb3Cer, Gb4Cer, and IV3 alpha GalNAc-Gb4Cer) and a mixture containing 160 ng each of three monosialogangliosides [GM3(NeuAc), GM2(NeuAc), and GM1(NeuAc)] were injected into the micro HPLC with programmed elution with isopropanol-n-hexane-water with or without ammonium hydroxide. Each glycosphingolipid was separated by mass chromatography and the obtained mass spectra were suitable for structural characterization. Thus, the characterization of glycosphingolipids was achieved with small amounts of materials, 160 ng each, and in mixtures.

Chromatography, High Pressure Liquid↗

PubMed1999

Integrated designs for gene discovery and characterization.

Recent advances, including near completion of the human genome map, ever improving high-throughput technologies, and successes in discovering chronic disease-related genes, have stimulated the further development of genetic epidemiology. The primary mission of genetic epidemiology is to discover and characterize genes, whether independent of or interactive with environmental factors, that cause human diseases. To accomplish such a mission, genetic epidemiology needs to integrate both genetic and epidemiologic approaches. One of the challenges facing such an integrated approach is the identification of study designs that are efficient for both gene discovery and characterization. Because designs for gene discovery alone and designs for gene characterization alone have been elaborated in the other two panels, the focus of this paper is to describe those designs that may be useful for discovery and characterization jointly, including case-family and case-control-family designs. Examples of integrated designs are described, and studies of breast cancer conducted at the Fred Hutchinson Cancer Research Center are used for illustration. Finally, related analytic issues are also discussed.

Breast Neoplasms↗

PubMed2000

Characterization of cells collected from the normal human ocular surface by contact lens cytology.

PURPOSE: In this investigation, we characterized cells collected from the normal human ocular surface using contact lens cytology (CLC). METHODS: Cells were characterized over the course of a day in three different ways. In experiment 1, we collected samples from 10 subjects six times during 1 day. Cell viability was determined by a calcein-ethidium assay. The same collection methods were used in experiment 2, but cell types were identified by fluorescent probes AE5 (corneal epithelium), AE1, AE3 (all epithelium), and T200 (all inflammatory cells). In experiment 3, cells were collected from five subjects two times in 1 day and characterized by fluorescent probes CD3 (T cells) and CD19 (B cells). For morning samples, we used an HLA-DR probe and transmission electron microscopy to examine the inflammatory activation of collected cells. RESULTS: We found viable and nonviable cells in all CLC samples, as well as an intermediate cell type that stained with both calcein and ethidium. There was a diurnal variation in cell numbers over the course of I day in viability and cell type assays, with greater cell numbers collected in the morning and evening, and fewest at midday. In the late afternoon and evening, there was an increase in corneal epithelial cell counts. There were more inflammatory cells in morning collections that included polymorphonuclear cells (PMNs). Many of these were HLA-DR+ and actively phagocytic, reflecting the immune activation of cells. CONCLUSION: The ocular surface is a dynamic environment characterized by cyclical shedding of the epithelium and active monitoring by immune cells.

Adolescent↗

PubMedDate not supplied

Additional value of magnetic resonance with spin echo T1-weighted imaging with fat suppression in characterization of soft tissue tumors.

