Distribution and evolution of het gene homologs in the basidiomycota

In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.

Obtaining regulatory T cells from uraemic patients awaiting kidney transplantation for use in clinical trials

Adoptive transfer of regulatory T cells (T(regs)) has been proposed for use as a cellular therapy to induce transplantation tolerance. Preclinical data are encouraging, and clinical trials with T(reg) therapy are anticipated. In this study, we investigate different strategies for the isolation and expansion of CD4(+) CD25(high) CD127(low) T(regs) from uraemic patients. We use allogeneic dendritic cells (DCs) as feeder cells for the expansion and compare T(reg) preparations isolated by either fluorescence activated cell sorting (FACS) or magnetic activated cell sorting (MACS) that have been expanded subsequently with either mature or tolerogenic DCs. Expanded T(reg) preparations have been characterized by their purity, cytokine production and in-vitro suppressive ability. The results show that T(reg) preparations can be isolated from uraemic patients by both FACS and MACS. Also, the type of feeder cells used in the expansion affects both the purity and the functional properties of the T(reg) preparations. In particular, FACS-sorted T(reg) preparations expanded with mature DCs secrete more interleukin (IL)-10 and granzyme B than FACS-sorted T(reg) preparations expanded with tolerogenic DCs. This is a direct comparison between different isolation techniques and expansion protocols with T(regs) from uraemic patients that may guide future efforts to produce clinical-grade T(regs) for use in kidney transplantation.

In vivo and in vitro liver cancer metabolism observed with hyperpolarized [5-(13)C]glutamine

Glutamine metabolism is, with its many links to oncogene expression, considered a crucial step in cancer metabolism and it is thereby a key target for alteration in cancer development. In particular, strong correlations have been reported between oncogene expression and expression and activity of the enzyme glutaminase. This mitochondrial enzyme, which is responsible for the deamidation of glutamine to form glutamate, is overexpressed in many tumour tissues. In animal models, glutaminase expression is correlated with tumour growth rate and it is readily possible to limit tumour growth by suppression of glutaminase activity. In principle, hyperpolarized (13)C MR spectroscopy can provide insight to glutamine metabolism and should hence be a valuable tool to study changes in glutaminase activity as tumours progress. However, no such successful in vivo studies have been reported, even though several good biological models have been tested. This may, at least partly, be due to problems in preparing glutamine for hyperpolarization. This paper reports a new and improved preparation of hyperpolarized [5-(13)C]glutamine, which provides a highly sensitive (13)C MR marker. With this preparation of hyperpolarized [5-(13)C]glutamine, glutaminase activity in vivo in a rat liver tumour was investigated. Moreover, this marker was also used to measure response to drug treatment in vitro in cancer cells. These examples of [5-(13)C]glutamine used in tumour models warrant the new preparation to allow metabolic studies with this conditionally essential amino acid.

Fewer invited talks by women in evolutionary biology symposia

Lower visibility of female scientists, compared to male scientists, is a potential reason for the under-representation of women among senior academic ranks. Visibility in the scientific community stems partly from presenting research as an invited speaker at organized meetings. We analysed the sex ratio of presenters at the European Society for Evolutionary Biology (ESEB) Congress 2011, where all abstract submissions were accepted for presentation. Women were under-represented among invited speakers at symposia (15% women) compared to all presenters (46%), regular oral presenters (41%) and plenary speakers (25%). At the ESEB congresses in 2001–2011, 9–23% of invited speakers were women. This under-representation of women is partly attributable to a larger proportion of women, than men, declining invitations: in 2011, 50% of women declined an invitation to speak compared to 26% of men. We expect invited speakers to be scientists from top ranked institutions or authors of recent papers in high-impact journals. Considering all invited speakers (including declined invitations), 23% were women. This was lower than the baseline sex ratios of early-mid career stage scientists, but was similar to senior scientists and authors that have published in high-impact journals. High-quality science by women therefore has low exposure at international meetings, which will constrain Evolutionary Biology from reaching its full potential. We wish to highlight the wider implications of turning down invitations to speak, and encourage conference organizers to implement steps to increase acceptance rates of invited talks.

