Capturing quantitative zooplankton information in the sea : Performance test of laser optical plankton counter and video plankton recorder in Calanus finmarchicus dominated summer situation

Author's accepted version (post-print).NOTICE: this is the author’s version of a work that was accepted for publication in Progress in Oceanography (2012). Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Progress in Oceanography (2012), 108. doi: http://dx.doi.org/10.1016/j.pocean.2012.10.005.We compared two optical plankton counters, the Laser Optical Plankton Counter (LOPC) and the Video Plankton Recorder (VPR) for their abundance estimates of Calanus finmarchicus during an early summer situation (June 2008) in two North Norwegian fjords. The LOPC was mounted on the VPR frame in order to sample the same body of water. The combined system of LOPC and VPR was operated by vertical profiling from the surface to 100 m of depth in several locations of the fjords representing different blooming conditions and zooplankton community structures. Data from the two instruments, as well as from CTD-F, were logged concurrently and retrieved on deck after about 15 depth profiles. Primary data were analysed according to standard routines, and choices made during sampling and analyses (sampling volume, selection of size range, transparency of particles, statistics) are discussed. Data were averaged for every 5, 10 and 15 m depth bins. The vertical profiles of C. finmarchicus CIV–CVI abundance that were obtained by LOPC and VPR, respectively, showed a striking similarity. No significant differences between profiles sampled by these two instruments were observed when data were binned into 15 m bins. At low abundances (<100 Calanus sp. L−1) profiles were significantly different when data were binned into 5- or 10-m bins. This is attributed to the small sampling volumes of the LOPC and the VPR, and to very patchy distributions of copepods, resulting in a high standard deviation between consecutive profiles. Based on the results we conclude that the time is mature for a more extensive use of optical instruments to estimate zooplankton abundances and distributions in the sea

Differences in PAR-2 activating potential by king crab (Paralithodes camtschaticus), salmon (Salmo salar), and bovine (Bos taurus) trypsin.

The manuscript version of this article, under a different title, is paper 3 of Anett Kristin Larsen's doctoral thesis which is available in Munin at http://hdl.handle.net/10037/2892Background: Salmon trypsin is shown to increase secretion of the pro-inflammatory cytokine interleukin (IL)-8 from human airway epithelial cells through activation of PAR-2. Secretion of IL-8 induced by king crab trypsin is observed in a different concentration range compared to salmon trypsin, and seems to be only partially related to PAR-2 activation. This report aim to identify differences in the molecular structure of king crab trypsin (Paralithodes camtschaticus) compared to salmon (Salmo salar) and bovine trypsin (Bos taurus) that might influence the ability to activate protease-activated receptor-2 (PAR-2). Results: During purification king crab trypsin displayed stronger binding capacity to the anionic column used in fast protein liquid chromatography compared to fish trypsins, and was identified as a slightly bigger molecule. Measurements of enzymatic activity yielded no obvious differences between the trypsins tested. Molecular modelling showed that king crab trypsin has a large area with strong negative electrostatic potential compared to the smaller negative areas in bovine and salmon trypsins. Bovine and salmon trypsins also displayed areas with strong positive electrostatic potential, a feature lacking in the king crab trypsin. Furthermore we have identified 3 divergent positions (Asp196, Arg244, and Tyr247) located near the substrate binding pocket of king crab trypsin that might affect the binding and cleavage of PAR-2. Conclusion: These preliminary results indicate that electrostatic interactions could be of importance in binding, cleavage and subsequent activation of PAR-2

Brain-type and liver-type fatty acid-binding proteins: new tumor markers for renal cancer?

