A stepwise framework for the normalization of array CGH data

Background  

In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effects from non-biological sources that can introduce biases in the estimated ratios. These biases should be removed before drawing conclusions about the relative levels of DNA. The performance of existing gene expression microarray normalization strategies has not been evaluated for removing systematic biases encountered in array-based comparative genomic hybridization (CGH), which aims to detect single copy gains and losses typically in samples with heterogeneous cell populations resulting in only slight shifts in signal ratios. The purpose of this work is to establish a framework for correcting the systematic sources of variation in high density CGH array images, while maintaining the true biological variations.     

Natural history of cervical intraepithelial neoplasia: a meta-analysis

OBJECTIVE: To determine the probabilities of transition of stages in the cervical cancer by conducting a meta-studies on the topic. STUDY DESIGN: We identified health states of interest in the natural history of cervical precancer, identified all possible papers that could meet selection criteria, developed relevance and acceptability criteria for inclusion, then thoroughly reviewed the selected studies. To determine the transition probability data we used a random effects model. We determined probabilities for 4 health state transitions. The 6-month mean predictive transition probability (95% confidence intervals with "prediction interval" in parentheses) for high grade squamous intraepithelial lesions (HSIL) to cancer was 0.0037 (0.00004, 0.03386), for low grade squamous intraepithelial lesions (LSIL) to HSIL was 0.0362 (0.00055, 0.23220), for HSIL to LSIL was 0.0282 (0.00027, 0.35782), and for LSIL to normal was 0.0740 (0.00119, 0.42672). CONCLUSION: The transition probabilities between cervical cancer health states for 6-month intervals are small; however, the cumulative risk of cervical cancer is significant. Markers to identify the cervical precursors that will lead to the transition to cervical cancer are needed.     

Post-release survival and riverine movements of Gulf of Mexico sturgeon (Acipenser oxyrinchus desotoi Acipenseriformes) following induced spawning

Post‐release survival and upstream movement of Gulf of Mexico sturgeon (Acipenser oxyrinchus desotoi) in the Suwannee River, Florida, were examined following induced spawning using carp pituitary extract (CPE). Six mature females (one CPE‐treated and five control) and 12 mature males (five CPE‐treated and seven control) were implanted with ultrasonic tags in March 2001 during their ingress into the Suwannee River. All CPE‐treated sturgeon and 10 of the 12 control fish were relocated using ultrasonic telemetry during 4 months following their release, resulting in 100% survival of treated fish and 83% known survival of control fish. Two control fish (one female and one male) could not be relocated after 2 weeks post‐release. CPE treatment did not result in mortality but did affect upstream movement behavior, with CPE‐treated males moving upstream at a significantly slower rate than control males and females. Similarly, the maximum observed distance that the fish moved upstream differed among control fish (males and females) and treated males, with control fish moving further upstream than CPE‐treated males. The rate of upstream movement for the single CPE‐treated female was similar to the control females and the maximum upstream distance that this female was located was near a putative spawning area. In general, the environmental parameters of temperature, dissolved oxygen, and conductivity differed over the course of the study but did not differ between treatments and sexes. Treating sturgeon with CPE to induce spawning therefore did not cause mortality but did appear to slow the rate of upstream movement and maximum distance moved in male Gulf sturgeon.     

Zoosporangial root infection of tomato by Spongospora subterranea in hydroponic and glasshouse culture results in diminished plant growth

Tomato plants are highly susceptible to root infection by Spongospora subterranea and are commonly used as bioassay hosts. The impacts of root infection with S. subterranea on plant productivity and yield have been debated. Recent experiments with potato, the major economic host of S. subterranea, have indicated significantly reduced plant growth and potato yield following heavy infection. However, there have been very few similar studies that have examined the possible impacts of S. subterranea infection on tomato plant growth. Three tomato cultivars, “Grape,” “Roma” and “Truss,” were challenged with S. subterranea inoculum in hydroponic culture. Moderate to severe zoosporangial infections were observed with minor but statistically significant differences in susceptibility among the three tomato cultivars. Zoosporangial root infection in the absence of root gall formation resulted in significantly diminished shoot lengths and plant fresh weights in pathogen challenge tests conducted both in hydroponic culture and glasshouse‐grown plants in potting mix. Root lengths were reduced, but the differences were statistically significant in a single trial only. The findings from this study demonstrate that, as with potato, root infection by S. subterranea can result in reduced tomato plant growth and that root gall production associated with root infection was not necessary for this retardation of growth response. This further suggests that possible yield impacts in other crop species that are hosts for S. subterranea root infection are worthy of examination.     

