LIN28 promotes tumorigenesis in colorectal cancer but is not associated with metastatic spread.

Background: Tumor stem cells play a role in metastatic spread in colorectal cancer (CRC). The oncogene LIN28A/B, a prognostic marker in CRC, is involved in tumorigenesis and maintains stem cell function. Therefore, it was the aim of the present study to clarify whether LIN28A/B is involved in metastatic spread in CRC.

The FeoC [4Fe-4S] Cluster Is Redox-Active and Rapidly Oxygen-Sensitive.

The acquisition of iron is essential to establishing virulence among most pathogens. Under acidic and/or anaerobic conditions, most bacteria utilize the widely distributed ferrous iron (Fe) uptake (Feo) system to import metabolically-required iron. The Feo system is inadequately understood at the atomic, molecular, and mechanistic levels, but we do know it is composed of a main membrane component (FeoB) essential for iron translocation, as well as two small, cytosolic proteins (FeoA and FeoC) hypothesized to function as accessories to this process.

Over-expression of a human CD62L ecto-domain and a potential role of RNA pseudoknot structures in recombinant protein expression.

L-selectin (CD62L) is an extracellular protein with a lectin-like domain that mediates rolling adhesion of leukocytes to vascular endothelial cell surfaces. Currently, there are no solved structures for the ectodomain of CD62L, nor of CD62L in complex with its ligand. We have developed a rapid mammalian recombinant protein expression system using an amplifiable glutamine synthase based vector.

Mixed adenoneuroendocrine carcinoma of the ampulla of Vater: A case report.

Mixed adenoneuroendocrine carcinomas (MANECs) are rare biphasic tumour types, which are morphologically recognisable as both gland-forming and neuroendocrine neoplasms. Within the gastrointestinal tract, MANECs occur predominantly in the stomach or colorectum. The present study described a case of a MANEC originating from the ampullary region.

Genetic algorithm based approach to optimize phenotypical traits of virtual rice.

How to select and combine good traits of rice to get high-production individuals is one of the key points in developing crop ideotype cultivation technologies. Existing cultivation methods for producing ideal plants, such as field trials and crop modeling, have some limits. In this paper, we propose a method based on a genetic algorithm (GA) and a functional-structural plant model (FSPM) to optimize plant types of virtual rice by dynamically adjusting phenotypical traits.

Tumour budding with and without admixed inflammation: two different sides of the same coin?

Background: Tumour budding is an adverse prognostic indicator in colorectal cancer (CRC). Marked overall peritumoural inflammation has been associated with favourable outcome and may lead to the presence of isolated cancer cells due to destruction of invading cancer cell islets.

Methods: We assessed the prognostic significance of tumour budding and peritumoural inflammation in a cohort of 381 patients with CRC applying univariate and multivariate analyses.

A calculation method of plant similarity giving consideration to different plant features.

A method to compute the similarity between different plants is proposed, using features of a plant׳s topological structure and peripheral contour, as well as its geometry. The topological structures are described using tree graphs, and their similarity can be calculated based on the edit distance of these graphs. The peripheral contour of a plant is abstracted by its three-dimensional convex hull, which is projected in several directions.

Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement).

Creating supersecondary structures with BuildBeta.

BuildBeta is a feature of the ProteinShop software designed to thoroughly sample a protein conformational space given the protein's sequence of amino acids and secondary structure predictions. It targets proteins with beta sheets because they are particularly challenging to predict due to the complexity of sampling long-range strand pairings. Here we discuss some of the most difficult targets in the recent 9th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and show how BuildBeta can leverage some of the most successful methods in the category "template-free modeling" by augmenting their sampling capabilities.

PackHelix: a tool for helix-sheet packing during protein structure prediction.

The three-dimensional structure of a protein is organized around the packing of its secondary structure elements. Predicting the topology and constructing the geometry of structural motifs involving α-helices and/or β-strands are therefore key steps for accurate prediction of protein structure. While many efforts have focused on how to pack helices and on how to sample exhaustively the topologies and geometries of multiple strands forming a β-sheet in a protein, there has been little progress on generating native-like packings of helices on sheets.

Subdivision analysis of the trilinear interpolant.

Isosurfaces are fundamental volumetric visualization tools and are generated by approximating contours of trilinearly interpolated scalar fields. While a complete set of cases has recently been published by Nielson, the formal proof that these cases are the only ones possible and that they are topologically correct is difficult to follow. We present a more straightforward proof of the correctness and completeness of these cases based on a variation of the Dividing Cubes algorithm.

BuildBeta--a system for automatically constructing beta sheets.

We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with beta-sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long-range strand pairings. Using some basic packing principles, inverse kinematics (IK), and beta-pairing scores, this method creates all possible beta-sheet arrangements including those that have the correct packing of beta-strands.

