New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images

Background

Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions.

Methods and Results

In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin—3,3’-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images.

Validation

To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images.

Context

Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.     

Peptidylarginine deiminase gene is differentially expressed in freshwater and brackish water rainbow trout

Peptidylarginine deiminase (PADI)-like cDNA sequence was isolated from rainbow trout (Oncorhynchus mykiss). It consists of a 111-bp 5′-untranslated region, a 731-bp 3′-UTR, and a 2,010-bp open reading frame encoding a protein of 669 amino acids. In the presence of calcium ions, PADI enzymes catalyze the post-translational modification reaction generating citrulline residues. Mammalian PADI enzymes are involved in a number of regulatory processes during cell differentiation and development such as skin keratinization, myelin maturation, and histone deimination. Though five PADI isotypes have been isolated from mammals, in bony fish only one PADI enzyme is present, which contains conserved amino acid residues responsible for catalysis and calcium ion-binding. Sequence identity of piscine PADI protein sequences available at gene databases exceeds 67%. Phylogenetic analyses revealed that not only piscine, but also amphibian and avian PADI-like proteins share most identical amino acid residues with mammalian PADI2. mRNA level of trout PADI-like gene is high in skin, fin, gills, brain, and spleen of rainbow trout. Quantitative Real-Time RT-PCR revealed that PADI gene is differentially expressed in liver, trunk kidney, and spleen of two trout strains, the freshwater-cultured STEELHEAD trout and the brackish water strain BORN.     

The active site of an algal prolyl 4-hydroxylase has a large structural plasticity

Prolyl 4-hydroxylases (P4Hs) are 2-oxoglutarate dioxygenases that catalyze the hydroxylation of peptidyl prolines. They play an important role in collagen synthesis, oxygen homeostasis, and plant cell wall formation. We describe four structures of a P4H from the green alga Chlamydomonas reinhardtii, two of the apoenzyme at 1.93 and 2.90 A resolution, one complexed with the competitive inhibitor Zn2+, and one with Zn2+ and pyridine 2,4-dicarboxylate (which is an analogue of 2-oxoglutarate) at 1.85 A resolution. The structures reveal the double-stranded beta-helix core fold (jellyroll motif), typical for 2-oxoglutarate dioxygenases. The catalytic site is at the center of an extended shallow groove lined by two flexible loops. Mutagenesis studies together with the crystallographic data indicate that this groove participates in the binding of the proline-rich peptide-substrates. It is discussed that the algal P4H and the catalytic domain of collagen P4Hs have notable structural similarities, suggesting that these enzymes form a separate structural subgroup of P4Hs different from the hypoxia-inducible factor P4Hs. Key structural differences between these two subgroups are described. These studies provide first insight into the structure-function relationships of the collagen P4Hs, which unlike the hypoxia-inducible factor P4Hs use proline-rich peptides as their substrates.     

The Eucalyptus terpene synthase gene family

Background

Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and intra- specific variation of terpenes is common in eucalypts.

Results

The genome sequences of Eucalyptus grandis and E. globulus were mined for terpene synthase genes (TPS) and compared to other plant species. We investigated the relative expression of TPS in seven plant tissues and functionally characterized five TPS genes from E. grandis. Compared to other sequenced plant genomes, Eucalyptus grandis has the largest number of putative functional TPS genes of any sequenced plant. We discovered 113 and 106 putative functional TPS genes in E. grandis and E. globulus, respectively. All but one TPS from E. grandis were expressed in at least one of seven plant tissues examined. Genomic clusters of up to 20 genes were identified. Many TPS are expressed in tissues other than leaves which invites a re-evaluation of the function of terpenes in Eucalyptus.

Conclusions

Our data indicate that terpenes in Eucalyptus may play a wider role in biotic and abiotic interactions than previously thought. Tissue specific expression is common and the possibility of stress induction needs further investigation. Phylogenetic comparison of the two investigated Eucalyptus species gives insight about recent evolution of different clades within the TPS gene family. While the majority of TPS genes occur in orthologous pairs some clades show evidence of recent gene duplication, as well as loss of function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1598-x) contains supplementary material, which is available to authorized users.     

Stimulus saliency modulates pre-attentive processing speed in human visual cortex

The notion of a saliency-based processing architecture [1] underlying human vision is central to a number of current theories of visual selective attention [e.g., 2]. On this view, focal-attention is guided by an overall-saliency map of the scene, which integrates (sums) signals from pre-attentive sensory feature-contrast computations (e.g., for color, motion, etc.). By linking the Posterior Contralateral Negativity (PCN) component to reaction time (RT) performance, we tested one specific prediction of such salience summation models: expedited shifts of focal-attention to targets with low, as compared to high, target-distracter similarity. For two feature-dimensions (color and orientation), we observed decreasing RTs with increasing target saliency. Importantly, this pattern was systematically mirrored by the timing, as well as amplitude, of the PCN. This pattern demonstrates that visual saliency is a key determinant of the time it takes for focal-attention to be engaged onto the target item, even when it is just a feature singleton.     

