Characterization of Bacterial Isolates Collected from a Sheep Model of Osseointegration

Percutaneous osseointegrated implant technology provides a potential alternative to current socket prosthetics for individuals with limb loss. However, similar to other percutaneous devices, there remain concerns of periprosthetic infection. To understand this process of infection, bacterial isolates were collected and characterized from a sheep model of osseointegration. CSA-13, a novel cationic steroid antimicrobial, was used at the skin/implant interface in an attempt to reduce the rate of infection. Results indicated that in this application, normal flora and environmental organisms continued to colonize the skin/implant interface as well as cause infection in the presence of CSA-13. Two factors are believed to have contributed to this outcome: the delivery of CSA-13 and the lack of a skin seal at the skin/implant interface, which would create a biological barrier to infection.     

An innovative application of a small-scale motion analysis technique to quantify human skin deformation in vivo

This study highlights a new experimental method developed to measure full-field deformation of human skin in vivo. The technique uses a small-scale Qualisys (Sweden) 3D motion capture system and an array of reflective markers placed on the forearm of five healthy volunteers. A load of up to 1.5 N was applied to induce skin deformation by pulling a fine wire attached to the centre of the marker configuration. Loading and marker displacements were recorded simultaneously. 3D marker trajectory data was generated for three different load directions. Tests were repeated to investigate accuracy and repeatability. Calibration results indicate the accuracy of the motion capture system with an average residual of 0.05 mm. The procedure was found to be repeatable and accurate for five repeated tests of measured displacements with a maximum variance of 5%. Experimental data are presented to demonstrate robustness and the ability to produce significant outputs. For all five subjects, at 1 N load, the mean and standard deviations of skin axial and lateral displacements were found to be 11.7±1.6 mm and 12.3±3.3 mm, respectively. The axial displacements ratio (u₉₀/u₀) ranges from 0.63 to 1.45 with mean±standard deviation of 0.982±0.34 and 0.982±0.32 for left and right arms, respectively. The experiments generated useful and accurate data that can be used to study the viscoelastic, hyperelastic or anisotropic behaviour of human skin. The measured displacements will be analysed further to determine the mechanical properties of skin using inverse Finite Element Analysis and Ogden model.     

Differential suppression of tumor-specific CD8+ T cells by regulatory T cells

In the CT26 BALB/c murine model of colorectal carcinoma, depletion of regulatory T cells (Tregs) prior to tumor inoculation results in protective immunity to both CT26 and other BALB/c-derived tumors of diverse histological origin. In this paper, we show that cross-protection can be conferred by adoptively transferred CD8(+) CTLs. Other schedules for inducing immunity to CT26 have been described, but they do not lead to cross-protection. We show that Treg ablation facilitates the development of new CTL specificities that are normally cryptic, and have mapped the root epitope of one of these responses. This work has allowed us to demonstrate how the specificity of CTL responses to tumor Ags can be controlled via differential suppression of CTL specificities by Tregs, and how this can result in very different physiological outcomes.     

BioThesaurus: a web-based thesaurus of protein and gene names

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase. Currently covering more than two million proteins, BioThesaurus consists of over 2.8 million names extracted from multiple molecular biological databases according to the database cross-references in iProClass. The BioThesaurus web site allows the retrieval of synonymous names of given protein entries and the identification of protein entries sharing the same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus     

Substring selection for biomedical document classification

MOTIVATION: Attribute selection is a critical step in development of document classification systems. As a standard practice, words are stemmed and the most informative ones are used as attributes in classification. Owing to high complexity of biomedical terminology, general-purpose stemming algorithms are often conservative and could also remove informative stems. This can lead to accuracy reduction, especially when the number of labeled documents is small. To address this issue, we propose an algorithm that omits stemming and, instead, uses the most discriminative substrings as attributes. RESULTS: The approach was tested on five annotated sets of abstracts from iProLINK that report on the experimental evidence about five types of protein post-translational modifications. The experiments showed that Naive Bayes and support vector machine classifiers perform consistently better [with area under the ROC curve (AUC) accuracy in range 0.92-0.97] when using the proposed attribute selection than when using attributes obtained by the Porter stemmer algorithm (AUC in 0.86-0.93 range). The proposed approach is particularly useful when labeled datasets are small.     

Importance of short-term dynamics in carbon isotope ratios of ecosystem respiration (delta13C(R)) in a Mediterranean oak woodland and linkage to environmental factors

Temporal dynamics in carbon isotope ratios of ecosystem respiration (delta13C(R)) were evaluated on hourly, daily and annual timescales in a Mediterranean woodland. Emphasis was given to the periods of transition from wet to dry season and vice versa, when the system turns from a net carbon sink to a source. The constancy of nocturnal delta13C(R) was tested. The relationship between delta13C(R) (determined through Keeling plots) and environmental factors was evaluated through time-lag analysis. Delta13C(R) exhibited high annual variation (> 7). During the transition periods, delta13C(R) correlated significantly with factors influencing photosynthetic discrimination, soil respiration, and whole-canopy conductance. Time-lags differed between below- and above-ground variables, and between seasons. A shift in regression parameters with environmental factors indicated seasonal differences in ecosystem responsiveness (e.g. temperature acclimation). Delta13C(R) exhibited substantial nocturnal enrichment (> 4) from dusk to dawn. These data indicate pronounced short-term dynamics in delta13C(R) at hourly to daily timescales and a modulated response to environmental drivers. Substantial short-term changes in nocturnal delta13C(R) may have important implications for the sampling protocols of nocturnal Keeling plots.     

