Collagen targeting using multivalent protein-functionalized dendrimers

Collagen is an attractive marker for tissue remodeling in a variety of common disease processes. Here we report the preparation of protein dendrimers as multivalent collagen targeting ligands by native chemical ligation of the collagen binding protein CNA35 to cysteine-functionalized dendritic divalent (AB₂) and tetravalent (AB₄) wedges. The binding of these multivalent protein constructs was studied on collagen-immobilized chip surfaces as well as to native collagen in rat intestinal tissues. To understand the importance of target density we also created collagen-mimicking surfaces by immobilizing synthetic collagen triple helical peptides at various densities on a chip surface. Multivalent display of a weak-binding variant (CNA35-Y175K) resulted in a large increase in collagen affinity, effectively restoring the collagen imaging capacities for the AB₄ system. In addition, dissociation of these multivalent CNA35 dendrimers from collagen surfaces was found to be strongly attenuated.     

Comprehensive gene-expression survey identifies wif1 as a modulator of cardiomyocyte differentiation

During chicken cardiac development the proepicardium (PE) forms the epicardium (Epi), which contributes to several non-myocardial lineages within the heart. In contrast to Epi-explant cultures, PE explants can differentiate into a cardiomyocyte phenotype. By temporal microarray expression profiles of PE-explant cultures and maturing Epi cells, we identified genes specifically associated with differentiation towards either of these lineages and genes that are associated with the Epi-lineage restriction. We found a central role for Wnt signaling in the determination of the different cell lineages. Immunofluorescent staining after recombinant-protein incubation in PE-explant cultures indicated that the early upregulated Wnt inhibitory factor-1 (Wif1), stimulates cardiomyocyte differentiation in a similar manner as Wnt stimulation. Concordingly, in the mouse pluripotent embryogenic carcinoma cell line p19cl6, early and late Wif1 exposure enhances and attenuates differentiation, respectively. In ovo exposure of the HH12 chicken embryonic heart to Wif1 increases the Tbx18-positive cardiac progenitor pool. These data indicate that Wif1 enhances cardiomyogenesis.     

Standardised Mindfulness-Based Interventions in Healthcare: An Overview of Systematic Reviews and Meta-Analyses of RCTs

Background

Mindfulness-based therapies are being used in a wide range of common chronic conditions in both treatment and prevention despite lack of consensus about their effectiveness in different patient categories.

Objective

To systematically review the evidence of effectiveness MBSR and MBCT in different patient categories.

Methods

A systematic review and meta-analysis of systematic reviews of RCTs, using the standardized MBSR or MBCT programs. We used PRISMA guidelines to assess the quality of the included reviews and performed a random effects meta-analysis with main outcome measure Cohen’s d. All types of participants were considered.

Results

The search produced 187 reviews: 23 were included, covering 115 unique RCTs and 8,683 unique individuals with various conditions. Compared to wait list control and compared to treatment as usual, MBSR and MBCT significantly improved depressive symptoms (d=0.37; 95%CI 0.28 to 0.45, based on 5 reviews, N=2814), anxiety (d=0.49; 95%CI 0.37 to 0.61, based on 4 reviews, N=2525), stress (d=0.51; 95%CI 0.36 to 0.67, based on 2 reviews, N=1570), quality of life (d=0.39; 95%CI 0.08 to 0.70, based on 2 reviews, N=511) and physical functioning (d=0.27; 95%CI 0.12 to 0.42, based on 3 reviews, N=1015). Limitations include heterogeneity within patient categories, risk of publication bias and limited long-term follow-up in several studies.

Conclusion

The evidence supports the use of MBSR and MBCT to alleviate symptoms, both mental and physical, in the adjunct treatment of cancer, cardiovascular disease, chronic pain, depression, anxiety disorders and in prevention in healthy adults and children.     

A role for the Rab6B Bicaudal-D1 interaction in retrograde transport in neuronal cells

The Rab6 subfamily of small GTPases consists of three different isoforms: Rab6A, Rab6A' and Rab6B. Both Rab6A and Rab6A' are ubiquitously expressed whereas Rab6B is predominantly expressed in brain. Recent studies have shown that Rab6A' is the isoform regulating the retrograde transport from late endosomes via the Golgi to the ER and in the transition from anaphase to metaphase during mitosis. Since the role of Rab6B is still ill defined, we set out to characterize its intracellular environment and dynamic behavior. In a Y-2H search for novel Rab6 interacting proteins, we identified Bicaudal-D1, a large coiled-coil protein known to bind to the dynein/dynactin complex and previously shown to be a binding partner for Rab6A/Rab6A'. Co-immunoprecipitation studies and pull down assays confirmed that Bicaudal-D1 also interacts with Rab6B in its active form. Using confocal laser scanning microscopy it was established that Rab6B and Bicaudal-D1 co-localize at the Golgi and vesicles that align along microtubules. Furthermore, both proteins co-localized with dynein in neurites of SK-N-SH cells. Live cell imaging revealed bi-directional movement of EGFP-Rab6B structures in SK-N-SH neurites. We conclude from our data that the brain-specific Rab6B via Bicaudal-D1 is linked to the dynein/dynactin complex, suggesting a regulatory role for Rab6B in the retrograde transport of cargo in neuronal cells.     