OBJECTIVE: The aim of the study was to describe the signal intensity (SI) behavior of soft tissue tumors (STT) on spin echo (SE) T1 weighted images (WI) with fat suppression (FS) and to assess its additional value in tissue characterization. METHODS: MRI signal characteristics of 53 histological proven STT were discussed. Signal intensity behavior of STT could be classified in 4 types, representing specific tissues or tissue components. Type 1 was defined as low SI on both SE T1-WI and SE T1-WI with FS. Type 2 was defined as high SI on both sequences. Type 3 consisted of high SI on T1-WI and low SI on T1-WI with FS. Type 4 was defined as SI comparable with SI of normal muscle on T1-WI and SI higher than normal muscle on T1-WI with FS. The additional information concerning contrast enhancement is described. RESULTS: Type 1 SI behavior was noted in fibrous lesions, in hemosiderotic components, cysts, and myxoma. Type 2 was noted in lesions containing methemoglobin or melanin. Type 3 was specific for fatty tissue. Type 4 was noted in highly cellular parts and in lesions of vascular origin. The use of SE T1-WI with FS improved lesion conspicuity on T1-WI. CONCLUSIONS: E T1-WI with FS has additional value in the characterization of fibrous and hemosiderotic parts from cellular parts of lesions. It gives more confidence in characterization of neurogenic tumors and hemangioma's. Presence of methemoglobin and melanin are clearly discriminated from fatty tissue. Tumor conspicuity and inhomogeneity evaluation is improved. The use of SE T1-WI FS not only improves tumor conspicuity, but as tumor homogeneity and SI are important parameters in staging and characterization of STT, the use of SE T1-WI with FS will certainly be helpful. This may obviate the need for gadolinium administration.

Contrast Media↗

PubMedDate not supplied

Liver tumor characterization: comparison between liver-specific gadoxetic acid disodium-enhanced MRI and biphasic CT--a multicenter trial.

OBJECTIVE: In our multi center trial we compared the potentials of biphasic contrast-enhanced computed tomography (CT) and a novel tissue-specific magnetic resonance imaging (MRI) contrast agent gadoxetic acid disodium in liver lesion characterization. METHODS: A total of 176 patients with 252 liver lesions were analyzed. There were 104 malignant and 148 benign lesions. High-field strength (1.0 T or 1.5 T) MR systems with T1-and T2-weighted sequences were used with and without fat suppression. After gadoxetic acid disodium injection, dynamic imaging and hepatocyte phase MR imaging were performed. Biphasic with 150 mg I/kg of body weight (100-200 mL) spiral CT was also performed. Image reading consisted of on-site (by study investigators) and fully blinded off-site (by E.S.P; C.R; and A.S) evaluations. The classification (benign or malignant) and characterization (lesion type) outcomes of both techniques were assessed. All imaging results were verified against a standard of reference. RESULTS: Both on-site and off-site evaluations demonstrated increases in the lesion classification accuracy with gadoxetic acid disodium-enhanced MRI when compared with spiral CT. This improvement was also shown for characterization. Gadoxetic acid disodium was well tolerated. CONCLUSIONS: Gadoxetic acid disodium offers a safe and diagnostically powerful tool for the evaluation of patients with focal liver lesions with a reliable assessment of lesion classification and characterization.

Gadolinium DTPA↗

PubMed1998

Nondisruptive, in vivo method for biomechanical characterization of linear incision wound healing: preliminary report.

Previous work on in vivo biomechanical characterization of soft tissues and wound healing has led to the development of a methodology for nondisruptive, in vivo biomechanical analysis of linear incision wounds. The purpose of this preliminary study was to define nondisruptive biomechanical parameters that characterize progressive healing and compare them with an in vivo disruptive parameter of ultimate pressure at failure (in vivo strength). Male Sprague-Dawley rats (n = 60), each weighing 250 to 300 gm, were anesthetized and underwent creation of paired full-thickness linear incision wounds. The rats were divided into three groups (n = 10/group per time period): control group, nothing applied to either wound; carrier group, bovine serum albumin applied to each wound; transforming growth factor-beta2 group, transforming growth factor-beta2 in bovine serum albumin applied to each wound. On postoperative days 5 and 10, rats from each group underwent in vivo biomechanical testing using the Dimensional Analysis System (Dimensional Analysis Systems, Inc., Nashville, Tenn.). This computer-driven device integrates a video camera and processor with a vacuum controller, valve, and transducer to provide measurements of tissue deformation (in millimeters) and negative pressure (mmHg) as a multiaxial stress (vacuum) is applied to a wound. On each rat, one incision was tested disruptively and the other incision was tested nondisruptively. Disruptive data were measured as ultimate pressure (mmHg) at failure, or the amount of pressure required to disrupt the wound. Nondisruptive data were measured for tissue stiffness (kiloPascals) during application of negative pressure (maximum, 80 mmHg). On postoperative day 5, wounds treated with transforming growth factor-beta2 had significantly increased in vivo wound strength compared with carrier wounds. The nondisruptive parameter of tissue stiffness was also significantly increased for the transforming growth factor-beta2 treated wounds, thus supporting the disruptive data. On postoperative day 10, there was no difference in mean wound strength or mean tissue stiffness among any of the groups. These preliminary data represent the first report of in vivo, nondisruptive biomechanical characterization of linear incision wounds. The results suggest that through in vivo measurements of tissue stiffness, differences can be detected between treatment groups. Because the healing wound may be characterized without the need for disruption, this methodology should allow for consecutive, in vivo biomechanical testing of wounds in future wound healing studies.

