Systematic Parameterization, Storage, and Representation of Volumetric DICOM Data.

Tomographic medical imaging systems produce hundreds to thousands of slices, enabling three-dimensional (3D) analysis. Radiologists process these images through various tools and techniques in order to generate 3D renderings for various applications, such as surgical planning, medical education, and volumetric measurements. To save and store these visualizations, current systems use snapshots or video exporting, which prevents further optimizations and requires the storage of significant additional data.

Performance comparison of compression algorithms for archiving segmented volumetric binary medical data.

Archiving result of a segmentation task allows the representation of the segmented volume at a later time. The segmented volume can be stored in a binary format, which can be restored by a simple combination of the original data with this binary information. Since, the sizes of the segmented binary data have high memory requirements; a lossless compression method should be employed for efficient archiving.

Semi-automatic segmentation methods for 3-D visualization and analysis of the liver.

Pre-evaluation of donors prior to surgery of living donated liver transplantation is one of the challenging applications that computer aided systems are needed. The precise measurement of liver volume requires effective segmentation procedures, while three dimensional rendering of the segmented data provides demonstrative information to radiologists and surgeons before surgery. The Insight Toolkit provides effective algorithms for segmentation, which are also optimized for high computational performance and processing time.

Complex formation between malate dehydrogenase and isocitrate dehydrogenase from Bacillus subtilis is regulated by tricarboxylic acid cycle metabolites.

In Bacillus subtilis, recent in vivo studies revealed that particular enzymes of the tricarboxylic acid cycle form complexes that allow an efficient transfer of metabolites. Remarkably, a complex of the malate dehydrogenase (Mdh) (EC 1.1.

A novel method to analyze nucleocytoplasmic transport in vivo by using short peptide tags.

Regulated nucleocytoplasmic transport is of vital importance for maintaining the physiology of the cell, and disturbed nucleocytoplasmic shuttling of certain proteins has been found in a variety of diseases including cancer. The most frequently used procedure to analyze those processes is to fuse the protein of interest to a fluorescent protein such as GFP (green fluorescent protein)--a technique that is prone to impair normal protein function and subcellular localization. We report a novel approach to monitor nucleocytoplasmic transport processes in vivo by combining short TetR inducing peptide tags (TIP) with a TetR-controlled reporter gene in a human cell line.

High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis.

Background: In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a positive or a negative regulator.

Promoter strength driving TetR determines the regulatory properties of Tet-controlled expression systems.

Bacteria frequently rely on transcription repressors and activators to alter gene expression patterns in response to changes in the surrounding environment. Tet repressor (TetR) is a paradigm transcription factor that senses the environmental state by binding small molecule effectors, the tetracyclines. However, recently isolated peptides that act as inducers of TetR after having been fused to the C-terminus of a carrier protein, suggest that TetR can also regulate gene expression in a signal-transduction pathway.

Protein expression can be monitored in yeast by peptide-mediated induction of TetR-controlled gene expression.

The rapidly increasing number of completed genome sequences urgently calls for convenient and efficient methods for analysis of gene function and expression. TetR-inducing peptides (TIP) can induce reporter gene expression controlled by Tet repressor (TetR) when fused to a protein of choice which makes them a highly valuable tool for monitoring expression in vivo. However, TIP functionality has only been demonstrated in bacteria so far.

CcpA forms complexes with CodY and RpoA in Bacillus subtilis.

The Bacillus subtilis catabolite control protein A (CcpA) is a global transcriptional regulator that is controlled by interactions with the phosphoproteins histidine-containing protein (HPr)Ser46P and the catabolite responsive HPr (Crh)Ser46P and with low molecular weight effectors, depending on the availability of preferred carbon sources such as glucose. Distinct point mutations in CcpA abolish the regulation of some but not all target genes, suggesting additional interactions of CcpA. Therefore, in vivo crosslinking and MS were applied to identify CcpA complexes active in repression and activation.

Short peptides act as inducers, anti-inducers and corepressors of Tet repressor.

Protein allostery plays a pivotal role in many regulatory processes. Prominent examples are cell-surface receptors, which allosterically transmit ligand-generated signals to their cytoplasmic domains, or bacterial transcription factors, which alternate between a free conformation and a DNA-bound conformation in response to binding an effector molecule. The bacterial transcription factor Tet repressor (TetR) belongs to the latter category and is regarded as highly adapted to tetracyclines (tc's) as effectors.

An exclusive α/β code directs allostery in TetR-peptide complexes.

The allosteric mechanism of one of the best characterized bacterial transcription regulators, tetracycline repressor (TetR), has recently been questioned. Tetracycline binding induces cooperative folding of TetR, as suggested by recent unfolding studies, rather than switching between two defined conformational states, namely a DNA-binding-competent conformation and a non-DNA-binding conformation. Upon ligand binding, a host of near-native multiconformational structures collapse into a single, highly stabilized protein conformation that is no longer able to bind DNA.

Carbon source control of the phosphorylation state of the Bacillus subtilis carbon-flux regulator Crh in vivo.

Bacillus subtilis possesses carbon-flux regulating histidine protein (Crh), a paralog of the histidine protein (HPr) of the phosphotransferase system (PTS). Like HPr, Crh becomes (de)phosphorylated in vitro at residue Ser46 by the metabolite-controlled HPr kinase/phosphorylase HPrK/P. Depending on its phosphorylation state, Crh exerts regulatory functions in connection with carbohydrate metabolism.