Free-Living Protozoa in Two Unchlorinated Drinking Water Supplies,Identified by Phylogenic Analysis of 18S rRNA Gene Sequences

Free-living protozoan communities in water supplies may include hosts for Legionella pneumophila and other undesired bacteria, as well as pathogens. This study aimed at identifying free-living protozoa in two unchlorinated groundwater supplies, using cultivation-independent molecular approaches. For this purpose, samples (<20°C) of treated water, distributed water, and distribution system biofilms were collected from supply A, with a low concentration of natural organic matter (NOM) (<0.5 ppm of C), and from supply B, with a high NOM concentration (7.9 ppm of C). Eukaryotic communities were studied using terminal restriction fragment length polymorphism and clone library analyses of partial 18S rRNA gene fragments and a Hartmannella vermiformis-specific quantitative PCR (qPCR). In both supplies, highly diverse eukaryotic communities were observed, including free-living protozoa, fungi, and metazoa. Sequences of protozoa clustered with Amoebozoa (10 operational taxonomic units [OTUs]), Cercozoa (39 OTUs), Choanozoa (26 OTUs), Ciliophora (29 OTUs), Euglenozoa (13 OTUs), Myzozoa (5 OTUs), and Stramenopiles (5 OTUs). A large variety of protozoa were present in both supplies, but the estimated values for protozoan richness did not differ significantly. H. vermiformis was observed in both supplies but was not a predominant protozoan. One OTU with the highest similarity to Acanthamoeba polyphaga, an opportunistic human pathogen and a host for undesired bacteria, was observed in supply A. The high level of NOM in supply B corresponded with an elevated level of active biomass and with elevated concentrations of H. vermiformis in distributed water. Hence, the application of qPCR may be promising in elucidating the relationship between drinking water quality and the presence of specific protozoa.Free-living protozoa are ubiquitous in natural freshwater environments (7, 38, 51, 71) but also proliferate in engineered water systems, including water treatment systems (3, 47, 70), distribution systems (6, 75), and tap water installations inside buildings (54, 69). Concentrations of protozoa, determined using cultivation methods and microscopy, range from <1 to 10⁴ cells liter⁻¹ in treated water (3, 47, 70, 75) and from <1 to 7 × 10⁵ cells liter⁻¹ in distribution systems (6, 61, 64, 75). Genera of free-living protozoa commonly observed in these systems and in tap water installations include Acanthamoeba, Echinamoeba, Hartmannella, Platyamoeba, Vahlkampfia, and Vannella (47, 58, 69, 70). In warm water systems, certain free-living protozoa, e.g., Acanthamoeba spp. (57), Balamuthia mandrillaris (62), Echinamoeba exandans (16), Hartmannella spp. (39, 56), Naegleria spp. (49, 57), Tetrahymena spp. (18, 33), and Vahlkampfia jugosa (56), serve as hosts for Legionella pneumophila, the etiologic agent of Legionnaires'' disease. High concentrations of L. pneumophila are generally associated with the proliferation of host protozoa in biofilms (38, 53). In addition, other amoeba-resistant, potentially pathogenic bacteria, e.g., Burkholderia spp. (28) and Mycobacterium spp. (37), have been observed in man-made aquatic environments (24). Free-living protozoa may enhance the multiplication of bacteria, serve as a transmission vector, or serve as a shelter against unfavorable environmental conditions, such as the presence of disinfectants. Furthermore, certain free-living protozoa are human pathogens, e.g., Naegleria fowleri (81), Balamuthia mandrillaris (77), and Acanthamoeba spp. (12) can cause encephalitis. Acanthamoeba spp. have also been associated with keratitis in persons wearing contact lenses (31).Free-living protozoa feed on bacteria, algae, fungi, other protozoa, and organic detritus in biofilms or in the planktonic phase, thereby affecting the structure of microbial communities. In turn, the community of free-living protozoa depends on the diversity and abundance of bacteria in the biofilm and in the planktonic phase (26, 50, 51, 55, 63, 65). Water quality is a critical factor for biofilm formation in distribution systems and tap water installations and therefore will affect the abundance and diversity of free-living protozoa in these systems (72, 78). However, information about the presence and identity of free-living protozoa in water supplies in relation to the quality of treated water is scarce, which may be attributed to the limitations of microscopic techniques and cultivation methods for detection and identification of these organisms, e.g., low detection limits and selectivity for specific groups (19).In this study, we applied a variety of cultivation-independent techniques, viz., quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP) analysis, and cloning and sequencing of eukaryotic 18S rRNA gene fragments, for the detection and identification of free-living protozoa predominating in two unchlorinated groundwater supplies. The concentrations of dissolved natural organic matter (NOM) in treated water at the plant were <0.5 mg C liter⁻¹ and 7.9 mg C liter⁻¹, covering the entire range of NOM concentrations in drinking water in The Netherlands. The objectives of the study were (i) to elucidate the identities of and diversity in the free-living protozoa predominating in these two different water supplies and (ii) to trace the presence of host protozoa for L. pneumophila and pathogenic free-living protozoa. The study revealed that treated water and biofilms in the distribution systems of both water supplies contained a large variety of free-living protozoa, including protozoan hosts for Legionella bacteria.     