Animals↗

PubMed1996

Human phenol sulfotransferase pharmacogenetics: STP1 gene cloning and structural characterization.

Sulfate conjugation catalysed by phenol sulfotransferase (PST) is an important pathway in the metabolism of many drugs. Two isoforms of PST have been characterized biochemically in human tissues-a thermostable (TS), or phenol-metabolizing (P) and a thermolabile (TL), or monoamine-metabolizing (M) form. Pharmacogenetic studies of TS and TL PST activities in the human blood platelet showed that the activities of these two isoforms were regulated by separate genetic polymorphisms. Subsequently, a series of TS PST cDNAs were cloned, and, based on sequence homology, those cDNAs could be classified as members of two separate subgroups, designated here as 'TS PST1' and 'TS PST2'-indicating the existence of three rather than two PST isoforms; TS PST1, TS PST2 and TL PST. The genes encoding TS PST2, STP2, and TL PST, STM, have been cloned, structurally characterized and mapped to chromosome 16-the same chromosome on which the TS PST1 gene, STP1, is localized. As a step toward molecular pharmacogenetic studies of sulfate conjugation in humans, we set out to clone and structurally characterize STP1, the remaining uncharacterized human PST gene. We found that STP1 spanned approximately 4.4 kb and contained 9 exons. The first two exons, IA and IB, were identified by performing 5'-rapid amplification of cDNA ends (RACE) with human liver cDNA as template. Exons IA and IB were noncoding and represented two different cDNA 5'-untranslated region sequences. No canonical TATA box sequences were present within the 5'-flanking regions of the gene, i.e. regions flanking exons IA and IB. Finally, use of the long polymerase chain reaction made it possible to determine that STP1 is located approximately 45 kb 5'-upstream from STP2 on the short arm of human chromosome 16. Cloning and structural characterization of STP1, when combined with knowledge of the structures of STP2 and STM, will make it possible to study the molecular basis for the genetic regulation of PST activity in human tissue.

Amino Acid Sequence↗

PubMed2003

Characterization of allergenic food proteins for improved diagnostic methods.

PURPOSE OF REVIEW: Diagnostic decision points for food allergen-specific serum IgE concentration and for skin prick test results have been established for several foods, reducing the requirement for food challenges in a number of patients. Many patients, however, still need to undergo oral food challenges because their food-specific IgE level is in the undefined range. In addition, diagnostic decision points could not be established for several foods. It appears that measurement of serum specific IgE concentrations to individual allergens is superior to determination of specific IgE to the crude food extract containing allergenic and nonallergenic proteins. This review will outline recent advantages in characterization of food allergens as well as the relevance of this knowledge for use in recently developed protein microarray technology. RECENT FINDINGS: Protein microarrays have been developed to profile allergen-specific IgE antibodies from human serum with the advantage of screening hundreds of allergens in parallel using minute amounts of blood. This technology, however, requires prior knowledge of the proteins to be studied. The identification and characterization of clinically relevant allergens have increased dramatically within the last several years. Relevant new allergens have been identified, especially in tree nuts and seeds. Interestingly, most of these allergens belong to the same family of seed storage proteins. In addition, known food allergens have been further characterized and IgE-binding sites have been determined. Moreover, 'informative' peptides shown to be predictive for the persistence of food allergy have been identified. SUMMARY: The combination of food allergen characterization and protein or peptide microarray technology will enable us to develop improved diagnostic tools in food allergy.