Intra-articular hyaluronic acid for the treatment of osteoarthritis of the knee: systematic review and meta-analysis

Background

Osteoarthritis of the knee affects up to 10% of the elderly population. The condition is frequently treated by intra-articular injection of hyaluronic acid. We performed a systematic review and meta-analysis of randomized controlled trials to assess the effectiveness of this treatment.

Methods

We searched MEDLINE, EMBASE, CINAHL, BIOSIS and the Cochrane Controlled Trial Register from inception until April 2004 using a combination of search terms for knee osteoarthritis and hyaluronic acid and a filter for randomized controlled trials. We extracted data on pain at rest, pain during or immediately after movement, joint function and adverse events.

Results

Twenty-two trials that reported usable quantitative information on any of the predefined end points were identified and included in the systematic review. Even though pain at rest may be improved by hyaluronic acid, the data available from these studies did not allow an appropriate assessment of this end point. Patients who received the intervention experienced a reduction in pain during movement: the mean difference on a 100-mm visual analogue scale was –3.8 mm (95% confidence interval [CI] –9.1 to 1.4 mm) after 2–6 weeks, –4.3 mm (95% CI –7.6 to –0.9 mm) after 10–14 weeks and –7.1 mm (95% CI –11.8 to –2.4 mm) after 22–30 weeks. However, this effect was not compatible with a clinically meaningful difference (expected to be about 15 mm on the visual analogue scale). Furthermore, the effect was exaggerated by trials not reporting an intention-to-treat analysis. No improvement in knee function was observed at any time point. Even so, the effect of hyaluronic acid on knee function was more favourable when allocation was not concealed. Adverse events occurred slightly more often among patients who received the intervention (relative risk 1.08, 95% CI 1.01 to 1.15). Only 4 trials explicitly reported allocation concealment, had blinded outcome assessment and presented intention-to-treat data.

Interpretation

According to the currently available evidence, intra-articular hyaluronic acid has not been proven clinically effective and may be associated with a greater risk of adverse events. Large trials with clinically relevant and uniform end points are necessary to clarify the benefit–risk ratio.Osteoarthritis affects about 10% of the population over 55 years of age. Of those, one-quarter are severely disabled.¹ The condition is characterized by degeneration of the articular cartilage and subsequent subchondral bone changes. The underlying mechanisms remain unknown, but the glycosaminoglycan–proteoglycan matrix may play a major role.²Hyaluronic acid, a glycosaminoglycan, is widely used for the treatment of osteoarthritis of the knee. A survey of 2 general practices in the United Kingdom showed that about 15% of patients with osteoarthritis received intra-articular treatment with glucosamine sulfates.³ The costs of such treatment are significant. At present, 1 syringe of hyaluronic acid costs at least Can$130 (US$110). The treatment of knee osteoarthritis is covered by the US Medicare program but not by provincial formularies in Canada. In Austria (which has 8 million inhabitants) more than 10 million euros (approximately US$12 million or Can$15 million) is spent by social insurance programs annually for hyaluronic acid preparations (excluding the cost of application).Hyaluronic acid has beneficial effects in vitro.⁴ Because of its viscoelastic quality, it may replace synovial fluid. Furthermore, it may reduce the perception of pain. Beneficial molecular and cellular effects have also been reported.^2,4 Hyaluronic acid is frequently applied by intra-articular injection, but the evidence concerning its clinical relevance is conflicting. The European League against Rheumatism (EULAR) recommends the intra-articular application of hyaluronic acid as “category 2” evidence (at least 1 controlled study without randomization).⁵ The American College of Rheumatology recommends intra-articular hyaluron therapy for patients with no response to nonpharmacologic therapy and simple analgesics.⁶ In contrast, other specialists have concluded that “hyaluronate sodium is not efficacious” in the treatment of osteoarthritis.⁷ The first state-of-the-art systematic review and meta-analysis was published recently,⁸ and its authors concluded “that intra-articular hyaluronic acid, at best, has a small effect.” We performed a systematic review and meta-analysis of the effect of intra-articular hyaluronic acid for the treatment of osteoarthritis of the knee. In contrast to 2 previous meta-analyses on this subject,^8,9 we used a different approach to data synthesis and interpretation: instead of analyzing a composite effect size over time, we allocated trial data, when possible, to 3 outcome groups that we assumed would be relevant for patients with osteoarthritis. We specifically looked at pain at rest, pain during exercise and joint function as distinct outcomes, measured repeatedly over time. In addition, we assessed adverse events and the impact of both trial quality and molecular mass of the product. This analysis allows us to provide important additional insight into the effects of intra-articular administration of hyaluronic acid for the treatment of osteoarthritis of the knee.     

