Proteome analysis of virus–host cell interaction: rabies virus replication in Vero cells in two different media

The use of Vero cells for rabies vaccine production was recommended from the WHO in 2005. A controlled production process is necessary to reduce the risk of contaminants in the product. One step towards this is to turn away from animal-derived components (e.g. serum, trypsin, bovine serum albumin) and face a production process in animal component-free medium. In this study, a proteomic approach was applied, using 2-D differential gel electrophoresis and mass spectrometry to compare rabies virus propagation in Vero cells under different cultivation conditions in microcarrier culture. Protein alterations were investigated for uninfected and infected Vero cells over a time span from 1 to 8 days post-infection in two different types of media (serum-free versus serum-containing media). For mock-infected cells, proteins involved in stress response, redox status, protease activity or glycolysis, and protein components in the endoplasmic reticulum were found to be differentially expressed comparing both cultivation media at all sampling points. For virus-infected cells, additionally changes in protein expression involved in general cell regulation and in calcium homeostasis were identified under both cultivation conditions. The fact that neither of these additional proteins was identified for cells during mock infection, but similar protein expression changes were found for both systems during virus propagation, indicates for a specific response of the Vero cell proteome on rabies virus infection.     

In vitro vRNA–vRNA interactions in the H1N1 influenza A virus genome

The genome of influenza A virus consists of eight-segmented, single-stranded, negative-sense viral RNAs (vRNAs). Each vRNA contains a central coding region that is flanked by noncoding regions. It has been shown that upon virion formation, the eight vRNAs are selectively packaged into progeny virions through segment-specific packaging signals that are located in both the terminal coding regions and adjacent noncoding regions of each vRNA. Although recent studies using next-generation sequencing suggest that multiple intersegment interactions are involved in genome packaging, contributions of the packaging signals to the intersegment interactions are not fully understood. Herein, using synthesized full-length vRNAs of H1N1 WSN (A/WSN/33 [H1N1]) virus and short vRNAs containing the packaging signal sequences, we performed in vitro RNA binding assays and identified 15 intersegment interactions among eight vRNAs, most of which were mediated by the 3′- and 5′-terminal regions. Interestingly, all eight vRNAs interacted with multiple other vRNAs, in that some bound to different vRNAs through their respective 3′- and 5′-terminal regions. These in vitro findings would be of use in future studies of in vivo vRNA–vRNA interactions during selective genome packaging.     

An integrated in silico approach to understand protein–protein interactions: human meprin-β with fetuin-A

Abstract

Human meprin-β, a zinc metalloprotease belonging to the astacin family, have been found to be associated with many pathological conditions like inflammatory bowel disease, fibrosis and neurodegenerative disease. The inhibition of meprin-β by various inhibitors, both macromolecular and small molecules, is crucial in the control of several diseases. Human fetuin-A, a negative acute phase protein involved in inflammatory disease, has recently been identified as an endogenous inhibitor for meprin-β. In this computational study, an integrated in silico approach was performed using existing structural information of meprin-β coupled with ab initio modelling of human fetuin-A to predict a rational model of the complex through protein–protein docking. Further, the models were optimized and validated to generate an ensemble of conformations through extensive molecular dynamics simulation. Virtual alanine scanning mutagenesis was explored to identify hotspot residues on both proteins significant for protein–protein interaction (PPI). The results of the study provide structural insight into PPI between meprin-β and fetuin-A which can be useful in designing molecules to modulate meprin-β activity.

Communicated by Ramaswamy H. Sarma     

Efficiency of Plasmocin™ on various mammalian cell lines infected by mollicutes in comparison with commonly used antibiotics in cell culture: a local experience

Mycoplasma contamination is a deleterious event for cell culture laboratories. Plasmocin™ is used to prevent and eradicate mycoplasma infections from cell. In this study, 80 different mammalian cell lines from various sources; human, monkey, mice, hamster and rat were used to study and evaluate plasmocin™ efficiency and compare it to commonly used antibiotics such as BM-cyclin, ciprofloxacin and mycoplasma removal agent (MRA). It was shown that mycoplasma infections were eradicated by plasmocin™, BM-cyclin, ciprofloxacin and MRA in 65%, 66.25%, 20%, and 31.25%, respectively, of infected cell cultures. However, re-infection with mycoplasmas after the period of 4 months occurred in 10–80% of the studied cell lines. Cell cytotoxicity and culture death was observed in 25, 17.5 and 10% of the treated cells, for plasmocin™, BM-cyclin and MRA, respectively. In this study, Plasmocin™ showed strong ability to eradicate mollicutes from our cell lines with minimal percentage of regrowth. However, due to its high cell cytotoxicity it should be used with caution especially when dealing with expensive or hard-to-obtain cell lines. Amongst the antibiotics tested, BM-cyclin was shown to remove mycoplasma with the highest efficiency.     

