Overgrowth of a mouse model of Simpson– Golabi–Behmel syndrome is partly mediated by Indian Hedgehog

Loss‐of‐function mutations of Glypican 3 (Gpc3) cause the Simpson–Golabi–Behmel overgrowth syndrome (SGBS), and developmental overgrowth is observed in Gpc3‐null mice, a mouse model for SGBS. We recently reported that GPC3 inhibits Hedgehog (Hh) signalling by inducing its endocytosis and degradation. Here, we show that the developmental overgrowth observed in Gpc3‐null mice is, at least in part, a consequence of the hyperactivation of the Hh pathway. We bred Gpc3‐null mice with mice that are Hh signalling‐deficient owing to the lack of Indian Hh (Ihh), one of the three mammalian Hhs. We found that the Gpc3‐null mice showed a 29.9% overgrowth in an Ihh wild‐type background, whereas an Ihh‐null background partly rescues the overgrowth caused by the lack of Gpc3 as the double mutants were 19.8% bigger than the Ihh‐null mice. Consistent with the role of GPC3 in Hh endocytosis and degradation, the Gpc3‐null mice show increased levels of Ihh protein and signalling, but similar levels of Ihh messenger RNA.     

Bacterial diversity patterns along a gradient of primary productivity

Primary productivity is a key determinant of biodiversity patterns in plants and animals but has not previously been shown to affect bacterial diversity. We examined the relationship between productivity and bacterial richness in aquatic mesocosms designed to mimic small ponds. We observed that productivity could influence the composition and richness of bacterial communities. We showed that, even within the same system, different bacterial taxonomic groups could exhibit different responses to changes in productivity. The richness of members of the Cytophaga‐Flavobacteria‐Bacteroides group exhibited a significant hump‐shaped relationship with productivity, as is often observed for plant and animal richness in aquatic systems. In contrast, we observed a significant U‐shaped relationship between richness and productivity for α‐proteobacteria and no discernable relationship for β‐proteobacteria. We show, for the first time, that bacterial diversity varies along a gradient of primary productivity and thus make an important step towards understanding processes responsible for the maintenance of bacterial biodiversity.     

S‐adenosyl‐l‐methionine usage during climacteric ripening of tomato in relation to ethylene and polyamine biosynthesis and transmethylation capacity

S‐adenosyl‐l ‐methionine (SAM) is the major methyl donor in cells and it is also used for the biosynthesis of polyamines and the plant hormone ethylene. During climacteric ripening of tomato (Solanum lycopersicum ‘Bonaparte’), ethylene production rises considerably which makes it an ideal object to study SAM involvement. We examined in ripening fruit how a 1‐MCP treatment affects SAM usage by the three major SAM‐associated pathways. The 1‐MCP treatment inhibited autocatalytic ethylene production but did not affect SAM levels. We also observed that 1‐(malonylamino)cyclopropane‐1‐carboxylic acid formation during ripening is ethylene dependent. SAM decarboxylase expression was also found to be upregulated by ethylene. Nonetheless polyamine content was higher in 1‐MCP‐treated fruit. This leads to the conclusion that the ethylene and polyamine pathway can operate simultaneously. We also observed a higher methylation capacity in 1‐MCP‐treated fruit. During fruit ripening substantial methylation reactions occur which are gradually inhibited by the methylation product S‐adenosyl‐l ‐homocysteine (SAH). SAH accumulation is caused by a drop in adenosine kinase expression, which is not observed in 1‐MCP‐treated fruit. We can conclude that tomato fruit possesses the capability to simultaneously consume SAM during ripening to ensure a high rate of ethylene and polyamine production and transmethylation reactions. SAM usage during ripening requires a complex cellular regulation mechanism in order to control SAM levels.     

