bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial diversity in alpine tundra soils correlates with snow cover dynamics
Authors: Zinger Lucie , Shahnavaz Bahar , Baptist Florence , Geremia Roberto A , Choler Philippe 
Published: March 2009

Abstract
The temporal and spatial snow cover dynamics is the primary factor controlling the plant communities' composition and biogeochemical cycles in arctic and alpine tundra. However, the relationships between the distribution of snow and the diversity of soil microbial communities remain largely unexplored. Over a period of 2 years, we monitored soil microbial communities at three sites, including contiguous alpine meadows of late and early snowmelt locations (LSM and ESM, respectively). Bacterial and fungal communities were characterized by using molecular fingerprinting and cloning/sequencing of microbial ribosomal DNA extracted from the soil. Herein, we show that the spatial and temporal distribution of snow strongly correlates with microbial community composition. High seasonal contrast in ESM is associated with marked seasonal shifts for bacterial communities; whereas less contrasted seasons because of long-lasting snowpack in LSM is associated with increased fungal diversity. Finally, our results indicate that, similar to plant communities, microbial communities exhibit important shifts in composition at two extremes of the snow cover gradient. However, winter conditions lead to the convergence of microbial communities independently of snow cover presence. This study provides new insights into the distribution of microbial communities in alpine tundra in relation to snow cover dynamics, and may be helpful in predicting the future of microbial communities and biogeochemical cycles in arctic and alpine tundra in the context of a warmer climate.
Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium
Authors: Rodrigues Debora F , da C Jesus Ederson , Ayala-del-Río Hector L , Pellizari Vivian H , Gilichinsky David , Sepulveda-Torres Lycely , Tiedje James M 
Published: March 2009

Abstract
The genera Exiguobacterium and Psychrobacter have been frequently detected in and isolated from polar permafrost and ice. These two genera have members that can grow at temperatures as low as −5 and −10 °C, respectively. We used quantitative PCR (Q-PCR) to quantify members of these genera in 54 soil or sediment samples from polar, temperate and tropical environments to determine to what extent they are selected by cold environments. These results were further analyzed by multiple linear regression to identify the most relevant environmental factors corresponding to their distribution. Exiguobacterium was detected in all three climatic zones at similar densities, but was patchier in the temperate and tropical samples. Psychrobacter was present in almost all polar samples, was at highest densities in Antarctica sediment samples, but was in very low densities and infrequently detected in temperate and tropical soils. Clone libraries, specific for the 16S rRNA gene for each genus, were constructed from a sample from each climatic region. The clone libraries were analyzed for α and β diversities, as well as for variation in population structure by using analysis of molecular variance. Results confirm that both genera were found in all three climatic zones; however, Psychrobacter populations seemed to be much more diverse than Exiguobacterium in all three climatic zones. Furthermore, Psychrobacter populations from Antarctica are different from those in Michigan and Puerto Rico, which are similar to each other.
Loss of 26S Proteasome Function Leads to Increased Cell Size and Decreased Cell Number in Arabidopsis Shoot Organs
Authors: Kurepa Jasmina , Wang Songhu , Li Yan , Zaitlin David , Pierce Andrew J. , Smalle Jan A. 
Published: March 2009

Abstract
Although the final size of plant organs is influenced by environmental cues, it is generally accepted that the primary size determinants are intrinsic factors that regulate and coordinate cell proliferation and cell expansion. Here, we show that optimal proteasome function is required to maintain final shoot organ size in Arabidopsis (Arabidopsis thaliana). Loss of function of the subunit regulatory particle AAA ATPase (RPT2a) causes a weak defect in 26S proteasome activity and leads to an enlargement of leaves, stems, flowers, fruits, seeds, and embryos. These size increases are a result of increased cell expansion that compensates for a reduction in cell number. Increased ploidy levels were found in some but not all enlarged organs, indicating that the cell size increases are not caused by a higher nuclear DNA content. Partial loss of function of the regulatory particle non-ATPase (RPN) subunits RPN10 and RPN12a causes a stronger defect in proteasome function and also results in cell enlargement and decreased cell proliferation. However, the increased cell volumes in rpn10-1 and rpn12a-1 mutants translated into the enlargement of only some, but not all, shoot organs. Collectively, these data show that during Arabidopsis shoot development, the maintenance of optimal proteasome activity levels is important for balancing cell expansion with cell proliferation rates.
Antibodies to Helicobacter pylori and CagA protein are associated with the response to antibacterial therapy in patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma
Authors: Sumida Tomonori , Kitadai Yasuhiko , Hiyama Toru , Shinagawa Kei , Tanaka Miwako , Kodama Michiyo , Masuda Hiroshi , Ito Masanori , Tanaka Shinji , Yoshihara Masaharu , Chayama Kazuaki 
Published: March 2009