Allergens↗

PubMed2003

Establishment and characterization of a continuous human chondrosarcoma cell line, ch-2879: comparative histologic and genetic studies with its tumor of origin.

Chondrosarcomas are malignant cartilage-forming tumors that represent the second most common malignant solid tumor of bone. These biologically poorly understood neoplasms vary considerably in clinical presentation and biologic behavior. Chemotherapy and radiation therapy are generally ineffective. Here we describe the establishment and characterization of a new human chondrosarcoma cell line named ch-2879, and we compare the cell line with its tumor of origin. The cell line was established from a recurrent grade 3 chondrosarcoma of the chest wall and characterized by growth kinetics and morphologic studies. Immunocytochemistry and RT-PCR were performed to examine the expression of cartilage-specific phenotypes. Genetic characterization was performed using cytogenetics, fluorescence in situ hybridization, flow cytometry, and molecular techniques for analysis of the genes implicated in cell cycle control, amplification of MDM2, CDK4, and Cyclin D1, and mutations in the p53 gene. ch-2879 cells were subcultured for more than 80 passages. They expressed vimentin, HNK-1, HBA-71, Ki-67, cyclin D1, Fli-1, S-100, p21, p27, and p53 and were negative for cytokeratin, EMA, p14, p16, MDM2, Rb, and c-erb-b2 antigens. Cytogenetically the recurrent tumor showed a hyperhaploid karyotype with clonal numerical and structural abnormalities. The sole structural abnormality was a chromosome derivative of a t(1;21) translocation. The cell line at passage 3 showed two populations: the hyperhaploid and an exactly duplicated, hypotriploid population. After the 18th passage, only the hypotriploid population was present. The cells expressed collagen 2. Molecular comparison of the primary and recurrent tumor evidenced an in vivo molecular change consisting of a deletion of 9p21 genes in the recurrence, probably caused by a selection process. Because of its gene expression profile, including expression of genes implicated in chondrogenesis in uncoated plastic dishes, this cell line may prove useful for cellular and molecular studies as well as studies of chondrosarcoma characterization and treatment.

Bone Neoplasms↗

PubMed2005

Lung nodule detection and characterization with multi-slice CT.

The influence of MSCT on nodule detection and characterization will be discussed. The objective is to improve understanding of the clinical issues involved in nodule detection, characterization, and management in light of technological advances. Topics to be covered are noninvasive characterization techniques, such as morphologic and density inspection on CT, nodule enhancement techniques, CT-PET, temporal nodule size assessment, and computer aided diagnosis for both detection and characterization.

Humans↗

PubMed2026

Admission whole-blood transcriptomic characterization of a neutrophil-predominant systemic immune response in patients with acute traumatic brain injury.

BACKGROUND: Acute traumatic brain injury (TBI) is accompanied by systemic immune responses, but their whole-blood transcriptomic features at hospital arrival remain incompletely characterized. We aimed to characterize these features in patients with acute TBI compared with healthy controls. METHODS: In this single-center prospective observational study, we performed whole-blood RNA sequencing on hospital-arrival samples from 42 patients with acute TBI and 21 healthy controls. Analyses included differential expression (limma-voom; FDR < 0.05, |log2FC| > 0.7), functional enrichment, Ingenuity Pathway Analysis, CIBERSORTx LM22 deconvolution, and per-sample neutrophil degranulation signature scoring. RESULTS: Differential expression analysis identified 996 upregulated and 863 downregulated genes, with marked upregulation of inflammation-, innate immunity-, and neutrophil-related genes including DUSP1, HMGB2, MMP9, and S100A8. Canonical pathways with positive IPA z-scores included Neutrophil degranulation, Neutrophil Extracellular Trap Signaling Pathway, and Toll-like Receptor Signaling; upstream regulators included TNF, IL1B, IFNG, and STAT3. Deconvolution identified 7 of 22 differing subsets (q < 0.05), with relatively higher myeloid and lower lymphoid fractions in TBI. The Neutrophil degranulation signature score correlated with Injury Severity Score within TBI (Spearman ρ = +0.55; q < 0.001). CONCLUSIONS: Admission whole-blood transcriptomics characterized a neutrophil-predominant systemic transcriptional response in patients with acute TBI. This response was also evident among patients without major extracranial injury and was associated with total ISS. However, because the study lacked an appropriately matched non-TBI trauma comparator, the findings should be interpreted as a descriptive characterization of a systemic injury response accompanying TBI and do not establish a TBI-specific molecular signature or mechanism.

