Application of several molecular techniques to study numerically predominant Bifidobacterium spp. and Bacteroidales order strains in the feces of healthy children

Bifidobacteria and Bacteroides-like bacteria are strictly anaerobic nonpathogenic members of human intestinal microflora. Here we describe an analysis of the species and subspecies composition of these bacterial populations in healthy children using a combination of culture and molecular methods at two different time points. It was found that B. bifidum and B. longum are the most common dominant taxons in infants aged between 8 and 16 months. The majority of the infants carried several dominant Bifidobacterium strains belonging to different species. Examination of the dominant bifidoflora in some of these children after a 5-year period showed major shifts in both species and strain composition, but the dominant strains remained unchanged in two children. The majority of dominant Bacteroides-like isolates belonged to species B. vulgatus and B. uniformis, but members of genera Alistipes and Barnesiella were common too. In addition, a novel approach to species identification of Bacteroidales order bacteria using amplified ribosomal DNA restriction analysis (ARDRA) is described.     

Serdin1/Lrrc10 is dispensable for mouse development

We have previously identified Serdin1/Lrrc10 as a cardiac-specific message that is expressed early in murine heart development and encodes a novel leucine-rich protein. A high degree of evolutionary conservation with respect to protein sequence, cardiac-specific expression, and cis-regulatory elements suggested that LRRC10 has an important and conserved function in cardiac development. Recently, the zebrafish lrrc10 knockdown models were described with a dramatic early defect in heart looping which supported the notion that Serdin1/Lrrc10 is likely to be essential for heart development in all vertebrates. To determine Lrrc10 function in mammalian cardiac development, we have disrupted the Lrrc10 gene in mice. We report here that, in striking contrast to the zebrafish lrrc10 knockdown, Lrrc10-null mice develop normally and exhibit no discernable phenotype.     

Divalent cation coordination and mode of membrane interaction in cyclotides: NMR spatial structure of ternary complex Kalata B7/Mn2+/DPC micelle

The cyclotides are the family of hydrophobic bioactive plant peptides, characterized by a circular protein backbone and three knot forming disulfide bonds. It is believed that membrane activity of the cyclotides underlines their antimicrobial, cytotoxic and hemolytic properties, but the specific interactions with divalent cations can be also involved. To assess the mode of membrane interaction and divalent cation coordination in cyclotides, the spatial structure of the Möbius cyclotide Kalata B7 from the African perennial plant Oldenlandia affinis was determined in the presence of anisotropic membrane mimetic (dodecylphosphocholine micelles). The model of peptide/cation/micelle complex was built using 5-doxylstearate and Mn²⁺ relaxation probes. Results show that the peptide binds to the micelle surface with relatively high affinity by two hydrophobic loops (loop 2 – Thr⁶-Leu⁷ and loop 5 – Trp¹⁹-Ile²¹). The partially hydrated divalent cation is coordinated by charged side-chain of Glu³, aromatic side chain of Tyr¹¹ and free carbonyls of Thr⁴ and Thr⁹, and is located in direct contact with the polar head-groups of detergent. The comparison with data about other cyclotides indicates that divalent cation coordination is the invariant property of all cyclotides, but the mode of peptide/membrane interactions is varied. Probably, the specific cation/peptide interactions play a major, but yet not known, role in the biological activity of the cyclotides.     

Abiotic immobilization of nitrate in two soils of relic <Emphasis Type="Italic">Abies pinsapo</Emphasis>-fir forests under Mediterranean climate

Evidence for abiotic immobilization of nitrogen (N) in soil is accumulating, but remains controversial. Identifying the fate of N from atmospheric deposition is important for understanding the N cycle of forest ecosystems. We studied soils of two Abies pinsapo fir forests under Mediterranean climate seasonality in southern Spain—one with low N availability and the other with symptoms of N saturation. We hypothesized that biotic and abiotic immobilization of nitrate (NO₃ ⁻) would be lower in soils under these forests compared to more mesic temperate forests, and that the N saturated stand would have the lowest rates of NO₃ ⁻ immobilization. Live and autoclaved soils were incubated with added ¹⁵NO₃ ⁻ (10 μg N g⁻¹ dry soil; 99% enriched) for 24 h, and the label was recovered as total dissolved-N, NO₃ ⁻, ammonium (NH₄ ⁺), or dissolved organic-N (DON). To evaluate concerns about possible iron interference in analysis of NO₃ ⁻ concentrations, both flow injection analysis (FIA) and ion chromatography (IC) were applied to water extracts, soluble iron was measured in both water and salt extracts, and standard additions of NO₃ ⁻ to salt extracts were analyzed. Good agreement between FIA and IC analysis, low concentrations of soluble Fe, and 100% (±3%) recovery of NO₃ ⁻ standard additions all pointed to absence of an interference problem for NO₃ ⁻ quantification. On average, 85% of the added ¹⁵NO₃ ⁻ label was recovered as ¹⁵NO₃ ⁻, which supports our hypothesis that rates of immobilization were generally low in these soils. A small amount (mean = 0.06 μg N g⁻¹ dry soil) was recovered as ¹⁵NH₄ ⁺ in live soils and none in sterilized soils. Mean recovery as DO¹⁵N ranged from 0.6 to 1.5 μg N g⁻¹ dry soil, with no statistically significant effect of sterilization or soil type, indicating that this was an abiotic process that occurred at similar rates in both soils. These results demonstrate a detectable, but modest rate of abiotic immobilization of NO₃ ⁻ to DON, supporting our first hypothesis. These mineral soils may not have adequate carbon availability to support the regeneration of reducing microsites needed for high rates of NO₃ ⁻ reduction. Our second hypothesis regarding lower expected abiotic immobilization in soils from the N-saturated site was not supported. The rates of N deposition in this region may not be high enough to have swamped the capacity for soil NO₃ ⁻ immobilization, even in the stand showing some symptoms of N saturation. A growing body of evidence suggests that soil abiotic NO₃ ⁻ immobilization is common, but that rates are influenced by a combination of factors, including the presence of plentiful available carbon, reduced minerals in anaerobic microsites and adequate NO₃ ⁻ supply.     

