Abandoning aggression but maintaining self-nonself discrimination as a first stage in ant supercolony formation

An ant supercolony is a very large entity with very many queens. Although normal colonies of small extent and few queens remain distinct, a supercolony is integrated harmoniously over a large area [1, 2]. The lack of aggression is advantageous: Aggression is costly, involving direct and indirect losses and recognition errors [3, 4]. Indeed, supercolonial ants are among the ecologically most successful organisms [5-7]. But how supercolonies arise remains mysterious [1, 2, 8]. Suggestions include that reduced within-colony relatedness or reduced self-nonself discrimination would foster supercolony formation [1, 2, 5, 7, 9-12]. However, one risks confusing correlation and causality in deducing the evolution from distinct colonies to supercolonies when observing established supercolonies. It might help to follow up observations of another lack of aggression, that between single-queened colonies in some ant species. We show that the single-queened Lasius austriacus lacks aggression between colonies and occasionally integrates workers across colonies but maintains high within-colony relatedness and self-nonself discrimination. Provided that the ecological framework permits, reduced aggression might prove adaptive for any ant colony irrespective of within-colony relatedness. Abandoning aggression while maintaining discrimination might be a first stage in supercolony formation. This adds to the emphasis of ecology as central to the evolution of cooperation in general [13].     

The dTDP-4-dehydro-6-deoxyglucose reductase encoding fcd gene is part of the surface layer glycoprotein glycosylation gene cluster of Geobacillus tepidamans GS5-97T

The glycan chain of the S-layer protein of Geobacillus tepidamans GS5-97(T) consists of disaccharide repeating units composed of L-rhamnose and D-fucose, the latter being a rare constituent of prokaryotic glycoconjugates. Although biosynthesis of nucleotide-activated L-rhamnose is well established, D-fucose biosynthesis is less investigated. The conversion of alpha-D-glucose-1-phosphate into thymidine diphosphate (dTDP)-4-dehydro-6-deoxyglucose by the sequential action of RmlA (glucose-1-phosphate thymidylyltransferase) and RmlB (dTDP-glucose-4,6-dehydratase) is shared between the dTDP-D-fucose and the dTDP-L-rhamnose biosynthesis pathway. This key intermediate is processed by the dTDP-4-dehydro-6-deoxyglucose reductase Fcd to form dTDP-alpha-D-fucose. We identified the fcd gene in G. tepidamans GS5-97(T) by chromosome walking and performed functional characterization of the recombinant 308-amino acid enzyme. The in vitro activity of the enzymatic cascade (RmlB and Fcd) was monitored by high-performance liquid chromatography and the reaction product was confirmed by (1)H and (13)C nuclear magnetic resonance spectroscopy. This is the first characterization of the dTDP-alpha-D-fucopyranose biosynthesis pathway in a Gram-positive organism. fcd was identified as 1 of 20 open reading frames contained in a 17471-bp S-layer glycosylation (slg) gene cluster on the chromosome of G. tepidamans GS5-97(T). The sgtA structural gene is located immediately upstream of the slg gene cluster with an intergenic region of 247 nucleotides. By comparison of the SgtA amino acid sequence with the known glycosylation pattern of the S-layer protein SgsE of Geobacillus stearothermophilus NRS 2004/3a, two out of the proposed three glycosylation sites on SgtA could be identified by electrospray ionization quadrupole-time-of-flight mass spectrometry to be at positions Ser-792 and Thr-583.     

Cell polarity development and protein trafficking in hepatocytes lacking E-cadherin/beta-catenin-based adherens junctions

Using a mutant hepatocyte cell line in which E-cadherin and beta-catenin are completely depleted from the cell surface, and, consequently, fail to form adherens junctions, we have investigated adherens junction requirement for apical-basolateral polarity development and polarized membrane trafficking. It is shown that these hepatocytes retain the capacity to form functional tight junctions, develop full apical-basolateral cell polarity, and assemble a subapical cortical F-actin network, although with a noted delay and a defect in subsequent apical lumen remodeling. Interestingly, whereas hepatocytes typically target the plasma membrane protein dipeptidyl peptidase IV first to the basolateral surface, followed by its transcytosis to the apical domain, hepatocytes lacking E-cadherin-based adherens junctions target dipeptidyl peptidase IV directly to the apical surface. Basolateral surface-directed transport of other proteins or lipids tested was not visibly affected in hepatocytes lacking E-cadherin-based adherens junctions. Together, our data show that E-cadherin/beta-catenin-based adherens junctions are dispensable for tight junction formation and apical lumen biogenesis but not for apical lumen remodeling. In addition, we suggest a possible requirement for E-cadherin/beta-catenin-based adherens junctions with regard to the indirect apical trafficking of specific proteins in hepatocytes.     

Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies

MOTIVATION: In proteomics, reverse database searching is used to control the false match frequency for tandem mass spectrum/peptide sequence matches, but reversal creates sequences devoid of patterns that usually challenge database-search software. RESULTS: We designed an unsupervised pattern recognition algorithm for detecting patterns with various lengths from large sequence datasets. The patterns found in a protein sequence database were used to create decoy databases using a Monte Carlo sampling algorithm. Searching these decoy databases led to the prediction of false positive rates for spectrum/peptide sequence matches. We show examples where this method, independent of instrumentation, database-search software and samples, provides better estimation of false positive identification rates than a prevailing reverse database searching method. The pattern detection algorithm can also be used to analyze sequences for other purposes in biology or cryptology. AVAILABILITY: On request from the authors. SUPPLEMENTARY INFORMATION: http://bioinformatics.psb.ugent.be/.     

Quantitation of Guggenheimella bovis and treponemes in bovine tissues related to digital dermatitis

Digital dermatitis is an inflammation of uncertain aetiology in the skin of the foot of cattle. In 2005, a novel microorganism, Guggenheimella bovis, was isolated from the advancing front of digital dermatitis lesions, suggesting a possible role in pathogenesis. In the present study, tissue samples of 20 affected cows were examined by quantitative PCR for G. bovis, treponemes and the total eubacterial load. High numbers of eubacteria and treponemes were found in most lesions, whereas only a few lesions contained Guggenheimella, and only at low concentrations. The results argue against the relevance of G. bovis in the aetiology of digital dermatitis in cattle, but are consistent with a role for treponemes.     

Combinatorial materials research applied to the development of new surface coatings IV. A high-throughput bacterial biofilm retention and retraction assay for screening fouling-release performance of coatings

A high-throughput bacterial biofilm retention screening method has been augmented to facilitate the rapid analysis and down-selection of fouling-release coatings for identification of promising candidates. Coatings were cast in modified 24-well tissue culture plates and inoculated with the marine bacterium Cytophaga lytica for attachment and biofilm growth. Biofilms retained after rinsing with deionised water were dried at ambient laboratory conditions. During the drying process, retained biofilms retracted through a surface de-wetting phenomenon on the hydrophobic silicone surfaces. The retracted biofilms were stained with crystal violet, imaged, and analysed for percentage coverage. Two sets of experimental fouling-release coatings were analysed with the high-throughput biofilm retention and retraction assay (HTBRRA). The first set consisted of a series of model polysiloxane coatings that were systematically varied with respect to ratios of low and high MW silanol-terminated PDMS, level of cross-linker, and amount of silicone oil. The second set consisted of cross-linked PDMS-polyurethane coatings varied with respect to the MW of the PDMS and end group functionality. For the model polysiloxane coatings, HTBRRA results were compared to data obtained from field immersion testing at the Indian River Lagoon at the Florida Institute of Technology. The percentage coverage calculations of retracted biofilms correlated well to barnacle adhesion strength in the field (R(2)=0.82) and accurately identified the best and poorest performing coating compositions. For the cross-linked PDMS-polyurethane coatings, the HTBRRA results were compared to combinatorial pseudobarnacle pull-off adhesion data and good agreement in performance was observed. Details of the developed assay and its implications in the rapid discovery of new fouling-release coatings are discussed.     

A Highlights from MBoC Selection: Peptide TFP5/TP5 derived from Cdk5 activator P35 provides neuroprotection in the MPTP model of Parkinson’s disease

Parkinson’s disease (PD) is a chronic neurodegenerative disorder characterized by the loss of dopamine neurons in the substantia nigra, decreased striatal dopamine levels, and consequent extrapyramidal motor dysfunction. Recent evidence indicates that cyclin-dependent kinase 5 (Cdk5) is inappropriately activated in several neurodegenerative conditions, including PD. To date, strategies to specifically inhibit Cdk5 hyperactivity have not been successful without affecting normal Cdk5 activity. Previously we reported that TFP5 peptide has neuroprotective effects in animal models of Alzheimer’s disease. Here we show that TFP5/TP5 selective inhibition of Cdk5/p25 hyperactivation in vivo and in vitro rescues nigrostriatal dopaminergic neurodegeneration induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP/MPP+) in a mouse model of PD. TP5 peptide treatment also blocked dopamine depletion in the striatum and improved gait dysfunction after MPTP administration. The neuroprotective effect of TFP5/TP5 peptide is also associated with marked reduction in neuroinflammation and apoptosis. Here we show selective inhibition of Cdk5/p25 ­hyperactivation by TFP5/TP5 peptide, which identifies the kinase as a potential therapeutic target to reduce neurodegeneration in Parkinson’s disease.     