Comparative proteome profiling of host–pathogen interactions: insights into the adaptation mechanisms of Francisella tularensis in the host cell environment

The intracellular pathogens have the unique capacity to sense the host cell environment and to respond to it by alteration in gene expression and protein synthesis. Proteomic analysis of bacteria exposed directly to the host cell milieu might thus greatly contribute to the elucidation of processes leading to bacterial adaptation and proliferation inside the host cell. Here we have performed a global proteome analysis of a virulent Francisella tularensis subsp. holarctica strain during its intracellular cycle within the macrophage-like murine cell line J774.2 using the metabolic pulse-labeling of bacterial proteins with ³⁵S-methionine and ³⁵S-cysteine in various periods of infection. The two-dimensional gel analysis revealed macrophage-induced bacterial proteome changes in which 64 identified proteins were differentially expressed in comparison to controls grown in tissue culture medium. Nevertheless, activation of macrophages with interferon gamma before in vitro infection decreased the number of detected alterations in protein levels. Thus, these proteomic data indicate the F. tularensis ability to adapt to the intracellular hostile environment that is, however, diminished by prior interferon gamma treatment of host cells.     

Immune responses to Epstein–Barr virus: molecular interactions in the virus evasion of CD8+ T cell immunity

Persistent viruses have mechanisms for modulating the host immune responses that are essential for achieving a lifelong virus–host balance while minimizing the viral pathogenicity. Here we review some of the immune-modulating mechanisms evolved by the ubiquitous but potentially oncogenic Epstein–Barr virus, with particular emphasis on the molecular mechanisms of genes interfering with HLA class I antigen presentation.     

Identification of proteins bearing β1–6 branched N-glycans in human melanoma cell lines from different progression stages by tandem mass spectrometry analysis

The common structural alterations in the cell-surface glycoproteins concern the highly elevated expression of tri- and tetra-antennary β1–6-N-acetylglucosamine (β1–6 GlcNAc) bearing N-glycans, which are recognised by Phaseolus vulgaris agglutinin (PHA-L). In this report we identified proteins bearing β1–6 GlcNAc branched N-glycans in three human melanoma cell lines: WM35 — from the primary tumour site, as well as WM239 and WM9 from different metastatic sites: the skin and the lymph node, respectively, by tandem mass spectrometry (MS/MS) on PHA-L agarose bound material, followed by immunochemical identification. Our results show that melanoma cell lines differ from each other in the number of N-glycoproteins bearing β1–6 GlcNAc branched oligosaccharides. Among identified proteins the largest group consists of integrin subunits. In addition, L1-CAM, Mac-2 binding protein, melanoma cell adhesion molecule, intercellular adhesion molecule, melanoma associated antigen, tumour rejection antigen-1, melanoma-associated chondroitin sulfate proteoglycan 4 and lysosome-associated membrane protein (LAMP-1) were found. It was indicated that WM35 cell line showed the lowest number of proteins possessing β1–6 GlcNAc branched N-glycans in comparison to metastatic WM9 and WM239 cell lines. Our data suggest that changes in the number of proteins being a substrate for GlcNAc-TV are better correlated with melanoma development and progression than with expression of cell adhesion molecules.     

Regulated expression of the integrin α9β1 in the epithelium of the developing human gut and in intestinal cell lines: Relation with cell proliferation

The integrin α9β1 is one of the recently identified integrins whose expression is restricted to specialized tissues. Its exact function is still unknown. In the present study, we have analyzed the expression of the α9 subunit in human fetal and adult small intestinal and colonic epithelia as well as in intestinal cell lines by indirect immunofluorescence, immunoprecipitation, Western blot, and Northern blot. In intact tissues, the antigen was restricted to the basolateral domain of epithelial cells in intestinal crypts at the fetal stage and was absent in the adult. The α9β1 integrin was also detected in the intestinal cell lines HIEC-6 and Caco-2/15. The presence of α9β1 in HIEC-6 was found to be consistent with their proliferative crypt-like status. In Caco-2/15 cells, the integrin was present at high levels in proliferating cells but was downregulated when cells cease to grow and undertake their differentiation. EGF treatment, which is known to maintain Caco-2/15 cells in a proliferative state, resulted in higher levels of α9 as compared to control cells. Taken together, these observations suggest a relation between integrin α9β1 expression and proliferation in human intestinal cells. J. Cell. Biochem. 71:536–545, 1998. © 1998 Wiley-Liss, Inc.     

