The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data

A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies.     

System for the expression of recombinant hemoproteins in Escherichia coli

Expression of recombinant hemoproteins in Escherichia coli is often limited because a vast majority of the protein produced lacks the heme necessary for function. This is compounded by the fact that standard laboratory strains of E. coli have a limited capacity to withdraw heme from the extracellular environment. We are developing a new tool designed to increase the heme content of our proteins of interest by simply supplementing the expression medium with low concentrations of hemin. This hemoprotein expression (HPEX) system is based on plasmids (pHPEX1-pHPEX3) that encode an outermembrane-bound heme receptor (ChuA) from E. coli O157:H7. This heme receptor, and others like it, confers on the host the ability to more effectively internalize exogenous heme. Transformation of a standard laboratory E. coli protein expression strain (BL-21 [DE3]) with the pHPEX plasmid led to the expression of a new protein with the appropriate molecular weight for ChuA. The receptor was functional as demonstrated by the ability of the transformant to grow on iron-deficient media supplemented with hemin, an ability that the unmodified expression strain lacked. Expression of our proteins of interest, catalase-peroxidases, using this system led to a dramatic and parallel increase in heme content and activity. On a per-heme basis, the spectral and kinetic properties of HPEX-derived catalase-peroxidase were the same as those observed for catalase-peroxidases expressed in standard E. coli-based systems. We suggest that the pHPEX plasmids may be a useful addition to other E. coli expression systems and may help address a broad range of problems in hemoprotein structure and function.     

Five labdane derivatives from Koanophyllon conglobatum

A re-investigation of the aerial parts of Koanophyllon conglobatum afforded six new diterpenes, five labdanes and one seco-labdane, as well as two hydroperoxides which may be artefacts.     

Handheld photoacoustic probe to detect both melanoma depth and volume at high speed in vivo

We applied a linear‐array‐based photoacoustic probe to detect melanin‐containing melanoma tumor depth and volume in nude mice in vivo. This system can image melanomas at five frames per second (fps), which is much faster than our previous handheld single transducer system (0.1 fps). We first theoretically show that, in addition to the higher frame rate, almost the entire boundary of the melanoma can be detected by the linear‐array‐based probe, while only the horizontal boundary could be detected by the previous system. Then we demonstrate the ability of this linear‐array‐based system in measuring both the depth and volume of melanoma through phantom, ex vivo, and in vivo experiments. The volume detection ability also enables us to accurately calculate the rate of growth of the tumor, which is an important parameter in quantifying the tumor activity. Our results show that this system can be used for clinical melanoma diagnosis and treatment in humans at the bedside.

Linear‐array‐based PA images of melanoma acquired in vivo on day 3 ( a ) and day 6 ( b ).     

P3b Reflects Periodicity in Linguistic Sequences

Temporal predictability is thought to affect stimulus processing by facilitating the allocation of attentional resources. Recent studies have shown that periodicity of a tonal sequence results in a decreased peak latency and a larger amplitude of the P3b compared with temporally random, i.e., aperiodic sequences. We investigated whether this applies also to sequences of linguistic stimuli (syllables), although speech is usually aperiodic. We compared aperiodic syllable sequences with two temporally regular conditions. In one condition, the interval between syllable onset was fixed, whereas in a second condition the interval between the syllables’ perceptual center (p-center) was kept constant. Event-related potentials were assessed in 30 adults who were instructed to detect irregularities in the stimulus sequences. We found larger P3b amplitudes for both temporally predictable conditions as compared to the aperiodic condition and a shorter P3b latency in the p-center condition than in both other conditions. These findings demonstrate that even in acoustically more complex sequences such as syllable streams, temporal predictability facilitates the processing of deviant stimuli. Furthermore, we provide first electrophysiological evidence for the relevance of the p-center concept in linguistic stimulus processing.     

Genome-wide gene amplification during differentiation of neural progenitor cells in vitro

DNA sequence amplification is a phenomenon that occurs predictably at defined stages during normal development in some organisms. Developmental gene amplification was first described in amphibians during gametogenesis and has not yet been described in humans. To date gene amplification in humans is a hallmark of many tumors. We used array-CGH (comparative genomic hybridization) and FISH (fluorescence in situ hybridization) to discover gene amplifications during in vitro differentiation of human neural progenitor cells. Here we report a complex gene amplification pattern two and five days after induction of differentiation of human neural progenitor cells. We identified several amplified genes in neural progenitor cells that are known to be amplified in malignant tumors. There is also a striking overlap of amplified chromosomal regions between differentiating neural progenitor cells and malignant tumor cells derived from astrocytes. Gene amplifications in normal human cells as physiological process has not been reported yet and may bear resemblance to developmental gene amplifications in amphibians and insects.     