Detection of Protozoan Hosts for Legionella pneumophila in Engineered Water Systems by Using a Biofilm Batch Test

Legionella pneumophila proliferates in aquatic habitats within free-living protozoa, 17 species of which have been identified as hosts by using in vitro experiments. The present study aimed at identifying protozoan hosts for L. pneumophila by using a biofilm batch test (BBT). Samples (600 ml) collected from 21 engineered freshwater systems, with added polyethylene cylinders to promote biofilm formation, were inoculated with L. pneumophila and subsequently incubated at 37°C for 20 days. Growth of L. pneumophila was observed in 16 of 18 water types when the host protozoan Hartmannella vermiformis was added. Twelve of the tested water types supported growth of L. pneumophila or indigenous Legionella anisa without added H. vermiformis. In 12 of 19 BBT flasks H. vermiformis was indicated as a host, based on the ratio between maximum concentrations of L. pneumophila and H. vermiformis, determined with quantitative PCR (Q-PCR), and the composition of clone libraries of partial 18S rRNA gene fragments. Analyses of 609 eukaryotic clones from the BBTs revealed that 68 operational taxonomic units (OTUs) showed the highest similarity to free-living protozoa. Forty percent of the sequences clustering with protozoa showed ≥99.5% similarity to H. vermiformis. None of the other protozoa serving as hosts in in vitro studies were detected in the BBTs. In several tests with growth of L. pneumophila, the protozoa Diphylleia rotans, Echinamoeba thermarum, and Neoparamoeba sp. were identified as candidate hosts. In vitro studies are needed to confirm their role as hosts for L. pneumophila. Unidentified protozoa were implicated as hosts for uncultured Legionella spp. grown in BBT flasks at 15°C.Legionella pneumophila, the causative agent of Legionnaires'' disease, is a common inhabitant of natural freshwater environments and human-made water systems, including cooling towers, whirlpools, air-conditioning systems, and installations for warm tap water (14). In the aquatic environment L. pneumophila proliferates within certain free-living protozoa, which serve as its hosts (15, 30, 59). Environmental factors favoring the growth and survival of L. pneumophila in freshwater systems include a water temperature between 20°C and 45°C (41, 60) and the presence of biofilms and sediments on which the protozoan hosts can graze (30, 41, 56).Rowbotham (44) was the first to report the growth of L. pneumophila within free-living amoebae, which belonged to the genera Acanthamoeba and Naegleria. In vitro studies with cocultures have revealed that 14 species of amoebae, viz., Acanthamoeba spp. (1, 35, 44, 53), Balamuthia mandrillaris (47), Echinamoeba exundans (15), Hartmannella spp. (43), Naegleria spp. (38, 44, 53), and Vahlkampfia jugosa (43); the slime mold Dictyostelium discoideum (20, 48); and two species of the ciliate genus Tetrahymena (15, 26) can serve as hosts for L. pneumophila. Recently, it has been reported that L. pneumophila can also replicate within the intestinal tract of the microbiovorous nematode Caenorhabditis elegans (3).A number of the free-living protozoa mentioned above and others, e.g., Vannella spp. and Saccamoeba spp., have been observed in aquatic environments from which L. pneumophila was cultivated or in which it was detected with PCR (4, 42, 51, 52). However, it remains unknown which of these protozoa actually serve as hosts for L. pneumophila in the aquatic environment, including human-made water systems. Moreover, it cannot be excluded that free-living protozoa other than those tested in vitro can serve as hosts for L. pneumophila as well. Information is also lacking about protozoan hosts for Legionella anisa (13, 49), which is frequently present in water installations in temperate regions (11, 62). Furthermore, it is unknown which free-living protozoa serve as hosts for uncultured Legionella bacteria that can grow at temperatures of about 15°C (61; B. A. Wullings, G. Bakker, and D. van der Kooij, submitted for publication).L. pneumophila can proliferate in samples of surface water, effluent of wastewater treatment plants, potable water, and water from cooling towers incubated at 25°C, 35°C, or 37°C (28, 45, 56). Consequently, incubation of freshwater samples can be used to amplify protozoan hosts for L. pneumophila and other Legionella spp. In this study, different human-made water types were investigated using a biofilm batch test (BBT) system to (i) amplify and subsequently identify predominating, known, and yet-undescribed hosts for L. pneumophila and (ii) identify potential protozoan hosts for Legionella bacteria that can grow at 15°C.     