gene expression↗

PubMed1991

Adaptive processing techniques based on hidden Markov models for characterizing very small channel currents buried in noise and deterministic interferences.

Techniques for characterizing very small single-channel currents buried in background noise are described and tested on simulated data to give confidence when applied to real data. Single channel currents are represented as a discrete-time, finite-state, homogeneous, Markov process, and the noise that obscures the signal is assumed to be white and Gaussian. The various signal model parameters, such as the Markov state levels and transition probabilities, are unknown. In addition to white Gaussian noise, the signal can be corrupted by deterministic interferences of known form but unknown parameters, such as the sinusoidal disturbance stemming from AC interference and a drift of the base line owing to a slow development of liquid-junction potentials. To characterize the signal buried in such stochastic and deterministic interferences, the problem is first formulated in the framework of a Hidden Markov Model and then the Expectation Maximization algorithm is applied to obtain the maximum likelihood estimates of the model parameters (state levels, transition probabilities), signals, and the parameters of the deterministic disturbances. Using fictitious channel currents embedded in the idealized noise, we first show that the signal processing technique is capable of characterizing the signal characteristics quite accurately even when the amplitude of currents is as small as 5-10 fA. The statistics of the signal estimated from the processing technique include the amplitude, mean open and closed duration, open-time and closed-time histograms, probability of dwell-time and the transition probability matrix. With a periodic interference composed, for example, of 50 Hz and 100 Hz components, or a linear drift of the baseline added to the segment containing channel currents and white noise, the parameters of the deterministic interference, such as the amplitude and phase of the sinusoidal wave, or the rate of linear drift, as well as all the relevant statistics of the signal, are accurately estimated with the algorithm we propose. Also, if the frequencies of the periodic interference are unknown, they can be accurately estimated. Finally, we provide a technique by which channel currents originating from the sum of two or more independent single channels are decomposed so that each process can be separately characterized. This process is also formulated as a Hidden Markov Model problem and solved by applying the Expectation Maximization algorithm. The scheme relies on the fact that the transition matrix of the summed Markov process can be construed as a tensor product of the transition matrices of individual processes.

Algorithms↗

PubMed1993

Identification of a fifth neutralizable site on type O foot-and-mouth disease virus following characterization of single and quintuple monoclonal antibody escape mutants.

A monoclonal antibody (C3) produced against foot-and-mouth disease virus type O1Caseros was found to neutralize quadrivalent monoclonal antibody escape mutant (G67) of foot-and-mouth disease virus type O1Kaufbeuren. This mutant had been characterized at the sequence level as having distinct changes affecting four non-overlapping neutralizable sites. The C3 monoclonal antibody was used to prepare a quintuple escape mutant from the G67 and a single escape mutant from the parental O1Kaufbeuren viruses. Polyclonal post-vaccinated and infected cattle sera as well as polyclonal mouse and guinea-pig sera, which neutralized the quadrivalent mutant, no longer neutralized the quintuple mutant, indicating that a fifth site had been identified and that changing the fifth site eliminated all neutralization. The site was characterized using serological techniques and found to be conformationally dependent, trypsin-sensitive and independent of sites previously characterized by monoclonal antibodies. Amino acid sequencing comparing parental, single C3 and quintuple mutants showed that a single change from a glutamine to a histidine, at amino acid 149 in the structural protein VP1, (1D) characterized the C3 mutation. The fifth site probably represents a conformational epitope which is formed due to the interaction of the VP1 loop region with other surface amino acids.