The fibroblast growth factor binding protein is a novel interaction partner of FGF-7, FGF-10 and FGF-22 and regulates FGF activity: implications for epithelial repair.

The fibroblast growth factor-binding protein (FGF-BP) binds and activates FGF-1 and FGF-2, thereby contributing to tumor angiogenesis. In this study, we identified novel binding partners of FGF-BP, and we provide evidence for a role of this protein in epithelial repair processes. We show that expression of FGF-BP increases after injury to murine and human skin, in particular in keratinocytes.

ProteinShop: a tool for interactive protein manipulation and steering.

We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user.

Hierarchical molecular modelling with ellipsoids.

Protein and DNA structures are represented at varying levels of details using ellipsoidal RGBA textured splats. The splat texture at each level is generated by rendering its children in a hierarchical model, from a distribution of viewing directions, and averaging the result. For rendering, the ellipsoids to be used are chosen adaptively, depending on the distance to the viewpoint.

Image-space visibility ordering for cell projection volume rendering of unstructured data.

Projection methods for volume rendering unstructured data work by projecting, in visibility order, the polyhedral cells of the mesh onto the image plane, and incrementally compositing each cell's color and opacity into the final image. Normally, such methods require an algorithm to determine a visibility order of the cells. The Meshed Polyhedra Visibility Order (MPVO) algorithm can provide such an order for convex meshes by considering the implications of local ordering relations between cells sharing a common face.

Quantitative detection of circulating tumor cells in cutaneous and ocular melanoma and quality assessment by real-time reverse transcriptase-polymerase chain reaction.

Purpose: Inconsistent reports on the detection of melanoma cells in peripheral blood by reverse transcriptase-PCR (RT-PCR) have resulted in uncertainty on the prognostic value of circulating melanoma cells.

Experimental Design: We developed real-time RT-PCR assays for quantitation of tyrosinase, MelanA/MART1, and gp100 and for porphobilinogen deaminase housekeeping gene. Melanoma tissue (n = 18), peripheral blood samples from healthy donors (n = 21), and patients with cutaneous (n = 122) and uveal (n = 64) melanoma from our institution were analyzed.

Quantitative real-time RT-PCR for detection of disseminated tumor cells in peripheral blood of patients with colorectal cancer using different mRNA markers.

The detection of disseminated tumor cells in peripheral blood from colorectal cancer patients by RT-PCR could be an attractive method for selecting patients for adjuvant therapy. We here report on real-time RT-PCR assays (LightCycler) to quantitate potential mRNA markers. We investigated specimens from colon carcinoma and normal colon mucosa tissues, cell lines, blood samples from 129 patients with colorectal cancer (all stages) and 58 reference blood samples (healthy donors, persons suffering from inflammatory bowel or infectious diseases).

Long-term freedom from recurrence in 2 stage IV melanoma patients following vaccination with tyrosinase peptides.

We report here on 2 patients who received adjuvant vaccination with an HLA-A2- or HLA-A24-restricted tyrosinase peptide, respectively, and GM-CSF for frequently relapsing stage IV melanoma. Following resection of metastases and irradiation of brain metastases in 1 patient, both patients were without evidence of disease when receiving the first vaccination. While the patients had had 9 and 12, respectively, mostly s.

Minimal residual disease in melanoma.

A number of specific genes encoding for melanosomal proteins are selectively expressed in melanocytes and melanomas. For detection of circulating melanoma cells, the expression of the tyrosinase gene is most widely used. Several cohorts of melanoma patients from single institutions have been analyzed by various research groups for the presence of circulating melanoma cells in all stages of disease.

Reliability of PCR-based detection of occult tumour cells: lessons from real-time RT-PCR.

For the molecular detection of rare tumour cells in clinical samples, real-time reverse transcription-polymerase chain reaction (RT-PCR) offers two important advantages over conventional RT-PCR assays: the results are quantitative and, perhaps more importantly, it facilitates exact sensitivity controls on a per sample basis as well as exact comparison of different assay protocols. We report here on quantitative results obtained with different protocols for RNA isolation and cDNA synthesis for amplification of beta2-microglobulin transcripts using the light cycler system. Furthermore, housekeeping gene-specific PCRs were compared with PCRs specific for an artificial transcript (internal standard) detected simultaneously at a level comparable to the wild-type sequence.

Nested quantitative real time PCR for detection of occult tumor cells.

Quantification of tumor mRNA markers expressed by occult circulating tumor cells may be of prognostic value in a variety of neoplasms and disease stages. We therefore developed a novel real time nested polymerase chain reaction (PCR) assay to quantify rare transcripts using the light cycler system. Tyrosinase mRNA expressed by melanocytes and melanoma cells was used as a model.