In vitro secretion of transforming growth factor alpha (TGF-α): A comparison of the A431 cell line with three human oesophageal squamous cell carcinoma lines

Transforming growth factor alpha (TGF-) is a single chain polypeptide which exists in a variety of forms differing in molecular weight. These forms are variously present in normal and neoplastic cells. Of particular interest are TGF-'s well-known mitogenic properties. The transition from a normal to a neoplastic cellular state results from signalling defects that may depend upon,iter alia, abonormal levels of expression and secretion of TGF-. It is known that the secretion of TGF- may be enhanced appreciably by agents such as phorbol 12-myristate 13-acetate (PMA), serum factors and epidermal growth factor (EGF). Here, we compare the efficacy of these three agents in the elevation of TGF- secretion in the well studied A431 cell line with their previously undocumented efficacy in certain interesting, but little known, human oesophageal squamous cell carcinoma (SCC) lines.     

Monoclonal antibodies that react with human band 3 residues 542–555 recognize different conformations of this protein in uninfected andPlasmodium falciparum infected erythrocytes

A monoclonal antibody generated against synthetic peptides patterned on amino acids 542–555 of human band 3, designated 1F4, specifically immunostainedPlasmodium falciparum-infected erythrocytes and inhibited the cytoadherence ofP. falciparum-infected erythrocytes to C32 amelanotic melanoma cells. 1F4 did not recognize intact band 3 protein on immunoblots, however it was reactive towards proteolytic fragments of band 3.The binding region of another murine monoclonal antibody previously reported to recognize the membrane spanning domain of human band 3, designated B6, was found to also recognize residues 542–555, however its properties differed from 1F4. Mab B6 recognized both infected and uninfected red cells, and reacted only with intact band 3 on immunoblots. Mab B6 was without effect on cytoadherence.These results demonstrate that monoclonal antibodies reactive against a common peptide sequence may bind to different conformations of the peptide sequence and suggest that the adherent competency ofP. falciparum-infected erythrocytes may result from a change in the surface topography of human band 3 protein.Abbreviations ELISA Enzyme-Linked Immunosorbent Assay - KLH Keyhole Limpet Hemocyanin - PBS Phosphate Buffered Saline - Mab Monoclonal Antibody - PMSF Phenylmethyl sulfonyl fluoride - i.p. intraperitoneum - TBS Tris Buffered Saline - H₂DIDS dihydro 4,4-diisothocyanostilbene-2,2-disulfonic acid - DIDS 4,4-diisothiocyanostilbene-2,2-disulfonic acid     

A comprehensive study of Sansalvamide A derivatives: The structure–activity relationships of 78 derivatives in two pancreatic cancer cell lines

We report an extensive structure–activity relationship (SAR) of 78 compounds active against two pancreatic cancer cell lines. Our comprehensive evaluation of these compounds utilizes SAR that allow us to evaluate which features of potent compounds play a key role in their cytotoxicity. This is the first report of 19 new second-generation structures, where these new compounds were designed from the first generation of 59 compounds. These 78 structures were tested for their cytotoxicity and this is the first report of their activity against two pancreatic cancer cell lines. Our results show that out of 78 compounds, three compounds are worth pursuing as leads, as they show potency of ?55% in both cancer cell lines. These three compounds all have a common structural motif, two consecutive d-amino acids and an N-methyl moiety. Further, of these three compounds, two are second-generation structures, indicating that we can incorporate and utilize data from the first generation to design potency into the second generation. Finally, one analog is in the mid nanomolar range, and has the lowest IC₅₀ of any reported San A derivative. These analogs share no structural homology to current pancreatic cancer drugs, and are cytotoxic at levels on par with existing drugs treating other cancers. Thus, we have established Sansalvamide A as an excellent lead for killing multiple pancreatic cancer cell lines.     

A comparison of four different fine root production estimates with ecosystem carbon balance data in a Fagus–Quercus mixed forest

The controversy on how to measure fine root production of forests (P) most accurately continues. We applied four different approaches to determine annual rates of P in an old-growth temperate Fagus sylvatica–Quercus petraea stand: sequential soil coring with minimum–maximum calculation, sequential coring with compartmental flow calculation, the ingrowth core method, and a recently developed root chamber method for measuring the growth of individual fine roots in situ. The results of the four destructive approaches differed by an order of magnitude and, thus, are likely to introduce large errors in estimating P. The highest annual rates of P were obtained from the sequential coring approach with compartmental flow calculation, intermediate rates by sequential coring with minimum–maximum calculation, and low ones by both the root growth chamber and ingrowth core approaches. A carbon budget for the stand was set up based on a model of annual net carbon gain by the canopy and measurements on carbon sink strength (annual leaf, branch and stem growth). The budget implied that a maximum of 27% of the net carbon gain was available for allocation to fine root growth. When compared to the carbon budget data, the sequential coring/compartmental flow approach overestimated annual fine root production substantially; whereas the ingrowth core and root growth chamber approaches grossly underestimated P rates. With an overestimation of about 25% the sequential coring/minimum–maximum approach demonstrated the best agreement with the carbon budget data. It is concluded that the most reliable estimate of P in this temperate forest will be obtained by applying the sequential coring/minimum–maximum approach, conducted with a large number of replicate samples taken on a few dates per season, in conjunction with direct root growth observation by minirhizotrons.     