BACKGROUND: Renal cell carcinoma (RCC) is the most common renal neoplasm. Cancer tissue is often characterized by altered energy regulation. Fatty acid-binding proteins (FABP) are involved in the intracellular transport of fatty acids (FA). We examined the level of brain-type (B) and liver-type (L) FABP mRNA and the protein expression profiles of both FABPs in renal cell carcinoma. METHODS: Paired tissue samples of cancerous and noncancerous kidney parts were investigated. Quantitative RT-PCR, immunohistochemistry and western blotting were used to determine B- and L-FABP in tumor and normal tissues. The tissue microarray (TMA) contained 272 clinico-pathologically characterized renal cell carcinomas of the clear cell, papillary and chromophobe subtype. SPSS 17.0 was used to apply crosstables (chi2-test), correlations and survival analyses. RESULTS: B-FABP mRNA was significantly up-regulated in renal cell carcinoma. In normal tissue B-FABP mRNA was very low or often not detectable. RCC with a high tumor grading (G3 + G4) showed significantly lower B-FABP mRNA compared with those with a low grading (G1 + G2). Western blotting analysis detected B-FABP in 78% of the cases with a very strong band but in the corresponding normal tissue it was weak or not detectable. L-FABP showed an inverse relationship for mRNA quantification and western blotting. A strong B-FABP staining was present in 52% of the tumor tissues contained in the TMA. In normal renal tissue, L-FABP showed a moderate to strong immunoreactivity in proximal tubuli. L-FABP was expressed at lower rates compared with the normal tissues in 30.5% of all tumors. There was no correlation between patient survival times and the staining intensity of both FABPs. CONCLUSION: While B-FABP is over expressed in renal cell carcinoma in comparison to normal renal tissues L-FABP appears to be reduced in tumor tissue. Although the expression behavior was not related to the survival outcome of the RCC patients, it can be assumed that these changes indicate fundamental alterations in the fatty metabolism in the RCC carcinogenesis. Further studies should identify the role of both FABPs in carcinogenesis, progression and with regard to a potential target in RCC

Renal cell neoplasias: reversion-inducing cysteine-rich protein with Kazal motifs discriminates tumor subtypes, while extracellular matrix metalloproteinase inducer indicates prognosis

BACKGROUND: Matrix metalloproteinases can promote invasion and metastasis, which are very frequent in renal cell carcinoma even at the time of diagnosis. Knowing the reversion-inducing cysteine-rich protein with Kazal motifs (RECK) as an inhibitor of matrix metalloproteinases and the extracellular matrix metalloproteinase inducer (EMMPRIN) protein as inducer, we aimed to determine their expression, localization and possible antagonistic action in the pathogenesis and progression of renal cell tumors in a retrospective study. METHODS: Tumor and adjacent normal tissues of 395 nephrectomized patients were immunostained for RECK and EMMPRIN on a tissue microarray. RESULTS: RECK strongly decreased in renal cell carcinoma compared to normal counterparts (Wilcoxon signed rank test, P < 0.001), and it discriminated tumor entities showing the highest expression in oncocytomas. EMMPRIN, however, could be significantly correlated to pT stage and Fuhrman grading (Spearman’s correlation coefficient r(s) = 0.289 and r(s) = 0.382, respectively). Higher expression of EMMPRIN was associated with decreased overall survival in Kaplan-Meier analysis (P < 0.001), and the EMMPRIN level could independently predict survival for cases without metastasis and involvement of lymph nodes. Decreased RECK expression was confirmed by Western blotting in tissue of eight normal/tumor matches of patients after radical nephrectomy, whereas the EMMPRIN pattern appeared to be heterogeneous. CONCLUSIONS: We propose RECK down regulation in renal cell carcinoma to be an early event that facilitates tumor formation and progression. EMMPRIN, however, as a prognostic tumor marker, increases only when aggressiveness is proceeding and could add an additional step to invasive properties of renal cell carcinoma

The third helix of the homeodomain of paired class homeodomain proteins acts as a recognition helix both for DNA and protein interactions

The transcription factor Pax6 is essential for the development of the eyes and the central nervous system of vertebrates and invertebrates. Pax6 contains two DNA-binding domains; an N-terminal paired domain and a centrally located homeodomain. We have previously shown that the vertebrate paired-less isoform of Pax6 (Pax6ΔPD), and several other homeodomain proteins, interact with the full-length isoform of Pax6 enhancing Pax6-mediated transactivation from paired domain-DNA binding sites. By mutation analyses and molecular modeling we now demonstrate that, surprisingly, the recognition helix for specific DNA binding of the homeodomains of Pax6 and Chx10 interacts with the C-terminal RED subdomain of the paired domain of Pax6. Basic residues in the recognition helix and the N-terminal arm of the homeodomain form an interaction surface that binds to an acidic patch involving residues in helices 1 and 2 of the RED subdomain. We used fluorescence resonance energy transfer assays to demonstrate such interactions between Pax6 molecules in the nuclei of living cells. Interestingly, two mutations in the homeodomain recognition helix, R57A and R58A, reduced protein–protein interactions, but not DNA binding of Pax6ΔPD. These findings suggest a critical role for the recognition helix and N-terminal arm of the paired class homeodomain in protein–protein interactions