The aim of this study was to clarify predictive factors for response to eradication therapy in cases of Helicobacter pylori (H. pylori)‐positive API2–MALT1‐negative gastric mucosa‐associated lymphoid tissue (MALT) lymphoma. Sixty‐six patients who were examined for H. pylori infection and the presence of the API2–MALT1 chimeric transcript and who underwent H. pylori eradication therapy as first‐line therapy, were enrolled in this study. Immunohistochemical markers (p53, Ki‐67, and BCL10), microsatellite instability, loss of heterozygosity, serum levels of antibodies (anti‐H. pylori and anti‐CagA), and markers for gastritis (gastrin and pepsinogens) were examined, and the results were compared between patients whose tumors regressed completely after eradication therapy (responders) and patients whose tumors did not regress (non‐responders). Of the 66 patients with localized gastric MALT lymphoma, 47 (71.2%) showed complete remission after eradication therapy. None of the H. pylori‐negative (n = 9) and/or API2–MALT1‐positive (n = 7) patients responded to antibacterial treatment. Of 44 patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma, 38 (86.4%) showed complete remission after eradication therapy. Titers of antibodies against H. pylori and CagA protein were significantly higher in the responders than in the non‐responders (P = 0.0235 and 0.0089, respectively). No significant difference between the groups was observed for the other factors. In conclusion, measurement of titers of serum antibodies to H. pylori and CagA protein may be useful for predicting the response to eradication therapy in patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma. (Cancer Sci 2009; 100: 1075–1081)
Deficiency of regulatory T cells in children with autoimmune neutropenia
Authors: Nakamura Kazuhiro , Miki Mizuka , Mizoguchi Yoko , Karakawa Syuhei , Sato Takashi , Kobayashi Masao 
Published: March 2009

SummaryCD4+ 25+ regulatory T cells (Tregs) play a role in controlling the development and progression of autoimmunity. The transcription factors Foxp3 and NFATC2 (NFAT1) play key roles in regulating the development and function of Tregs. The present study examined the involvement of Tregs in the pathophysiology of autoimmune neutropenia in children. Tregs were analysed by flow cytometry, based on the expressions of CD4, CD25, and intracellular Foxp3. The expressions of FOXP3 and NFATC2 mRNA in the CD4+ 25+ cells were determined by quantitative real‐time polymerase chain reaction. The percentage of CD4+ 25high Tregs in patients with autoimmune neutropenia was significantly lower than that in age‐matched healthy subjects. The intracellular expression of Foxp3 of CD4+ 25+ cells in patients similarly decreased in comparison to that in healthy subjects. The expression of FOXP3 and NFATC2 mRNA of CD4+ 25+ cells in patients also significantly decreased in comparison to that in healthy subjects. These results suggest that the deficiency of Tregs might thus play an important role in the immunopathophysiology of autoimmune neutropenia in children.
Oct‐4A isoform is expressed in human cord blood‐derived CD133 stem cells and differentiated progeny
Authors: Howe M.  , Zhao J.  , Bodenburg Y. , McGuckin C. P.  , Forraz N.  , Tilton R. G.  , Urban R. J.  , Denner L.  
Published: March 2009

AbstractObjectives: This study aims to establish whether the pluripotent embryonic stem cell marker and nuclear transcription factor Oct‐4A isoform is expressed in human umbilical cord blood CD133 stem cells (CD133 cells) and their differentiated progeny.Materials and methods: CD133 cells were examined for expression of the embryonic stem cell marker Oct‐4A by reverse transcription–polymerase chain reaction using primers specific for the coding region of the Oct‐4A isoform. Immunocytochemistry and flow cytometry were performed using an antibody raised to a peptide from the unique amino‐terminal domain of the Oct‐4A isoform, that does not exist in the Oct‐4B isoform. Furthermore, specificity was confirmed by pre‐adsorption of the antibody with the peptide immunogen. Differentiation was determined before and after expansion in culture, by flow cytometry for haematopoietic stem cell and differentiation markers. For many studies, after 7 days of culture CD133‐positive and CD133‐negative cells were separated by flow cytometry for additional analyses. Multilineage haematopoietic proliferative potential was determined using colony‐forming assays.Results: Freshly isolated CD133 cells expressed Oct‐4A mRNA and protein. The cells proliferated rapidly in culture producing only a small proportion of CD133‐positive cells and a much larger proportion of non‐self‐renewing CD133‐negative cells. Proliferation was also associated with loss of other adult stem cell markers, gain of differentiated haematopoietic markers, and maintenance of potential to generate haematopoietic lineages. Oct‐4A mRNA and protein were expressed throughout these changes.Conclusions: Oct‐4A, which is associated with self‐renewal in embryonic stem cells, neither defines nor confers self‐renewal to CD133 stem cells.
Long‐term repeatability of winter basal metabolic rate and mass in a wild passerine
Authors: Broggi Juli , Hohtola Esa , Koivula Kari , Orell Markku , Nilsson Jan‐Åke 
Published: March 2009