Solitary Pulmonary Nodules in Organ Transplant Candidates and Recipients

The solitary pulmonary nodule (SPN) is a diagnostic and therapeutic challenge in solid organ transplant patients. Common causes of SPNs in solid organ transplant recipients are fungal and bacterial infections and post-transplant lymphoproliferative disorder, which carry high morbidity and mortality. Clinical and radiographic features such as timing after transplant and patterns of SPN might provide clues to the diagnosis but are nonspecific. SPNs mandate prompt, definitive evaluation.     

Monitoring urea transport in rat kidney in vivo using hyperpolarized ¹³C magnetic resonance imaging

Urea functions as a key osmolyte in the urinary concentrating mechanism of the inner medulla. The urea transporter UT-A1 is upregulated by antidiuretic hormone, facilitating faster equilibration of urea between the lumen and interstitium of the inner medullary collecting duct, resulting in the formation of more highly concentrated urine. New methods in dynamic nuclear polarization, providing ～50,000-fold enhancement of nuclear magnetic resonance signals in the liquid state, offer a novel means to monitor this process in vivo using magnetic resonance imaging. In this study, we detected significant signal differences in the rat kidney between acute diuretic and antidiuretic states, using dynamic (13)C magnetic resonance imaging following a bolus infusion of hyperpolarized [(13)C]urea. More rapid medullary enhancement was observed under antidiuresis, consistent with known upregulation of UT-A1.     

In vivo two-photon excited fluorescence microscopy reveals cardiac- and respiration-dependent pulsatile blood flow in cortical blood vessels in mice

Subtle alterations in cerebral blood flow can impact the health and function of brain cells and are linked to cognitive decline and dementia. To understand hemodynamics in the three-dimensional vascular network of the cerebral cortex, we applied two-photon excited fluorescence microscopy to measure the motion of red blood cells (RBCs) in individual microvessels throughout the vascular hierarchy in anesthetized mice. To resolve heartbeat- and respiration-dependent flow dynamics, we simultaneously recorded the electrocardiogram and respiratory waveform. We found that centerline RBC speed decreased with decreasing vessel diameter in arterioles, slowed further through the capillary bed, and then increased with increasing vessel diameter in venules. RBC flow was pulsatile in nearly all cortical vessels, including capillaries and venules. Heartbeat-induced speed modulation decreased through the vascular network, while the delay between heartbeat and the time of maximum speed increased. Capillary tube hematocrit was 0.21 and did not vary with centerline RBC speed or topological position. Spatial RBC flow profiles in surface vessels were blunted compared with a parabola and could be measured at vascular junctions. Finally, we observed a transient decrease in RBC speed in surface vessels before inspiration. In conclusion, we developed an approach to study detailed characteristics of RBC flow in the three-dimensional cortical vasculature, including quantification of fluctuations in centerline RBC speed due to cardiac and respiratory rhythms and flow profile measurements. These methods and the quantitative data on basal cerebral hemodynamics open the door to studies of the normal and diseased-state cerebral microcirculation.     

Current concepts in clinical radiation oncology

Based on its potent capacity to induce tumor cell death and to abrogate clonogenic survival, radiotherapy is a key part of multimodal cancer treatment approaches. Numerous clinical trials have documented the clear correlation between improved local control and increased overall survival. However, despite all progress, the efficacy of radiation-based treatment approaches is still limited by different technological, biological, and clinical constraints. In principle, the following major issues can be distinguished: (1) The intrinsic radiation resistance of several tumors is higher than that of the surrounding normal tissue, (2) the true patho-anatomical borders of tumors or areas at risk are not perfectly identifiable, (3) the treatment volume cannot be adjusted properly during a given treatment series, and (4) the individual heterogeneity in terms of tumor and normal tissue responses toward irradiation is immense. At present, research efforts in radiation oncology follow three major tracks, in order to address these limitations: (1) implementation of molecularly targeted agents and ‘omics’-based screening and stratification procedures, (2) improvement of treatment planning, imaging, and accuracy of dose application, and (3) clinical implementation of other types of radiation, including protons and heavy ions. Several of these strategies have already revealed promising improvements with regard to clinical outcome. Nevertheless, many open questions remain with individualization of treatment approaches being a key problem. In the present review, the current status of radiation-based cancer treatment with particular focus on novel aspects and developments that will influence the field of radiation oncology in the near future is summarized and discussed.