Predator–prey interactions in anurans of the tropical dry forests of the Colombian Caribbean: A functional approach

Anuran–prey selection might be mediated by traits, either by mismatches in predator and prey traits (preventing interactions) or by predator selection of prey traits (encouraging interactions). These effect traits could be summarized in two contrasting foraging strategies: “active” and “sit-and-wait” foragers. We evaluated whether anurans could be classified into groups of species sharing traits associated with their diet, and what is the relation between particular effect traits of anurans and their prey. We collected anurans and identified their stomach contents once during dry, minor, and major rain seasons in six dry forest sites in the Colombian Caribbean. For each of the 19 anuran species and 436 prey items, we registered six effect traits. We applied RLQ and fourth-corner methodologies to relate predator and prey traits through their interaction matrix. Predators were assigned to five groups according to their differences in locomotion, body shape, proportion of the jaw width, mode of tongue protrusion, and strata preferred. Regarding preys, species were assigned to four groups according to their gregariousness, body shape and hardness, defensive traits, and mobility. Body size of both, predators and prey, had a minor contribution in the group assignment. We found that predators using active search target low-mobility preys, whereas species using sit-and-wait strategy target highly nutritive prey that are difficult to manipulate. By linking amphibian diet with foraging strategies, we hope to contribute to the understanding of mechanisms behind anuran–prey food web patterns and to build more realistic models of functional response to changing environments.     

Genetic variants in TERT–CLPTM1L genetic region associated with several types of cancer: A meta-analysis

Background

TERT–CLPTM1L genomic region has been extensively associated with several types of cancer. However, results were inconsistent. We performed this meta-analysis to estimate the association between TERT (rs2736100, rs2736098), as well as CLPTM1L (rs402710, rs401681) polymorphisms and cancer risk.

Methods

Electronic search in PubMed, EMBASE and China National Knowledge Infrastructure (CNKI) was conducted to select the studies. Studies containing available genotype frequencies of those 4 polymorphisms were chosen, and overall odds ratio (OR) with 95% confidence interval (CI) was used to assess the association.

Results

The final meta-analysis included 16 published case–control studies. Increased cancer risk was found between TERT-rs2736100, as well as CLPTM1L-rs402710 and cancer susceptibility. In addition, we found an increased risk of cancer in both rs2736098 and rs401681 homozygous variant genetic model.

Conclusions

This meta-analysis suggested that TERT–CLPTM1L genomic region was associated with increased risk of cancer. To validate the association between these polymorphisms and cancer susceptibility, further studies with larger participants are needed.     

Spatiotemporal change in land use patterns of coupled human–environment system with an integrated monitoring approach: A case study of Lianyungang,China

There is an urgent need to quantitatively monitor the spatiotemporal pattern–process interactions of coupled human–environment systems in rapidly urbanizing areas. In this study, we mainly referred to structural(not functional) aspects of land-use pattern, and especially, we targeted at landscape composition and landscape fragmentation. We applied an integrated monitoring approach, to a case study of a new and fast-growing city in the east coast of China. This approach included gradient, spatial overlay and square blocks sampling analysis. The results showed that (1) over the past seven years, the urbanization intensified with its percentage of construction land from 8.19% in 2004 through 17.15% in 2008 to 25.79% in at the cost of more fragmentized agricultural land system and loss of wetland ecosystems; (2) Lianyungang is experiencing rapid urban expansions over the 2004–2008 and 2008–2011 periods in a dispersed and leapfrogged but not compact form; (3) the hypothesis of urban expansion following a process of diffusion and coalescence proposed by Dietzel et al. (2005) were confirmed again by this study; (4) the relationship between patch density of construction land and the degree of urbanization was characterized as an inverted Ushape pattern. Moreover, this study revealed the threshold of the changes of landscape fragmentation while the degree of urbanization is increasing until about 20–40% for Lianyungang city, which should be carefully applied to other places; (5) mean patch size follows an exponential growth or a quadratic growth in the process of urbanization in this study, which is new finding that has not been revealed by other relative case studies reviewed and stand the tests.