Down-regulation of the pro-apoptotic XIAP associated factor-1 (XAF1) during progression of clear-cell renal cancer

BACKGROUND: Decreased expression of the interferon-stimulated, putative tumour suppressor gene XAF1 has been shown to play a role during the onset, progression and treatment failure in various malignancies. However, little is yet known about its potential implication in the tumour biology of clear-cell renal cell cancer (ccRCC). METHODS: This study assessed the expression of XAF1 protein in tumour tissue obtained from 291 ccRCC patients and 68 normal renal tissue samples, utilizing immunohistochemistry on a tissue-micro-array. XAF1 expression was correlated to clinico-pathological tumour features and prognosis. RESULTS: Nuclear XAF1 expression was commonly detected in normal renal- (94.1%) and ccRCC (91.8%) samples, without significant differences of expression levels. Low XAF1 expression in ccRCC tissue, however, was associated with progression of tumour stage (p = 0.040) and grade (p < 0.001). Low XAF1 tumour levels were also prognostic of significantly shortened overall survival times in univariate analysis (p = 0.018), but did not provide independent prognostic information. CONCLUSION: These data suggest down-regulation of XAF1 expression to be implicated in ccRCC progression and implies that its re-induction may provide a therapeutic approach. Although the prognostic value of XAF1 in ccRCC appears to be limited, its predictive value remains to be determined, especially in patients with metastatic disease undergoing novel combination therapies of targeted agents with Interferon-alpha

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries

Implementing Motivational Interviewing for Exercise with Depressed Adults

Background: Depression can negatively impact all aspects of life including physical health, financial stability, and job security. Motivational Interviewing (MI) reflects a counseling style based on five general principles: reflective listening, developing a discrepancy between the patient’s goals, values and their current behavior, avoiding argument and direct confrontation, adjusting to client resistance instead of opposing directly, and finally, supporting self-efficacy and optimism. Exercise can improve mood, lessen the course of depression, and can provide benefits in addition to antidepressants. However, many with mental illness do not get enough exercise and this can compound their illness. Objective: The purpose of this DNP project was to determine the barriers and facilitators of employing Motivational Interviewing (MI) for exercise in an outpatient mental health clinic in Northern Arizona Methodology: Patients were interviewed pre and post MI intervention, as well as administered PHQ-9 pre and post MI intervention. Written responses were analyzed for commonalities in their survey questions. Setting: West Yavapai Guidance Clinic in Prescott Valley, AZ. Participants: There were five patients that met project guidelines for depression during the convenience sampling period. Results: Response rate among participants was 60%, with 80% female and 20% male. The PHQ-9 scores was lower at the one month follow up after the MI intervention for two participants and stayed the same for the third. Commonalties that were identified were “relaxed,” “peaceful,” and “nature,” as well as “dogs.” Barriers were “time” and “weather.” Conclusion: The five participants reported depression and were identified as having depression on the PHQ-9. The three who followed up reported that they thought of exercise more frequently, and linked it to their mental health. With this small sample size there exhibited a positive association between targeting people’s behavior via MI on exercise, and subsequent improvement in PHQ-9 scores, as well as positive thoughts regarding mental health and exercise

Homology Modeling of Transporter Proteins

Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological importance. Several presently used therapeutic compounds elucidate their effects by targeting membrane transporter proteins, including anti-arrhythmic, anesthetic, antidepressant, anxiolytic and diuretic drugs. The lack of three-dimensional structures of human transporters hampers experimental studies and drug discovery. In this chapter, the use of homology modeling for generating structural models of membrane transporter proteins is reviewed. The increasing number of atomic resolution structures available as templates, together with improvements in methods and algorithms for sequence alignments, secondary structure predictions, and model generation, in addition to the increase in computational power have increased the applicability of homology modeling for generating structural models of transporter proteins. Different pitfalls and hints for template selection, multiple-sequence alignments, generation and optimization, validation of the models, and the use of transporter homology models for structure-based virtual ligand screening are discussed