Anoikis evasion in inflammatory breast cancer cells is mediated by Bim-EL sequestration

Inflammatory breast cancer (IBC) is a rare and highly invasive type of breast cancer, and patients diagnosed with IBC often face a very poor prognosis. IBC is characterized by the lack of primary tumor formation and the rapid accumulation of cancerous epithelial cells in the dermal lymphatic vessels. Given that normal epithelial cells require attachment to the extracellular matrix (ECM) for survival, a comprehensive examination of the molecular mechanisms underlying IBC cell survival in the lymphatic vessels is of paramount importance to our understanding of IBC pathogenesis. Here we demonstrate that, in contrast to normal mammary epithelial cells, IBC cells evade ECM-detachment-induced apoptosis (anoikis). ErbB2 and EGFR knockdown in KPL-4 and SUM149 cells, respectively, causes decreased colony growth in soft agar and increased caspase activation following ECM detachment. ERK/MAPK signaling was found to operate downstream of ErbB2 and EGFR to protect cells from anoikis by facilitating the formation of a protein complex containing Bim-EL, LC8, and Beclin-1. This complex forms as a result of Bim-EL phosphorylation on serine 59, and thus Bim-EL cannot localize to the mitochondria and cause anoikis. These results reveal a novel mechanism that could be targeted with innovative therapeutics to induce anoikis in IBC cells.Inflammatory breast cancer (IBC) is a rare and highly invasive type of breast cancer, and patients diagnosed with IBC often face a very poor prognosis. The 5-year survival rate for patients with IBC is <40%, while the 5-year survival rate of all other breast cancers combined is approximately 90%.^{1, 2, 3, 4} This poor prognosis can be attributed to a number of factors, including the propensity for misdiagnosis of the disease due to its unique clinical presentation.^{5, 6, 7} In contrast to most breast cancers, IBC is characterized by the lack of discernible primary tumor formation and the accumulation of cancerous epithelial cells in the dermal lymphatic vessels.⁸ This lodging of IBC cells in the dermal lymphatics manifests as what appears to be inflammation, oftentimes causing clinicians to incorrectly diagnose the malady. Given that IBC cells are inherently aggressive, misdiagnosis is particularly problematic as a correct diagnosis or appropriate treatment is prolonged until more advanced disease is discovered. Thus it is imperative to gain a better understanding of the unique molecular mechanisms underlying IBC pathogenesis so that improved therapies can be designed to specifically eliminate IBC cells in a manner that improves patient outcome.Unfortunately, few treatment options exist that are specifically designed to combat IBC. A review of nearly 400 IBC patients treated at The University of Texas MD Anderson Cancer Center between 1974 and 2005 demonstrated that there has been no significant improvement in prognosis for patients with IBC over the past 30 years.¹ Many recent studies have focused on assessing the efficacy of chemotherapeutic regimens in IBC cells/patients where success had previously been observed only in the treatment of non-IBCs.^{9, 10} Some progress has been made in understanding the mechanisms underlying the invasive nature of IBC. For instance, Akt1 has been identified as a possible chemotherapeutic target that appears to be involved in the aggressive behavior of IBC cells.¹¹ Other studies have identified RhoC, which is overexpressed in 90% of IBC tissue samples, as a potent oncogene contributing to IBC pathogenesis.^{11, 12, 13, 14, 15} More recently, evidence implicating the membrane protein TIG1 and the receptor tyrosine kinase Axl in the oncogenic behavior of IBC cells has been uncovered.¹⁶ However, despite these advances, knowledge of the biological mechanisms underlying IBC pathogenesis remains fairly rudimentary, and additional research dedicated to understanding the unique molecular pathways involved in IBC progression remains essential.Given that IBC cells do not form a palpable primary tumor and instead flourish in suspension in the lymph of the dermal lymphatic vessels, we hypothesized that IBC cells must have an inherent ability to survive in the absence of attachment to the extracellular matrix (ECM). Normal mammary epithelial cells require attachment to the ECM to inhibit anoikis, which is defined as caspase-dependent cell death caused by ECM detachment.¹⁷ It has become clear that tumor progression and metastasis require cancer cells to inhibit anoikis, oftentimes through alterations in intracellular signaling pathways.^{18, 19, 20} Interestingly, previous studies have shown that ErbB2 and EGFR, which are hyperactivated in a substantial percentage of IBC patients,²¹ can effectively antagonize the anoikis program to facilitate anchorage-independent growth.^{22, 23, 24, 25, 26, 27, 28} However, a detailed examination of the molecular mechanisms underlying anoikis inhibition in IBC cells has yet to be completed. In this study, we demonstrate that signaling from EGFR and ErbB2 through ERK/MAPK has a major role in the ability of IBC cells to survive in the absence of ECM attachment. Surprisingly, we have discovered that ERK-mediated anoikis suppression in IBC cells is not due to targeting of the pro-apoptotic protein Bim-EL for degradation that has previously been observed in mammary epithelial cells.^{23, 27} Rather, ERK activation in IBC cells promotes the formation of a protein complex containing Bim-EL, Beclin-1, and LC8, which functions to sequester Bim-EL from the mitochondria and thereby block anoikis. In support of the importance of this signaling pathway in IBC patients, five of the seven IBC patient samples assayed showed discernible Bim-EL staining. Collectively, these data identify a novel mechanism utilized by IBC cells to survive during ECM detachment and reveal a potential target for the development of anoikis-inducing chemotherapeutics targeting IBC cells.