The fate of effector T cells in vivo is determined during activation and differs for CD4+ and CD8+ cells

Effector T cells generated in the mesenteric lymph nodes (mLN) are known to accumulate in mLN and the tissue drained by them after circulating in the blood. Their accumulation is due less to preferential entry into mLN but more to preferential proliferation within mLN. The factors regulating the proliferation of effector T cells in vivo are unclear, and it is unknown whether they are different for CD4(+) and CD8(+) effector T cells. Rat T cells from mLN or peripheral lymph nodes (pLN) were stimulated polyclonally via the TCR and CD28 and injected i.v. into congenic recipients. Using three-color flow cytometry and immunohistochemistry, they were identified in mLN, pLN, and blood over time, and proliferation was determined by measuring bromodeoxyuridine incorporation. Only effector mLN T cells showed a significantly increased proliferation rate after entry into mLN compared with that in pLN (2.4 +/- 1.8% vs 0.8 +/- 0.4%). Proliferation among the injected cells was higher when they had contact with dendritic cells within mLN (9.0 +/- 4.3%) than when they did not (4.1 +/- 2.1%). Furthermore, effector mLN T cells which were observed 56 days after injection maintained the capacity for preferential proliferation within mLN. Interestingly, CD4(+) effector mLN T cells proliferated at a higher rate (4.8 +/- 0.7%), remaining in mLN, whereas CD8(+) effector mLN T cells proliferated at a lower rate (3.3 +/- 1.0%) and were able to leave the mLN into the blood. Elucidating the factors regulating the proliferation of effector T cells in vivo will help to modify their distribution for therapeutic purposes.     

Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds

Germination is a complex process, highly dependent on various environmental factors, including temperature and water availability. Germinating soybean seeds are especially vulnerable to unfavorable environmental conditions and exposure to long-term abiotic stresses may result in diminishing much of the yield and most importantly – restrained germination. In the present study, a proteomic approach was employed to analyze influence of cold and osmotic stress on roots of germinated soybean (Glycine max, L.) seeds. Seeds were germinating under continuous conditions of cold stress (+10 °C/H₂O), osmotic stress (+25 °C/−0.2 MPa) as well as cold and osmotic stress combined (+10 °C/−0.2 MPa). Proteome maps established for control samples and stress-treated samples displayed 1272 CBB-stained spots. A total of 59 proteins, present in both control and stress-treated samples and showing significant differences in volume, were identified with LC/nanoESI-MS. Identified proteins divided into functional categories, revealed 9 proteins involved in plant defense, 8 proteins responsible for plant destination and storage and 10 proteins involved in various tracks of carbohydrate metabolism. Furthermore, a number of proteins were assigned to electron transport, range of metabolic pathways, secondary metabolism, protein synthesis, embryogenesis and development, signal transduction, cellular transport, translocation and storage. By analyzing differences in expression patterns, it was possible to trace the soybean response to long-term abiotic stress as well as to distinguish similarities and differences between response to cold and osmotic stress.     

Protein Sets Define Disease States and Predict In Vivo Effects of Drug Treatment

Gaining understanding of common complex diseases and their treatments are the main drivers for life sciences. As we show here, comprehensive protein set analyses offer new opportunities to decipher functional molecular networks of diseases and assess the efficacy and side-effects of treatments in vivo. Using mass spectrometry, we quantitatively detected several thousands of proteins and observed significant changes in protein pathways that were (dys-) regulated in diet-induced obesity mice. Analysis of the expression and post-translational modifications of proteins in various peripheral metabolic target tissues including adipose, heart, and liver tissue generated functional insights in the regulation of cell and tissue homeostasis during high-fat diet feeding and medication with two antidiabetic compounds. Protein set analyses singled out pathways for functional characterization, and indicated, for example, early-on potential cardiovascular complication of the diabetes drug rosiglitazone. In vivo protein set detection can provide new avenues for monitoring complex disease processes, and for evaluating preclinical drug candidates.The application of reductionism and experimental manipulation in the 20^th century biological research has generated important insights into functional processes of life. Based on this successful paradigm, researchers rationally dissected multiple underlying molecular mechanisms of “living systems” and efficiently developed drugs. However, drugs or dietary interventions can interfere with numerous proteins in hundreds of different cell types in various tissues, not to mention potential crosstalk on various levels of biological organization. Not surprisingly, conventional in vitro and lengthy preclinical studies that target only specific marker molecules often missed out important but unexpected physiological effects of drug treatment. Although complex biological phenomena such as physiological outcomes of disease treatment depend on various individual molecules, they are based on in vivo network properties, which cannot be adequately described or explained by “parts of the sum” of mechanistic events.Soft-ionization mass spectrometry (MS) has been widely validated as a tool for precise quantitative analysis of biomolecules (1, 2), and isotope-labeling procedures were introduced to detect protein expression, primarily in cell culture models (3, 4). Previous attempts of using mass spectrometry for protein quantification in mammalian disease models were limited to analysis of a small number of usually abundant proteins, which made comprehensive pathway analysis and physiological outcome prediction impossible (5, 6). Recent technical pilot studies provided extensive information on the protein inventories of different mouse tissues (7, 8), and isotope-labeled mice have been introduced as a resource for accurate protein quantification (9).The development of diet-induced obesity and diabetes is a complex pathophysiological process involving a number of interacting organs, in which chronic hyperglycemia and hyperlipidemia lead to cumulative damaging effects on metabolic tissues such as skeletal muscle, liver, and adipose tissues. As we show here, disease processes and in particular physiological effects of drug treatment are largely determined by the actual cellular protein expression levels and post-translational modifications of proteins. Whereas analyses of single protein changes were mostly uninformative, quantitative protein set enrichment analysis was an efficient tool to monitor tissue-specific responses of anti-diabetic treatments. This approach allows for investigation of interacting molecular and physiological processes that occur on the pathway level, and enables sensitive, unbiased and robust diagnostic detection of treatments in vivo.In this pilot study, we compared the effects of the drug rosiglitazone (RSG)¹, which has been associated with a number of undesirable side effects (10), and the plant-derived amorfrutin A1 (A1) (11) in diet-induced obesity (DIO) mice. Both compounds'' antidiabetic effects appear to be derived from activation of the peroxisome proliferator-activated receptor gamma (PPARγ).     