Mars promotes dTACC dephosphorylation on mitotic spindles to ensure spindle stability

Microtubule-associated proteins (MAPs) ensure the fidelity of chromosome segregation by controlling microtubule (MT) dynamics and mitotic spindle stability. However, many aspects of MAP function and regulation are poorly understood in a developmental context. We show that mars, which encodes a Drosophila melanogaster member of the hepatoma up-regulated protein family of MAPs, is essential for MT stabilization during early embryogenesis. As well as associating with spindle MTs in vivo, Mars binds directly to protein phosphatase 1 (PP1) and coimmunoprecipitates from embryo extracts with minispindles and Drosophila transforming acidic coiled-coil (dTACC), two MAPs that function as spindle assembly factors. Disruption of binding to PP1 or loss of mars function results in elevated levels of phosphorylated dTACC on spindles. A nonphosphorylatable form of dTACC is capable of rescuing the lethality of mars mutants. We propose that Mars mediates spatially controlled dephosphorylation of dTACC, which is critical for spindle stabilization.     

Human tankyrases are aberrantly expressed in colon tumors and contain multiple epitopes that induce humoral and cellular immune responses in cancer patients

Purpose Tankyrases 1 and 2 are telomere-associated poly(ADP-ribose) polymerases (PARP) that can positively regulate telomere elongation and interact with multiple cellular proteins. Recent reports implicated tankyrases as tumor antigens and potential targets of anticancer treatment. We examined expression of tankyrases in colon tumors and immune response to these enzymes in patients with different types of cancer. Methods mRNA and protein expression was evaluated by quantitative real-time RT-PCR and Western blotting, respectively. Humoral immune response to recombinant tankyrases was investigated by modified enzyme-linked immunoassays. Cellular immune response was analysed by ELISPOT and ⁵¹Cr release assays. Results We found that both mRNA and protein levels of tankyrase 2 (TNKL) are upregulated in colon tumors. In contrast, protein level of tankyrase 1 (TNKS) is downregulated, while mRNA level shows variable changes. More than a quarter of colon cancer patients develop humoral immune response to at least one of the two tankyrases. In this study we mapped common and unique B-cell epitopes located in different domains of the two proteins. Additionally, we present evidence for T-cell responses both to epitopes that are unique for TNKL and to those shared between TNKL and TNKS. Conclusion Our study favors a biomarker usage of antibody response to tankyrases. Spontaneous CD8⁺ T-cell responses to these enzymes are rare and further investigation is needed to evaluate tankyrases as potential targets for cancer immunotherapy.     