Treatment of inflammatory bowel disease by chemokine receptor-targeted leukapheresis

Leukapheresis removes circulating leukocytes en route to the target organ. Hitherto unspecific matrixes have been used to remove leukocytes in inflammatory bowel disease (IBD). This report describes a novel selective leukapheresis column based on chemokine-chemokine receptor interaction. We found an increased expression of the gut homing chemokine receptor CCR9 on CD14(+) monocytes and on CD3(+) T lymphocytes from IBD patients. Biologically active CCL25 was coupled to a Sepharose matrix and demonstrated to selectively remove CCR9-expressing cells leaving other cell populations largely unaffected. A patient with active ulcerative colitis, was subjected to CCL25-column leukapheresis. Four days after treatment, he experienced clinical improvement and stable disease improvement ensued. The study illustrates that specific cells can be targeted using high affinity interactions, i.e., CCL25-CCR9 interactions to remove pathogenic gut-homing cells. Leukapheresis using the bCCL25 column should be investigated in a clinical phase I trial of patients with inflammatory bowel disease.

Schmidt decompositions of parametric processes II: vector four-wave mixing

In vector four-wave mixing, one or two strong pump waves drive two weak signal and idler waves, each of which has two polarization components. In this paper, vector four-wave mixing processes in a randomly-birefringent fiber (modulation interaction, phase conjugation and Bragg scattering) are studied in detail. For each process, the Schmidt decompositions of the coupling matrices facilitate the solution of the signal-idler equations and the Schmidt decomposition of the associated transfer matrix. The results of this paper are valid for arbitrary pump polarizations.

Schmidt decompositions of parametric processes I: basic theory and simple examples

Parametric devices based on four-wave mixing in fibers perform many signal-processing functions required by optical communication systems. In these devices, strong pumps drive weak signal and idler sidebands, which can have one or two polarization components, and one or many frequency components. The evolution of these components (modes) is governed by a system of coupled-mode equations. Schmidt decompositions of the associated transfer matrices determine the natural input and output mode vectors of such systems, and facilitate the optimization of device performance. In this paper, the basic properties of Schmidt decompositions are derived from first principles and are illustrated by two simple examples (one- and two-mode parametric amplification). In a forthcoming paper, several nontrivial examples relevant to current research (including four-mode parametric amplification) will be discussed.

Polarized neutron Laue diffraction on a crystal containing dynamically polarized proton spins

A polarized neutron Laue diffraction experiment on a single crystal of neodymium-doped lanthanum magnesium nitrate hydrate containing polarized proton spins is reported. By using dynamic nuclear polarization to polarize the proton spins, it is demonstrated that the intensities of the Bragg peaks can be enhanced or diminished significantly, whilst the incoherent background, due to proton spin disorder, is reduced. It follows that the method offers unique possibilities to tune continuously the contrast of the Bragg reflections and thereby represents a new tool for increasing substantially the signal-to-noise ratio in neutron diffraction patterns of hydrogenous matter.

The potential of dual-energy computed tomography for quantitative decomposition of soft tissues to water, protein and lipid in brachytherapy

Dosimetric accuracy of radiation treatment planning in brachytherapy depends on knowledge of tissue composition. It has been speculated that soft tissues can be decomposed to water, lipid and protein. The aim of our work is to evaluate the accuracy of such tissue decomposition. Selected abdominal soft tissues, whose average elemental compositions were taken from literature, were decomposed using dual energy computed tomography to water, lipid and protein via the three-material decomposition method. The quality of the decomposition was assessed using relative differences between (i) mass energy absorption and (ii) mass energy attenuation coefficients of the analyzed and approximated tissues. It was found that the relative differences were less than 2% for photon energies larger than 10 keV. The differences were notably smaller than the ones for water as the transport and dose scoring medium. The choice of the water, protein and lipid triplet resulted in negative elemental mass fractions for some analyzed tissues. As negative elemental mass fractions cannot be used in general purpose particle transport computer codes using the Monte Carlo method, other triplets should be used for the decomposition. These triplets may further improve the accuracy of the approximation as the differences were mainly caused by the lack of high-Z materials in the water, protein and lipid triplet.

Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation

PURPOSE

Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap.

EXPERIMENTAL DESIGN

Here, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860).

RESULTS

The meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate <1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup.

CONCLUSIONS

Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics.

Lactobacilli differently regulate expression and secretion of CXCL8 in urothelial cells

Modulation of the immune response is an established feature of certain lactobacilli. CXCL8 is an inflammatory chemokine released by the urinary tract mucosa after contact with uropathogenic Escherichia coli during urinary tract infection and is crucial for proper infiltration of immune cells. Nevertheless, persistently high levels of CXCL8 are associated with pathogenicity and malignancy. In this study, we tested twelve Lactobacillus strains for their ability to influence CXCL8 release from urothelial cells. We evaluated how strains from different Lactobacillus species could regulate CXCL8 in human 5637 urothelial cells, either resting cells or cells concomitantly challenged with heat-killed E. coli. A majority of the tested species altered CXCL8 release from the urothelial cells after 24 hours of stimulation. Most species increased CXCL8 release, whereas a few lactobacilli efficiently suppressed CXCL8 secretion from E. coli-challenged cells. While strong CXCL8 modulators such as Lactobacillus reuteri and Lactobacillus delbrueckii were unable to degrade CXCL8 in the extracellular environment, effects on IL8 transcription were evident for selected lactobacilli. Although IL8 transcription was affected by lactobacilli, the influence on mRNA transcript did not correlate to the impact on CXCL8 release. Phylogenetic analysis based on a 16S rRNA dendrogram of the tested lactobacilli and their effect on CXCL8 revealed some linkage to specific Lactobacillus groups. Testing the immunomodulatory nature of lactobacilli can prove important when selecting new probiotic microbes. Moreover, we believe that phylogenetic and phenotypic similarities could be used to analyse the traits governing such modulation.

Improving teamwork between students from two professional programmes in dental education

In Sweden, the National Board of Health and Welfare forecasts a decrease in dentists with 26% and an increase in dental hygienists with 47% until the year of 2023. This, together with changes in both epidemiology, especially of dental caries, and political priorities, calls for an effective and well-developed cooperation between dentists and dental hygienists in future dentistry. Hence, the aim of this project was to investigate whether highlighting teamwork during the undergraduate studies of dental students and dental hygiene students could improve the students' holistic view on patients as well as their knowledge of and insight into each other's future professions. Thirty-four dental students and 24 dental hygiene students participated in the study. At the beginning of their final year in undergraduate education, a questionnaire testing the level of knowledge of the dental hygienists' clinical competences was completed by both groups of students. In addition, activities intending to improve teamwork quality included the following: (i) a seminar with a dentist representing the Public Dental Health Services in Sweden, (ii) dental students as supervisors for dental hygiene students, (iii) planning and treatment for shared patients and (iv) students' presentations of the treatments and their outcomes at a final seminar. The project was ended by the students answering the above-mentioned questionnaire for the second time, followed by an evaluation of the different activities included in the study. The knowledge of dental hygienists' competences showed higher scores in almost all questions. Both groups of students considered the following aspects important: seminars with external participants, dental students acting as supervisors and planning and treating shared patients. By initiating and encouraging teamwork between dental students and dental hygiene students, it is possible to increase knowledge on dental hygienists' competence and also to develop and strengthen a holistic view on patients and dental work, thereby preparing both groups of students for their professional life.

Higher-capacity communication links based on two-mode phase-sensitive amplifiers

Optical communication links are usually made with erbium-doped fiber amplifiers, which amplify the signal waves in a phase-insensitive (PI) manner. They can also be made with parametric fiber amplifiers, in which the signal waves interact with idler waves. If information is transmitted using only the signals, parametric amplifiers are PI and their noise figures are comparable to those of erbium amplifiers. However, transmitting correlated information in the signals and idlers, or copying the signals prior to transmission, allows parametric amplifiers to be phase-sensitive (PS), which lowers their noise figures. The information capacities of two-mode PS links exceed those of the corresponding PI links by 2 b/s-Hz.