Closing the ‘phenotype gap’ in precision medicine: improving what we measure to understand complex disease mechanisms

The central concept underlying precision medicine is a mechanistic understanding of each disease and its response to therapy sufficient to direct a specific intervention. To execute on this vision requires parsing incompletely defined disease syndromes into discrete mechanistic subsets and developing interventions to precisely address each of these etiologically distinct entities. This will require substantial adjustment of traditional paradigms which have tended to aggregate high-level phenotypes with very different etiologies. In the current environment, where diagnoses are not mechanistic, drug development has become so expensive that it is now impractical to imagine the cost-effective creation of new interventions for many prevalent chronic conditions. The vision of precision medicine also argues for a much more seamless integration of research and development with clinical care, where shared taxonomies will enable every clinical interaction to inform our collective understanding of disease mechanisms and drug responses. Ideally, this would be executed in ways that drive real-time and real-world discovery, innovation, translation, and implementation. Only in oncology, where at least some of the biology is accessible through surgical excision of the diseased tissue or liquid biopsy, has “co-clinical” modeling proven feasible. In most common germline disorders, while genetics often reveal the causal mutations, there still remain substantial barriers to efficient disease modeling. Aggregation of similar disorders under single diagnostic labels has directly contributed to the paucity of etiologic and mechanistic understanding by directly reducing the resolution of any subsequent studies. Existing clinical phenotypes are typically anatomic, physiologic, or histologic, and result in a substantial mismatch in information content between the phenomes in humans or in animal ‘models’ and the variation in the genome. This lack of one-to-one mapping of discrete mechanisms between disease and animal models causes a failure of translation and is one form of ‘phenotype gap.’ In this review, we will focus on the origins of the phenotyping deficit and approaches that may be considered to bridge the gap, creating shared taxonomies between human diseases and relevant models, using cardiovascular examples.

     

Knowledge and Skill in Motion: Layers of Tibetan Medical Education in India

This article examines the transmission of Tibetan medical knowledge in the Himalayan region of Ladakh (India), taking three educational settings as ethnographic ports of entry. Each of these corresponds to a different operating mode in the standardisation of medical knowledge and learning processes, holding profound implications for the way this therapeutic tradition is known, valued, applied and passed on to the next generation. Being at the same time a cause and a consequence of intra-regional variability in Tibetan medicine, the three institutional forms coexist in constant interaction with one another. The authors render this visible by examining the ‘taskscapes’ that characterize each learning context, that is to say, the specific and interlocking sets of practices and tasks in which a practitioner must be skilled in order to be considered competent. The authors build upon this notion by studying two fields of transmission and practice, relating to medicine production and medical ethics. These domains of enquiry provide a rich grounding from which to examine the transition from enskilment to education, as well as the overlaps between them, and to map out the connections linking different educational forms to social and medical legitimacy in contemporary India.     