Visualization of the post‐Golgi vesicle‐mediated transportation of TGF‐β receptor II by quasi‐TIRFM

Transforming growth factor β receptor II (Tβ RII) is synthesized in the cytoplasm and then transported to the plasma membrane of cells to fulfil its signalling duty. Here, we applied live‐cell fluorescence imaging techniques, in particular quasi‐total internal reflection fluorescence microscopy, to imaging fluorescent protein‐tagged Tβ RII and monitoring its secretion process. We observed punctuate‐like Tβ RII‐containing post‐Golgi vesicles formed in MCF7 cells. Single‐particle tracking showed that these vesicles travelled along the microtubules at an average speed of 0.51 μm/s. When stimulated by TGF‐β ligand, these receptor‐containing vesicles intended to move towards the plasma membrane. We also identified several factors that could inhibit the formation of such post‐Golgi vesicles. Although the inhibitory mechanisms still remain unknown, the observed characteristics of Tβ RII‐containing vesicles provide new information on intracellular Tβ RII transportation. It also renders Tβ RII a good model system for studying post‐Golgi vesicle‐trafficking and protein transportation. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

New hypotheses about the structure–function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor‐like repeat A docking site using WaterMap

LDL cholesterol (LDL‐C) is cleared from plasma via cellular uptake and internalization processes that are largely mediated by the low‐density lipoprotein cholesterol receptor (LDL‐R). LDL‐R is targeted for lysosomal degradation by association with proprotein convertase subtilisin‐kexin type 9 (PCSK9). Gain of function mutations in PCSK9 can result in excessive loss of receptors and dyslipidemia. On the other hand, receptor‐sparing phenomena, including loss‐of‐function mutations or inhibition of PCSK9, can lead to enhanced clearance of plasma lipids. We hypothesize that desolvation and resolvation processes, in many cases, constitute rate‐determining steps for protein–ligand association and dissociation, respectively. To test this hypothesis, we analyzed and compared the predicted desolvation properties of wild‐type versus gain‐of‐function mutant Asp374Tyr PCSK9 using WaterMap, a new in silico method for predicting the preferred locations and thermodynamic properties of water solvating proteins (“hydration sites”). We compared these results with binding kinetics data for PCSK9, full‐length LDL‐R ectodomain, and isolated EGF‐A repeat. We propose that the fast k_on and entropically driven thermodynamics observed for PCSK9‐EGF‐A binding stem from the functional replacement of water occupying stable PCSK9 hydration sites (i.e., exchange of PCSK9 H‐bonds from water to polar EGF‐A groups). We further propose that the relatively fast k_off observed for EGF‐A unbinding stems from the limited displacement of solvent occupying unstable hydration sites. Conversely, the slower k_off observed for EGF‐A and LDL‐R unbinding from Asp374Tyr PCSK9 stems from the destabilizing effects of this mutation on PCSK9 hydration sites, with a concomitant increase in the persistence of the bound complex. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Eight polymorphic microsatellite markers developed in the green leaf bug,Lygus lucorum Meyer‐Dür (Hemiptera: Miridae)

We developed eight polymorphic microsatellite markers for the green leaf bug, Lygus lucorum Meyer‐Dür. The number of observed alleles per locus in 48 individuals ranged from three to 13, whereas the observed and expected heterozygosities ranged from 0.133 to 0.810 and from 0.236 to 0.886, respectively. Cross‐species amplifications were conducted both within and between generas, and the amplification results indicated that these primers enriched for L. lucorum Meyer‐Dür are species‐specific.     

Formation of truncated peptide by‐products via sequence‐specific formyl group transfer from Trp(For) residues to Nα in the course of Boc‐SPPS

(N^In)‐Formyl protective group of tryptophan has been introduced as a base/nucleophile‐labile protective group. It has long been known that a free Nα‐amino group of the peptide can serve as a nucleophile: an irreversible formyl N^In → NH₂ transfer is consistently observed when deformylation is performed last on an otherwise deprotected peptide that possesses free Nα‐amino group. Obviously, this particular side reaction should be expected any time free amino group is exposed to Trp(For), but, at the best of our knowledge, has never been reported in the course of Boc‐SPPS. In the present communication, we describe a set of appropriately designed model experiments that permitted to detect the title side reaction both in solution and in solid‐phase reactions. We observed intermolecular formyl group transfer with a model compound, Trp(For)‐NH₂. Importantly, we also observed this migration on solid support with the rate roughly estimated to be up to 1% of residues per minute. We also observed that the formyl‐group transfer reaction occurred in a sequence‐dependent manner and was suppressed to a non‐detectable level using ‘in situ neutralization’ technique. Because this side reaction is sequence dependent, there might be situations when the rate of the formation of N_α‐formyl termination by‐products is significant. In other cases, the N_α‐For truncated by‐products would not contaminate the final peptide significantly but still could be a source of microheterogeneity. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Targeted destruction of fungal structures of Erysiphe trifoliorum on flat leaf surfaces of Marchantia polymorpha