Glial cell-line derived neurotrophic factor-mediated RET signaling regulates spermatogonial stem cell fate

Normal spermatogenesis is essential for reproduction and depends on proper spermatogonial stem cell (SSC) function. Genes and signaling pathways that regulate SSC function have not been well defined. We report that glial cell-line-derived neurotrophic factor (GDNF) signaling through the RET tyrosine kinase/GFRA1 receptor complex is required for spermatogonial self-renewal in mice. GFRA1 and RET expression was identified in a subset of gonocytes at birth, was restricted to SSCs during normal spermatogenesis, and RET expressing cells were abundant in a cryptorchid model of SSC self-renewal. We used the whole-testis transplantation technique to overcome the limitation of neonatal lethality of Gdnf-, Gfra1-, and Ret-deficient mice and found that each of these genes is required for postnatal spermatogenesis and not for embryological testes development. Each mutant testis shows severe SSC depletion by Postnatal Day 7 during the first wave of spermatogenesis. These defects were due to lack of SSC proliferation and an inability of SSCs to maintain an undifferentiated state. Our results demonstrate that GDNF-mediated RET signaling is critical for the fate of undifferentiated spermatogonia and that abnormalities in this pathway may contribute to male infertility and testicular germ cell tumors.     

The 5-HT2A serotoninergic receptor is expressed in the MCF-7 human breast cancer cell line and reveals a mitogenic effect of serotonin

Serotonin (5-hydroxytryptamine, 5-HT) has been described as a mitogen in a variety of cell types and carcinomas. It exerts its mitogenic effect by interacting with a wide range of 5-HT receptor types. Certain studies suggest that some selective serotonin re-uptake inhibitors promote breast cancer in animals and humans. This study attempts to clarify the role of serotonin in promoting the growth of neoplastic mammary cells. Expression of the 5-HT(2A) serotoninergic receptor subtype in MCF-7 cells was determined by RT-PCR, Western blotting, and immunofluorescence analysis. The mitogenic effect of 5-HT on MCF-7 cells was determined by means of the MTT proliferation assay. We have demonstrated that the 5-HT(2A) receptor subtype is fully expressed in the MCF-7 human breast cancer cell line, in terms of encoding mRNA and receptor protein. Automated sequencing has confirmed that the 5-HT(2A) receptor present in this cell line is identical to the 5-HT(2A) receptor found in human platelets and in human cerebral cortex. Furthermore, this receptor was found by immunofluorescence to be on the plasma membrane. MTT proliferation assays revealed that 5-HT and DOI, a selective 5-HT(2A) receptor subtype agonist, stimulated MCF-7 cell. These results indicate that 5-HT plays a mitogenic role in neoplastic mammary cells. Our data also indicate that 5-HT exerts this positive growth effect on MCF-7 cells through, in part, the 5-HT(2A) receptor subtype, which is fully expressed in this cell line.     

c-kit delineates a distinct domain of progenitors in the developing kidney

Early inductive events in mammalian nephrogenesis depend on an interaction between the ureteric bud and the metanephric mesenchyme. However, mounting evidence points towards an involvement of additional cell types--such as stromal cells and angioblasts--in growth and patterning of the nephron. In this study, through analysis of the stem cell factor (SCF)/c-kit ligand receptor pair, we describe an additional distinct cell population in the early developing kidney. While SCF is restricted to the ureteric bud, c-kit-positive cells are located within the renal interstitium, but are negative for Foxd1, an established marker of stromal cells. In fact, the c-kit-positive domain is continuous with a central mesodermal cell mass ventral and lateral to the dorsal aorta, while Foxd1-expressing stromal cells are continuous with a dorsal perisomitic cell population suggesting distinct intraembryonic origins for these cell types. A subset of c-kit-positive cells expresses Flk-1 and podocalyxin, suggesting that this cell population includes angioblasts and their progenitors. c-kit activation is not required for the survival of these cells in vivo, because white spotting (c-kit(W/W)) mice, carrying a natural inactivating mutation of c-kit, display normal intrarenal distribution of the c-kit-positive cells at E13.5. In addition, early kidney development in these mutants is preserved up to the stage when anemia compromises global embryonic development. In contrast, under defined conditions in organ cultures of metanephric kidneys, c-kit-positive cells, including the Flk-1-positive subset, undergo apoptosis after treatment with STI-571, an inhibitor of c-kit tyrosine phosphorylation. This is associated with reductions in ureteric bud branching and nephron number. Conversely, exogenous SCF expands the c-kit-positive population, including Flk-1-positive angioblasts, and accelerates kidney development in vitro. These data suggest that ureteric bud-derived SCF elicits growth-promoting effects in the metanephric kidney by expanding one or more components of the interstitial c-kit-positive progenitor pool.