Matching the supply of bacterial nutrients to the nutritional demand of the animal host

Various animals derive nutrients from symbiotic microorganisms with much-reduced genomes, but it is unknown whether, and how, the supply of these nutrients is regulated. Here, we demonstrate that the production of essential amino acids (EAAs) by the bacterium Buchnera aphidicola in the pea aphid Acyrthosiphon pisum is elevated when aphids are reared on diets from which that EAA are omitted, demonstrating that Buchnera scale EAA production to host demand. Quantitative proteomics of bacteriocytes (host cells bearing Buchnera) revealed that these metabolic changes are not accompanied by significant change in Buchnera or host proteins, suggesting that EAA production is regulated post-translationally. Bacteriocytes in aphids reared on diet lacking the EAA methionine had elevated concentrations of both methionine and the precursor cystathionine, indicating that methionine production is promoted by precursor supply and is not subject to feedback inhibition by methionine. Furthermore, methionine production by isolated Buchnera increased with increasing cystathionine concentration. We propose that Buchnera metabolism is poised for EAA production at certain maximal rates, and the realized release rate is determined by precursor supply from the host. The incidence of host regulation of symbiont nutritional function via supply of key nutritional inputs in other symbioses remains to be investigated.     

In vivo recording of adult zebrafish electrocardiogram and assessment of drug-induced QT prolongation

In the last decade the zebrafish has become a major model organism for the study of development and organogenesis. To maximize the experimental utility of this organism, it will be important to establish methods for adult phenotyping. We previously proposed that the embryonic zebrafish may be useful in high-throughput screening for drug-induced cardiotoxicity. We now describe a method for the reproducible recording of the adult zebrafish ECG and illustrate its application in the investigation of QT-prolonging drugs. Zebrafish ECGs were obtained by inserting two needle electrodes through the ventral epidermis. Fish were perfused orally, and motion artifacts were eliminated with a paralytic dose of mu-conotoxin GIIIB. Test compounds were delivered via the perfusion system. Without a means of hydration and oxygenation, the fish succumb rapidly. The use of a perfusion system allowed stable recording for > 6 h. Baseline conduction intervals were as follows: PR, 66 ms (SD 14); QRS, 34 ms (SD 11); QT, 242 ms (SD 54); and R-R, 398 ms (SD 77). The known QT-prolonging agents astemizole, haloperidol, pimozide, and terfenadine caused corrected QT increases of 18% (SD 9), 16% (SD 11), 17% (SD 9), and 11% (SD 6), respectively. The control drugs clonidine, penicillin and propranolol did not prolong the corrected QT interval. In conclusion, perfusion and muscular paralysis allows stable, low-noise recording of zebrafish ECGs. Agents known to cause QT prolongation in humans caused QT prolongation in fish in each case. The development of rigorous tools for the phenotyping of adult zebrafish will complement the high-throughput assays currently under development for embryonic and larval fish.     

An in silico platform for the study of epithelial pre-invasive neoplastic development

To study the possible mechanisms of epithelial preneoplastic development we developed an integrated platform using a 3D agent-based model (ABM). This platform, named idefics, allows for the implementation of normal biological rules at the cell level that interact and generate the usual homeostatic equilibrium of epithelium as well as other abnormal processes that can disrupt this equilibrium. The structure of this model is based on data from multi-scale quantitative analysis of a unique collection of preneoplastic lesions of the lung, cervix, and oral epithelium, that have been collected in our lab in the last 25 years. In this paper, we are describing the different components of this platform and will present results from different simulations generated by the model.     

Hedgehog signaling via angiopoietin1 is required for developmental vascular stability

The molecular pathways by which newly formed, immature endothelial cell tubes remodel to form a mature network of vessels supported by perivascular mural cells are not well understood. The zebrafish iguana (igu) genetic mutant has a mutation in the daz-interacting protein 1 (dzip1), a member of the hedgehog signaling pathway. Loss of dzip1 results in decreased size of the cranial dorsal aortae, ultrastructural defects in perivascular mural cell recruitment and subsequent hemorrhage. Although hedgehog signaling is disrupted in igu mutants, we find no defects in vessel patterning or artery–vein specification. Rather, we show that the loss of angiopoietin1 (angpt1) expression in ventral perivascular mesenchyme is responsible for vascular instability in igu mutants. Over-expression of angpt1 or partial down-regulation of the endogenous Angpt1 antagonist angpt2 rescues hemorrhage. This is the first direct in vivo link between hedgehog signaling and the induction of vascular stability by recruitment of perivascular mural cells through angiopoietin signaling.