In this study, we observed the germination behaviour of airborne conidia from powdery mildews that settle on thalloid surfaces. We inoculated thalli (flat, sheet‐like leaf tissues) and gemmae (small, flat, sheet‐like leaf tissues that propagate asexually via bud‐like structures) of the common liverwort (Marchantia polymorpha) with conidia from tomato powdery mildew (Oidium neolycopersici; KTP‐02) and red clover powdery mildew (Erysiphe trifoliorum; KRCP‐4N) and examined their germination and subsequent appressorium formation under a high‐fidelity digital microscope. Conidial bodies and germ tubes of the inoculated KRCP‐4N conidia were destroyed on both the thalli and gemmae. The destruction of these fungal structures was observed only for KRCP‐4N conidia inoculated onto M. polymorpha on both leaf surfaces. No differences in destruction of the KRCP‐4N fungal structures between thalli and gemmae were observed. At 4 h post‐inoculation, destruction of the germ tube tip was observed when it reached the gemmae leaf surface. At 6 h post‐inoculation, the conidial bodies and germ tubes were destroyed. In contrast, KTP‐02 conidia were not destroyed and formed normal, well‐lobed appressoria on the surface of M. polymorpha gemmae.     

Mitochondrial DNA mutations in respiratory complex-I in never-smoker lung cancer patients contribute to lung cancer progression and associated with EGFR gene mutation

Mitochondrial DNA (mtDNA) mutations were reported in different cancers. However, the nature and role of mtDNA mutation in never‐smoker lung cancer patients including patients with epidermal growth factor receptor (EGFR) and KRAS gene mutation are unknown. In the present study, we sequenced entire mitochondrial genome (16.5 kb) in matched normal and tumors obtained from 30 never‐smoker and 30 current‐smoker lung cancer patients, and determined the mtDNA content. All the patients' samples were sequenced for KRAS (exon 2) and EGFR (exon 19 and 21) gene mutation. The impact of forced overexpression of a respiratory complex‐I gene mutation was evaluated in a lung cancer cell line. We observed significantly higher (P = 0.006) mtDNA mutation in the never‐smokers compared to the current‐smoker lung cancer patients. MtDNA mutation was significantly higher (P = 0.026) in the never‐smoker Asian compared to the current‐smoker Caucasian patients' population. MtDNA mutation was significantly (P = 0.007) associated with EGFR gene mutation in the never‐smoker patients. We also observed a significant increase (P = 0.037) in mtDNA content among the never‐smoker lung cancer patients. The majority of the coding mtDNA mutations targeted respiratory complex‐I and forced overexpression of one of these mutations resulted in increased in vitro proliferation, invasion, and superoxide production in lung cancer cells. We observed a higher prevalence and new relationship between mtDNA alterations among never‐smoker lung cancer patients and EGFR gene mutation. Moreover, a representative mutation produced strong growth effects after forced overexpression in lung cancer cells. Signature mtDNA mutations provide a basis to develop novel biomarkers and therapeutic strategies for never‐smoker lung cancer patients. J. Cell. Physiol. 227: 2451–2460, 2012. © 2011 Wiley Periodicals, Inc.     

Small Organic Solutes in Sticky Droplets from Orb Webs of the Spider Zygiella atrica (Araneae; Araneidae): β‐Alaninamide Is a Novel and Abundant Component

In northeastern North America, Zygiella atrica often build their orb webs near the ocean. We analyzed individual field‐built Z. atrica webs to determine if organic low‐molecular‐mass solutes (LMM) in their sticky droplets showed any unusual features not previously seen in orb webs of other species living in less salty environments. While two of the three most abundant organic LMM (putrescine (butane‐1,4‐diamine) and GABamide (4‐aminobutanamide)) are already well‐known from webs of inland spiders, the third major LMM, β‐alaninamide (3‐aminopropanamide), a homolog of GABamide, has not been detected in sticky droplets from any other araneoid spiders (27 species). It remains to be established, however, whether or not use of β‐alaninamide is related to proximity to saltwater. We observed variability in organic LMM composition in Z. atrica webs that appeared to be influenced more by an undetermined factor associated with different collecting locations and/or collection dates than by different genders or instars. Shifts in composition when adult females were transferred from the field to the laboratory were also observed. Structural similarities and inverse correlations among β‐alaninamide, GABamide, and N‐acetylputrescine suggest that they may form a series of LMM fulfilling essentially the same, as yet unknown, role in the webs of those species in which they occur.     