Local therapy of cancer with free IL-2

This is a position paper about the therapeutic effects of locally applied free IL-2 in the treatment of cancer. Local therapy: IL-2 therapy of cancer was originally introduced as a systemic therapy. This therapy led to about 20% objective responses. Systemic therapy however was very toxic due to the vascular leakage syndrome. Nevertheless, this treatment was a break-through in cancer immunotherapy and stimulated some interesting questions: Supposing that the mechanism of IL-2 treatment is both proliferation and tumoricidal activity of the tumor infiltrating cells, then locally applied IL-2 should result in a much higher local IL-2 concentration than systemic IL-2 application. Consequently a greater beneficial effect could be expected after local IL-2 application (peritumoral = juxtatumoral, intratumoral, intra-arterial, intracavitary, or intratracheal = inhalation). Free IL-2: Many groups have tried to prepare a more effective IL-2 formulation than free IL-2. Examples are slow release systems, insertion of the IL-2 gene into a tumor cell causing prolonged IL-2 release. However, logistically free IL-2 is much easier to apply; hence we concentrated in this review and in most of our experiments on the use of free IL-2. Local therapy with free IL-2 may be effective against transplanted tumors in experimental animals, and against various spontaneous carcinomas, sarcomas, and melanoma in veterinary and human cancer patients. It may induce rejection of very large, metastasized tumor loads, for instance advanced clinical tumors. The effects of even a single IL-2 application may be impressive. Not each tumor or tumor type is sensitive to local IL-2 application. For instance transplanted EL4 lymphoma or TLX9 lymphoma were not sensitive in our hands. Also the extent of sensitivity differs: In Bovine Ocular Squamous Cell Carcinoma (BOSCC) often a complete regression is obtained, whereas with the Bovine Vulval Papilloma and Carcinoma Complex (BVPCC) mainly stable disease is attained. Analysis of the results of local IL-2 therapy in 288 cases of cancer in human patients shows that there were 27% Complete Regressions (CR), 23% Partial Regressions (PR), 18% Stable Disease (SD), and 32% Progressive Disease (PD). In all tumors analyzed, local IL-2 therapy was more effective than systemic IL-2 treatment. Intratumoral IL-2 applications are more effective than peritumoral application or application at a distant site. Tumor regression induced by intratumoral IL-2 application may be a fast process (requiring about a week) in the case of a highly vascular tumor since IL-2 induces vascular leakage/edema and consequently massive tumor necrosis. The latter then stimulates an immune response. In less vascular tumors or less vascular tumor sites, regression may require 9–20 months; this regression is mainly caused by a cytotoxic leukocyte reaction. Hence the disadvantageous vascular leakage syndrome complicating systemic treatment is however advantageous in local treatment, since local edema may initiate tumor necrosis. Thus the therapeutic effect of local IL-2 treatment is not primarily based on tumor immunity, but tumor immunity seems to be useful as a secondary component of the IL-2 induced local processes. If local IL-2 is combined with surgery, radiotherapy or local chemotherapy the therapeutic effect is usually greater than with either therapy alone. Hence local free IL-2 application can be recommended as an addition to standard treatment protocols. Local treatment with free IL-2 is straightforward and can readily be applied even during surgical interventions. Local IL-2 treatment is usually without serious side effects and besides minor complaints it is generally well supported. Only small quantities of IL-2 are required. Hence the therapy is relatively cheap. A single IL-2 application of 4.5 million U IL-2 costs about 70 Euros. Thus combined local treatment may offer an alternative in those circumstances when more expensive forms of treatment are not available, for instance in resource poor countries.     

Recognition and degradation of myelin basic protein peptides by serum autoantibodies: novel biomarker for multiple sclerosis

The pathologic role of autoantibodies in autoimmune disease is widely accepted. Recently, we reported that anti-myelin basic protein (MBP) serum Abs from multiple sclerosis (MS) patients exhibit proteolytic activity toward the autoantigen. The aim of this study is to determine MBP epitopes specific for the autoantibodies in MS and compare these data with those from other neuronal disorders (OND), leading to the generation of new diagnostic and prognostic criteria. We constructed a MBP-derived recombinant "epitope library" covering the entire molecule. We used ELISA and PAGE/surface-enhanced laser desorption/ionization mass spectroscopy assays to define the epitope binding/cleaving activities of autoantibodies isolated from the sera of 26 MS patients, 22 OND patients, and 11 healthy individuals. The levels of autoantibodies to MBP fragments 48-70 and 85-170 as well as to whole MBP and myelin oligodendrocyte glycoprotein molecules were significantly higher in the sera of MS patients than in those of healthy donors. In contrast, selective reactivity to the two MBP fragments 43-68 and 146-170 distinguished the OND and MS patients. Patients with MS (77% of progressive and 85% of relapsing-remitting) but only 9% of patients with OND and no healthy donors were positive for catalysis, showing pronounced epitope specificity to the encephalitogenic MBP peptide 81-103. This peptide retained its substrate properties when flanked with two fluorescent proteins, providing a novel fluorescent resonance energy transfer approach for MS studies. Thus, anti-MBP autoantibody-mediated, epitope-specific binding and cleavage may be regarded as a specific characteristic of MS compared with OND and healthy donors and may serve as an additional biomarker of disease progression.     

Structural impact of the E113Q counterion mutation on the activation and deactivation pathways of the G protein-coupled receptor rhodopsin

Disruption of an interhelical salt bridge between the retinal protonated Schiff base linked to H7 and Glu113 on H3 is one of the decisive steps during activation of rhodopsin. Using previously established stabilization strategies, we engineered a stabilized E113Q counterion mutant that converted rhodopsin to a UV-absorbing photoreceptor with deprotonated Schiff base and allowed reconstitution into native-like lipid membranes. Fourier-transform infrared difference spectroscopy reveals a deprotonated Schiff base in the photoproducts of the mutant up to the active state Meta II, the absence of the classical pH-dependent Meta I/Meta II conformational equilibrium in favor of Meta II, and an anticipation of active state features under conditions that stabilize inactive photoproduct states in wildtype rhodopsin. Glu181 on extracellular loop 2, is found to be unable to maintain a counterion function to the Schiff base on the activation pathway of rhodopsin in the absence of the primary counterion, Glu113. The Schiff base becomes protonated in the transition to Meta III. This protonation is, however, not associated with a deactivation of the receptor, in contrast to wildtype rhodopsin. Glu181 is suggested to be the counterion in the Meta III state of the mutant and appears to be capable of stabilizing a protonated Schiff base in Meta III, but not of constraining the receptor in an inactive conformation.