Proteolytic processing of the receptor-type protein tyrosine phosphatase PTPBR7

The single-copy mouse gene Ptprr gives rise to different protein tyrosine phosphatase (PTP) isoforms in neuronal cells through the use of distinct promoters, alternative splicing, and multiple translation initiation sites. Here, we examined the array of post-translational modifications imposed on the PTPRR protein isoforms PTPBR7, PTP-SL, PTPPBSgamma42 and PTPPBSgamma37, which have distinct N-terminal segments and localize to different parts of the cell. All isoforms were found to be short-lived, constitutively phosphorylated proteins. In addition, the transmembrane isoform, PTPBR7, was subject to N-terminal proteolytic processing, in between amino acid position 136 and 137, resulting in an additional, 65-kDa transmembrane PTPRR isoform. Unlike for some other receptor-type PTPs, the proteolytically produced N-terminal ectodomain does not remain associated with this PTPRR-65. Shedding of PTPBR7-derived polypeptides at the cell surface further adds to the molecular complexity of PTPRR biology.     

Protein enrichment by capture-release based on strain-promoted cycloaddition of azide with bicyclononyne (BCN)

An enrichment strategy was devised for azide derivatized macromolecules, based on strain-promoted alkyne-azide cycloaddition (SPAAC) and a cleavable linker. A ring-strained alkyne, bicyclo[6.1.0]non-4-yne (BCN), was covalently attached to agarose beads via a hydrazine-sensitive linker. Benchmark studies of the resulting 'azido-trap' beads were performed with a fluorogenic coumarin derivative, leading to efficient capture of the azidocoumarin with concomitant fluorescence staining of the beads via SPAAC. The versatility of the beads for specific protein enrichment was shown by an effective and highly specific capture-release strategy for enrichment of azido-containing Candida antarctica lipase B (CalB) from a mixture of proteins. This approach is suited for selective enrichment of (glyco)proteins after metabolic incorporation of azides for subsequent (glyco)proteomics studies.     

Zinc inhibition of hepatic fructose metabolism in rats

The ability of Zn to modulate key metabolic processes was investigated in a study of gluconeogenesis in isolated hepatocytes from fasted rats. Zn (100 μM) inhibited glucose production from fructose by 41%, sorbitol by 28%; glycerol by 17%, and glyceraldehyde by 26%. Maximum inhibition of gluconeogenesis from fructose occurred at 25 μM Zn. Zn inhibited the rate of lactate production from fructose by 24% but not from sorbitol, glycerol, or glyceraldehyde. Fructose uptake by hepatocytes was not affected by Zn. A positive linear relationship (r=0.994) was obtained between inhibition by Zn of glucose and lactate production, indicating that a common step in both pathways is inhibited by Zn. The effect of Zn on fructokinase, aldolase-B, and triokinase activities was determined on semipurified rat liver enzyme preparations. Zn had no affect on triokinase activity but inhibited the two other enzymes in a dose-dependent manner, with the inhibition of aldolase-B being much greater than of fructokinase for concentrations of Zn between 2.5 and 20 μM. Zn increased the intracellular concentration of fructose-1-P in hepatocytes incubated with fructose, indicating a more potent Zn inhibition of aldolase-B than fructokinase. In addition, hepatocytes treated with Zn had decreased ATP and ADP concentrations, but had normal energy charge, suggesting an effect of Zn on adenine nucleotide degradation or synthesis. The demonstration that Zn inhibits two enzymes in fructose metabolism adds to the growing list of metabolic pathways that are catalyzed by enzymes that are sensitive to Zn.