Characterization of polymorphic microsatellite loci in a neotropical wood‐quail,Odontophorus leucolaemus

We developed a set of nine polymorphic microsatellite loci for black‐breasted wood‐quail, Odontophorus leucolaemus. We screened 50 individuals from Monteverde, Puntarenas Province, Costa Rica and found that locus‐specific allelic diversity ranges from two to 15 alleles (mean 10.2) and observed heterozygosity ranges from 0.24 to 0.96 (mean 0.78). These markers appear to be useful in other members of the Odontophorus genus.     

Novel microsatellite loci for the study of the black‐capped vireo (Vireo atricapillus)

We identified 14 novel polymorphic microsatellite loci in the black‐capped vireo (Vireo atricapillus). We also attempted to amplify and genotype these loci in other Vireo species, including the white‐eyed vireo (Vireo griseus), red‐eyed vireo (Vireo olivaceus), and blue‐headed vireo (Vireo solitarius). In 33 genotyped black‐capped vireos from two locations, total alleles ranged from six to 20, with observed heterozygosity ranging from 0.58 to 0.91 and expected heterozygosity from 0.65 to 0.93. Two loci had detectable levels of null alleles. Many of the loci were able to be amplified in the related Vireo species.     

Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis) on Newfoundland and Cape Breton Island

Island populations have long been important for understanding the dynamics and mechanisms of evolution in natural systems. While genetic drift is often strong on islands due to founder events and population bottlenecks, the strength of selection can also be strong enough to counteract the effects of drift. Here, we used several analyses to identify the roles of genetic drift and selection on genetic differentiation and diversity of Canada lynx (Lynx canadensis) across eastern Canada, including the islands of Cape Breton and Newfoundland. Specifically, we assessed whether we could identify a genetic component to the observed morphological differentiation that has been reported across insular and mainland lynx. We used a dinucleotide repeat within the promoter region of a functional gene that has been linked to mammalian body size, insulin‐like growth factor‐1 (IGF‐1). We found high genetic differentiation at neutral molecular markers but convergence of allele frequencies at the IGF‐1 locus. Thus, we showed that while genetic drift has influenced the observed genetic structure of lynx at neutral molecular markers, natural selection has also played a role in the observed patterns of genetic diversity at the IGF‐1 locus of insular lynx.     

An F‐box gene,CPR30, functions as a negative regulator of the defense response in Arabidopsis

Arabidopsis gain‐of‐resistance mutants, which show HR‐like lesion formation and SAR‐like constitutive defense responses, were used well as tools to unravel the plant defense mechanisms. We have identified a novel mutant, designated constitutive expresser of PR genes 30 (cpr30), that exhibited dwarf morphology, constitutive resistance to the bacterial pathogen Pseudomonas syringae and the dramatic induction of defense‐response gene expression. The cpr30‐conferred growth defect morphology and defense responses are dependent on ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), PHYTOALEXIN DEFICIENT 4 (PAD4), and NONRACE‐SPECIFIC DISEASE RESISTANCE 1 (NDR1). Further studies demonstrated that salicylic acid (SA) could partially account for the cpr30‐conferred constitutive PR1 gene expression, but not for the growth defect, and that the cpr30‐conferred defense responses were NPR1 independent. We observed a widespread expression of CPR30 throughout the plant, and a localization of CPR30‐GFP fusion protein in the cytoplasm and nucleus. As an F‐box protein, CPR30 could interact with multiple Arabidopsis‐SKP1‐like (ASK) proteins in vivo. Co‐localization of CPR30 and ASK1 or ASK2 was observed in Arabidopsis protoplasts. Based on these results, we conclude that CPR30, a novel negative regulator, regulates both SA‐dependent and SA‐independent defense signaling, most likely through the ubiquitin‐proteasome pathway in Arabidopsis.     

Induction of protective immunity by primed B-1 cells in Toxoplasma gondii -infected B cell-deficient mice

We examined the role of B‐1 cells in protection against Toxoplasma gondii infection using B cell‐deficient mice (μMT mice). We found that primed but not naïve B‐1 cells from wild‐type C57BL/6 mice protected B cell‐deficient recipients from challenge infection. All μMT mice transferred with primed B‐1 cells survived more than 5 months after T. gondii infection, whereas 100% of μMT mice transferred with naïve B‐1 cells succumbed by 18 days after infection. Additionally, high expression of both T help (Th) 1‐ and Th2‐type cytokines and a high level of nitric oxide production were observed in T. gondii‐infected μMT mice transferred with primed B‐1 cells. Thus, it was clearly demonstrated that B‐1 cells play an important role in host protection against T. gondii infection in μMT mice.     