Role of CcpA in polyhydroxybutyrate biosynthesis in a newly isolated Bacillus sp. MA3.3.

The ccpA gene was inactivated in the polyhydroxybutyrate (PHB)-producing strain Bacillus sp. MA3.3 in order to reduce glucose catabolite repression over pentoses and develop improved bacterial strains for the production of PHB from lignocellulosic hydrolysates.

Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.

In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by first forming a complex with the phosphoprotein HPr-Ser46-P. Bacillus subtilis CcpA functions as both a transcription repressor and activator and binds to more than 50 operators called catabolite response elements (cres).

Tetracycline sensing using novel doxycycline derivatives immobilized on different surface plasmon resonance biosensor surfaces.

Background: This article aims to explore novel doxycycline derivatives for analyzing low concentrations of tetracyclines in biological matrices and food in competitive assays.

Results: Surface plasmon resonance (SPR) was employed in an indirect competitive format using a bacterial tetracycline-dependent regulatory protein as receptor. Three doxycycline derivatives were synthesized and covalently bound to the surface of four different sensor chips.

Anhydrotetracycline-peptide conjugates as representatives for ligand-based transactivating systems.

Bioconjugates of anhydrotetracycline and minimal activation sequences (VP1, VP2) derived from the Herpes simplex virus protein VP16 were synthesized. Different ligation strategies were applied and the resulting molecules tested in HeLa cells expressing the reverse transactivator rtTA-S3 for activity. The data clearly demonstrate that the atc-peptide conjugates are able to penetrate the cell membrane.

Adjusting transgene expression levels in lymphocytes with a set of inducible promoters.

Background: Inducible gene expression systems are powerful research tools and could be of clinical value in the future, with lymphocytes being likely prime application targets. However, currently available regulatable promoters exhibit variation in their efficiency in a cell line-dependent-manner and are notorious for basal leakiness or poor inducibility. Data concerning the regulatory properties of different inducible promoters are scarce for lymphocytes.

Integrating segmentation methods from different tools into a visualization program using an object-based plug-in interface.

In medical visualization, segmentation is an important step prior to rendering. However, it is also a difficult procedure because of the restrictions imposed by variations in image characteristics, human anatomy, and pathology. Moreover, what is interesting from clinical point of view is usually not only an organ or a tissue itself, but also its properties together with adjacent organs or related vessel systems that are going in and coming out.

Click-chemistry-derived tetracycline-amino acid conjugates exhibiting exceptional potency and exclusive recognition of the reverse tet repressor.

A click-chemistry-based synthesis of biologically active doxycycline-amino acid conjugates is described. Starting from 9-aminodoxycycline derivatives and complementary functionalized amino acids, ligation was accomplished by copper(I)-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC). The final products were tested in a variety of TetR and revTetR systems, and the C-terminally linked phenylalanine conjugate 12 c exhibited high selectivity for revTetR over TetR.

Diarylpropane-1,3-dione derivatives as TetR-inducing tetracycline mimetics: Synthesis and biological investigations.

Synthesis, biological investigations and molecular docking studies of nonantibiotic and nontetracyclic inducers that feature a minimal key motif of the natural lead tetracycline are presented. The diarylpropane-1,3-dione motif was identified as the minimal substructure responsible for TetR induction by tetracyclines. The first nontetracyclic surrogates of the natural tetracyclines displayed significant inducing effects for TetR(BD)S135L, whereby the chlorohydroxyphenyl-substituted beta-diketone 31 displayed the highest activity.

Structural origins for selectivity and specificity in an engineered bacterial repressor-inducer pair.

The bacterial tetracycline transcription regulation system mediated by the tetracycline repressor (TetR) is widely used to study gene expression in prokaryotes and eukaryotes. To study multiple genes in parallel, a triple mutant TetR(K(64)L(135)I(138)) has been engineered that is selectively induced by the synthetic tetracycline derivative 4-de-dimethylamino-anhydrotetracycline (4-ddma-atc) and no longer by tetracycline, the inducer of wild-type TetR. In the present study, we report the crystal structure of TetR(K(64)L(135)I(138)) in the absence and in complex with 4-ddma-atc at resolutions of 2.

In vivo activation of tetracycline repressor by Cre/lox-mediated gene assembly.

Tetracycline repressor (TetR) bears an unstructured loop region between helices alpha8 and alpha9, which is moderately permissive to amino acid exchanges and length variations. Recognition sites for the site-specific recombinases Flp (FRT) or Cre (lox) were inserted in-frame into tetR, substituting some of this loop's codons. A number of the deduced TetR variants displayed efficient regulation in vivo, thus allowing the establishment of a new mode of TetR activation on the genetic level.

An RNA aptamer that induces transcription.

We identified an RNA aptamer that induces TetR-controlled gene expression in Escherichia coli when expressed in the cell. The aptamer was found by a combined approach of in vitro selection for TetR binding and in vivo screening for TetR induction. The smallest active aptamer folds into a stem-loop with an internal loop interrupting the stem.

Functionally important residues of the Tet repressor inducing peptide TIP determined by a complete mutational analysis.

Tet repressor (TetR) is widely used to control gene expression in pro- and eukaryotes. The mechanism of induction by its natural inducer tetracycline is well characterized. A 16-mer oligopeptide, called TIP, fused to thioredoxin A (TrxA) of Escherichia coli is an artificial inducer of TetR.