Amino Acid Sequence↗

PubMed2004

Glucan synthesis in the genus Lactobacillus: isolation and characterization of glucansucrase genes, enzymes and glucan products from six different strains.

Members of the genera Streptococcus and Leuconostoc synthesize various alpha-glucans (dextran, alternan and mutan). In Lactobacillus, until now, the only glucosyltransferase (GTF) enzyme that has been characterized is gtfA of Lactobacillus reuteri 121, the first GTF enzyme synthesizing a glucan (reuteran) that contains mainly alpha-(1-->4) linkages together with alpha-(1-->6) and alpha-(1-->4,6) linkages. Recently, partial sequences of glucansucrase genes were detected in other members of the genus Lactobacillus. This paper reports, for the first time, isolation and characterization of dextransucrase and mutansucrase genes and enzymes from various Lactobacillus species and the characterization of the glucan products synthesized, which mainly have alpha-(1-->6)- and alpha-(1-->3)-glucosidic linkages. The four GTF enzymes characterized from three different Lb. reuteri strains are highly similar at the amino acid level, and consequently their protein structures are very alike. Interestingly, these four Lb. reuteri GTFs have relatively large N-terminal variable regions, containing RDV repeats, and relatively short putative glucan-binding domains with conserved and less-conserved YG-repeating units. The three other GTF enzymes, isolated from Lactobacillus sakei, Lactobacillus fermentum and Lactobacillus parabuchneri, contain smaller variable regions and larger putative glucan-binding domains compared to the Lb. reuteri GTF enzymes.

Amino Acid Motifs↗

PubMed2005

Virus-induced gene silencing-based functional characterization of genes associated with powdery mildew resistance in barley.

We successfully implemented virus-induced gene silencing (VIGS) in barley (Hordeum vulgare) for the functional characterization of genes required for Mla13-mediated resistance toward the biotrophic barley pathogen Blumeria graminis f. sp. hordei. Initially, barley cultivars were screened for their ability to host the barley stripe mosaic virus (BSMV)-VIGS vector by allowing its replication and systemic movement without causing excessive symptoms. Phytoene desaturase silencing leading to photobleaching was used as a phenotypic marker alongside reverse transcription-PCR data to characterize the silencing response at the molecular level. Barley cultivar Clansman, harboring the Mla13 resistance gene, was chosen as the most suitable host for BSMV-VIGS-based functional characterization of Rar1, Sgt1, and Hsp90 in the Mla-mediated resistance toward powdery mildew. BSMV-induced gene silencing of these candidate genes, which are associated in many but not all race-specific pathways, proved to be robust and could be detected at both mRNA and protein levels for up to 21 d postinoculation. Systemic silencing was observed not only in the newly developed leaves from the main stem but also in axillary shoots. By examining fungal development from an incompatible mildew strain carrying the cognate Avr13 gene on plants BSMV silenced for Rar1, Sgt1, and Hsp90, a resistance-breaking phenotype was observed, while plants infected with BSMV control constructs remained resistant. We demonstrate that Hsp90 is a required component for Mla13-mediated race-specific resistance and that BSMV-induced VIGS is a powerful tool to characterize genes involved in pathogen resistance in barley.

Carrier Proteins↗

PubMed1998

Characterization of visually similar diffuse diseases from B-scan liver images using nonseparable wavelet transform.

This paper describes a new approach for texture characterization, based on nonseparable wavelet decomposition, and its application for the discrimination of visually similar diffuse diseases of liver. The proposed feature-extraction algorithm applies nonseparable quincunx wavelet transform and uses energies of the transformed regions to characterize textures. Classification experiments on a set of three different tissue types show that the scale/frequency approach, particularly one based on the nonseparable wavelet transform, could be a reliable method for a texture characterization and analysis of B-scan liver images. Comparison between the quincunx and the traditional wavelet decomposition suggests that the quincunx transform is more appropriate for characterization of noisy data, and practical applications, requiring description with lower rotational sensitivity.

Algorithms↗