Presence of SopE and mode of infection result in increased Salmonella‐containing vacuole damage and cytosolic release during host cell infection by Salmonella enterica

Salmonella enterica serovar Typhimurium (STM) is an invasive, facultative intracellular pathogen that has evolved sophisticated molecular mechanisms to establish an intracellular niche within a specialised vesicular compartment, the Salmonella‐containing vacuole (SCV). The loss of the SCV and release of STM into the cytosol of infected host cells was observed, and a bimodal intracellular lifestyle of STM in the SCV versus life in the cytosol is currently discussed. We set out to investigate the parameters affecting SCV integrity and cytosolic release. A fluorescent protein‐based cytosolic reporter approach was established to quantify, time‐resolved, and on a single cell level, the release of STM into the cytosol of host cells. We observed that the extent of SCV damage and cytosolic release is highly dependent on experimental conditions such as multiplicity of infection, type of host cell line, and STM strain background. Trigger invasion mediated by the Salmonella Pathogenicity Island 1‐encoded type III secretion system (SPI1‐T3SS) and its effector proteins promoted cytosolic release, whereas cytosolic bacteria were rarely observed if entry was mediated by zipper invasion. Presence of SPI1‐T3SS effector SopE was identified as major factor for damage of the SCV in the early phase after STM invasion and sopE‐expressing strains showed higher levels of cytosolic release.     

The Salmonella enterica giant adhesin SiiE binds to polarized epithelial cells in a lectin‐like manner

The invasion of polarized epithelial cells by Salmonella enterica requires the cooperative activity of the Salmonella pathogenicity island (SPI) 1‐encoded type III secretion system (T3SS) and the SPI4‐encoded giant non‐fimbrial adhesin SiiE. SiiE is a highly repetitive protein composed of 53 bacterial Ig (BIg) domains and mediates binding to the apical side of polarized epithelial cells. We analysed the binding properties of SiiE and observed lectin‐like activity. SiiE‐dependent cell invasion can be ablated by chemical or enzymatic deglycosylation. Lectin blockade experiments revealed that SiiE binding is specific for glycostructures with terminal N‐acetyl‐glucosamine (GlcNAc) and/or α 2,3‐linked sialic acid. In line with these data, we found that SiiE‐expressing Salmonella bind to the GlcNAc polymer chitin. Various recombinant SiiE fragments were analysed for host cell binding. We observed that C‐terminal portions of SiiE bind to the apical side of polarized cells and the intensity of binding increases with the number of BIg domains present in the recombinant proteins. Based on these results, we propose that SiiE mediates multiple interactions per molecule with glycoproteins and/or glycosylated phospholipids present in the apical membrane of polarized epithelial cells. Thisintimate binding enables the subsequent function of the SPI1‐T3SS, resulting in host cell invasion.     

Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline

The Lyme disease spirochete evades the host immune system by combinatorial variation of VlsE, a surface antigen. Antigenic variation occurs via segmental gene conversion from contiguous silent cassettes into the vlsE locus. Because of the high degree of similarity between switch variants and the size of vlsE, short‐read NGS technologies have been unsuitable for sequencing vlsE populations. Here we use PacBio sequencing technology coupled with the first fully‐automated software pipeline (VAST) to accurately process NGS data by minimizing error frequency, eliminating heteroduplex errors and accurately aligning switch variants. We extend earlier studies by showing use of almost all of the vlsE SNP repertoire. In different tissues of the same mouse, 99.6% of the variants were unique, suggesting that dissemination of Borrelia burgdorferi is predominantly unidirectional with little tissue‐to‐tissue hematogenous dissemination. We also observed a similar number of variants in SCID and wild‐type mice, a heatmap of location and frequency of amino acid changes on the 3D structure and note differences observed in SCID versus wild type mice that hint at possible amino acid function. Our observed selection against diversification of residues at the dimer interface in wild‐type mice strongly suggests that dimerization is required for in vivo functionality of vlsE.