Coalescent-based association mapping and fine mapping of complex trait loci

We outline a general coalescent framework for using genotype data in linkage disequilibrium-based mapping studies. Our approach unifies two main goals of gene mapping that have generally been treated separately in the past: detecting association (i.e., significance testing) and estimating the location of the causative variation. To tackle the problem, we separate the inference into two stages. First, we use Markov chain Monte Carlo to sample from the posterior distribution of coalescent genealogies of all the sampled chromosomes without regard to phenotype. Then, averaging across genealogies, we estimate the likelihood of the phenotype data under various models for mutation and penetrance at an unobserved disease locus. The essential signal that these models look for is that in the presence of disease susceptibility variants in a region, there is nonrandom clustering of the chromosomes on the tree according to phenotype. The extent of nonrandom clustering is captured by the likelihood and can be used to construct significance tests or Bayesian posterior distributions for location. A novelty of our framework is that it can naturally accommodate quantitative data. We describe applications of the method to simulated data and to data from a Mendelian locus (CFTR, responsible for cystic fibrosis) and from a proposed complex trait locus (calpain-10, implicated in type 2 diabetes).     

Photosynthetically oxygenated salicylate biodegradation in a continuous stirred tank photobioreactor

A consortium consisting of a Chlorella sorokiniana strain and a Ralstonia basilensis strain was able to carry out sodium salicylate biodegradation in a continuous stirred tank reactor (CSTR) using exclusively photosynthetic oxygenation. Salicylate biodegradation depended on algal activity, which itself was a function of microalgal concentration, light intensity, and temperature. Biomass recirculation improved the photobioreactor performance by up to 44% but the results showed the existence of an optimal biomass concentration above which dark respiration started to occur and the process efficiency started to decline. The salicylate removal efficiency increased by a factor of 3 when illumination was increased from 50-300 microE/m2.s. In addition, the removal rate of sodium salicylate was shown to be temperature-dependent, increasing from 14 to 27 mg/l.h when the temperature was raised from 26.5 to 31.5 degrees C. Under optimized conditions (300 microE/m2.s, 30 degrees C, 1 g sodium salicylate/l in the feed and biomass recirculation) sodium salicylate was removed at a maximum constant rate of 87 mg/l.h, corresponding to an estimated oxygenation capacity of 77 mg O2/l.h (based on a BOD value of 0.88 g O2/g sodium salicylate for the tested bacterium), which is in the range of the oxygen transfer capacity of large-scale mechanical surface aerators. Thus, although higher degradation rates were attained in the control reactor, the photobioreactor is a cost-efficient process which reduces the cost of aeration and prevents volatilization problems associated with the degradation of toxic volatile organic compounds under aerobic conditions.     

Dynamics of neutral lipid storage in yeast

Since energy storage is a basic metabolic process, the synthesis of neutral lipids occurs in all kingdoms of life. The yeast, Saccharomyces cerevisiae, widely accepted as a model eukaryotic cell, contains two classes of neutral lipids, namely steryl esters and triacylglycerols. Triacylglycerols are synthesized through two pathways governed by the acyl-CoA diacylglycerol acyltransferase Dga1p and the phospholipid diacylglycerol acyltransferase Lro1p, respectively. Steryl esters are formed by the two steryl ester synthases Are1p and Are2p, two enzymes with overlapping function which also catalyze triacylglycerol formation, although to a minor extent. Storage of neutral lipids is tightly linked to the biogenesis of so called lipid particles. The role of this compartment in lipid homeostasis and its interplay with other organelles involved in neutral lipid dynamics, especially the endoplasmic reticulum and the plasma membrane, are subject of current investigations. In contrast to neutral lipid formation, mobilization of triacylglycerols and steryl esters in yeast are less characterized at the molecular level. Only recently, the triacylglycerol lipase Tgl3p was identified as the first yeast enzyme of this kind by function. Genes and gene products governing steryl ester mobilization still await identification. Besides biochemical properties of enzymes involved in yeast neutral lipid synthesis and degradation, regulatory aspects of these pathways and cell biological consequences of neutral lipid depletion will be discussed in this minireview.