Comprehensive proteomic datasets for studying adipocyte–macrophage cell–cell communication

Cellular communication is a fundamental process in biology. The interaction of adipocytes with macrophages is a key event in the development of common diseases such as type 2 diabetes. We applied an established bilayer cell coculture system and comprehensive MS detection to analyse on a proteome‐wide scale the paracrine interaction of murine adipocytes and macrophages. Altogether, we identified 4486 proteins with at least two unique peptides, of which 2392 proteins were informative for 3T3‐L1 adipocytes and 2957 proteins for RAW 264.7 macrophages. Further, we observed over 12000 phosphorylation sites, of which we could assign 3200 informative phosphopeptides with a single phosphosite for adipocytes and 4514 for macrophages. Using protein set enrichment and phosphosite analyses, we deciphered regulatory protein pathways involved in cellular stress and inflammation, which can contribute to metabolic impairment of cells including insulin resistance and other disorders. The generated datasets provide a holistic, molecular pathway‐centric view on the interplay of adipocytes and macrophages in disease processes and a resource for further studies.     

DNA damage in peripheral blood of patients with chronic obstructive pulmonary disease (COPD)

Chronic obstructive pulmonary disease (COPD) is a condition characterized by chronic airway inflammation and remodeling, lung parenchymal inflammation, and destruction resulting in expiratory airflow obstruction, hyperinflation of the lung with loss of elastic recoil, and impairment of gas exchange. Skeletal muscles in individuals with COPD generate free radicals at rest, and production increases during contractile activity. Overproduction of free radicals may result in oxidant-antioxidant imbalance in favor of oxidants. This study evaluated the levels of genetic damage in peripheral blood of patients with COPD using the cytokinesis-blocked micronucleus (CBMN) and the comet assays. The study was conducted with 25 patients with COPD and 25 controls matched for age and sex. Results of both comet and CBMN assays showed an increase in the level of DNA damage. In the group of patients with COPD, the mean frequency of binucleate cells with micronuclei was 6.72+/-3.02, and in the control group, 4.20+/-2.08 (p=0.00233). Mean comet value was 26.84+/-19.61 in patients with COPD and 7.25+/-7.57 in the control group (p=0.00004). The increased frequency of micronuclei in patients with COPD was primarily assigned to clastogenic events and DNA amplification because the frequency of nucleoplasmic bridges and buds was also increased. Oxidative stress in lung cells is a constant source of free radicals that damage genetic material of both lung and circulating cells.     

A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer

To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.     

Protein-Coated Nanoparticles Are Internalized by the Epithelial Cells of the Female Reproductive Tract and Induce Systemic and Mucosal Immune Responses

The female reproductive tract (FRT) includes the oviducts (fallopian tubes), uterus, cervix and vagina. A layer of columnar epithelium separates the endocervix and uterus from the outside environment, while the vagina is lined with stratified squamous epithelium. The mucosa of the FRT is exposed to antigens originating from microflora, and occasionally from infectious microorganisms. Whether epithelial cells (ECs) of the FRT take up (sample) the lumen antigens is not known. To address this question, we examined the uptake of 20–40 nm nanoparticles (NPs) applied vaginally to mice which were not treated with hormones, epithelial disruptors, or adjuvants. We found that 20 and 40 nm NPs are quickly internalized by ECs of the upper FRT and within one hour could be observed in the lymphatic ducts that drain the FRT, as well as in the ileac lymph nodes (ILNs) and the mesenteric lymph nodes (MLNs). Chicken ovalbumin (Ova) conjugated to 20 nm NPs (NP-Ova) when administered vaginally reaches the internal milieu in an immunologically relevant form; thus vaginal immunization of mice with NP-Ova induces systemic IgG to Ova antigen. Most importantly, vaginal immunization primes the intestinal mucosa for secretion of sIgA. Sub-cutaneous (s.c) boosting immunization with Ova in complete Freund''s adjuvant (CFA) further elevates the systemic (IgG1 and IgG2c) as well as mucosal (IgG1 and sIgA) antibody titers. These findings suggest that the modes of antigen uptake at mucosal surfaces and pathways of antigen transport are more complex than previously appreciated.