Summary

Basal metabolic rate (BMR) is an important trait in the study of energy management of an individual, especially in small wintering passerines from the north which have one of the highest energy turnover rates in vertebrates. Laboratory studies have shown the trait to be repeatable and heritable, despite its plastic nature. However there is currently a lack of empirical data from wild passerine populations.
We studied within‐ and between‐year repeatability of BMR, body mass and mass‐independent BMR from two populations of wintering great tits (Parus major) at the northern range of their distribution.
We found body mass, BMR and mass‐independent BMR to be highly repeatable both within and between years.
Our results provide the first evidence from a wild small passerine that, despite a large environmentally induced variation in metabolic rate, individuals show consistent metabolic strategies over periods even longer than a year.
Homeotherm species exposed to new or changing environmental conditions may be able to evolve specific energetic strategies in the wild, as previously found in captive species.
Effect of simulated environmental change on alpine soil arthropods
Authors: HÅGVAR SIGMUND , KLANDERUD KARI 
Published: March 2009

AbstractThe effects of environmental change on soil animal communities are poorly known. Norwegian mountains are subject to both atmospheric nitrogen deposition and increased temperature. In a nutrient poor alpineDryasheath in south Norway, soil arthropods were studied after 4 years of simulated environmental change by warming and/or nutrient addition. Warming alone only affected three low‐density Collembola species, while nutrient addition, with or without warming, greatly changed the dominance hierarchy of the microarthropod community. Certain Collembola species with a short (1 year) life cycle and predatory Gamasina mites increased markedly in density. These groups may have been favored by increased litter production, as plant biomass and litter producing graminoids and forbs increased significantly in plots with nutrient addition and nutrient addition combined with warming. Microarthropods with a longer life cycle, such as Oribatida and certain Collembola, were generally unaffected by nutrient addition and probably need more time to respond. The number of Oribatida taxa was, however, reduced in plots with nutrient addition, both with and without warming. A ground‐living species of Coccoidea (Homoptera) declined in plots with nutrient addition and warming compared with only warming, probably due to reduced cover of its host plantDryas. The density of Diptera larvae (Sciaridae and Chironomidae) was unaffected by the treatments. Our results show that increased nutrient availability in nutrient poor alpine soils may have large but different effects on different taxa of soil animals. Species with short life cycles reacted first. Nutrient addition and nutrient addition combined with warming resulted in several effects below ground on microarthropods as previously shown above ground on plants: Increased biomass, high dominance of a few rapid‐growing species, contrasting responses of closely related species, and a reduction in species numbers. These short‐term responses may have profound long‐term effects in this alpine ecosystem.
Annual emissions of dissolved CO2, CH4, and N2O in the subsurface drainage from three cropping systems
Authors: MINAMIKAWA KAZUNORI , NISHIMURA SEIICHI , SAWAMOTO TAKUJI , NAKAJIMA YASUHIRO , YAGI KAZUYUKI 
Published: March 2009

AbstractIndirect emission of nitrous oxide (N2O), associated with nitrogen (N) leaching and runoff from agricultural lands is a major source of atmospheric N2O. Recent studies have shown that carbon dioxide (CO2) and methane (CH4) are also emitted via these pathways. We measured the concentrations of three dissolved greenhouse gases (GHGs) in the subsurface drainage from field lysimeter that had a shallow groundwater table. Aboveground fluxes of CH4 and N2O were monitored using an automated closed‐chamber system. The annual total emissions of dissolved and aboveground GHGs were compared among three cropping systems; paddy rice, soybean and wheat, and upland rice.The annual drainage in the paddy rice, the soybean and wheat, and the upland rice plots was 1435, 782, and 1010 mm yr−1, respectively. Dissolved CO2 emissions were highest in the paddy rice plots, and were equivalent to 1.05–1.16% of the carbon storage in the topsoil. Dissolved CH4 emissions were also higher in the paddy rice plots, but were only 0.03–0.05% of the aboveground emissions. Dissolved N2O emissions were highest in the upland rice plots, where leached N was greatest due to small crop biomass. In the soybean and wheat plots, large crop biomass, due to double cropping, decreased the drainage volume, and thus decreased dissolved GHG emissions. Dissolved N2O emissions from both the soybean and wheat plots and the upland rice plots were equivalent to 50.3–67.3% of the aboveground emissions. The results indicate that crop type and rotation are important factors in determining dissolved GHG emissions in the drainage from a crop field.
Impact of human immunodeficiency virus 1 infection and inflammation on the composition and yield of cervical mononuclear cells in the female genital tract
Authors: Nkwanyana Nonhlanhla N. , Gumbi Pamela P. , Roberts Lindi , Denny Lynette , Hanekom Willem , Soares Andreia , Allan Bruce , Williamson Anna‐Lise , Coetzee David , Olivier Abraham J. , Burgers Wendy A. , Passmore Jo‐Ann 
Published: March 2009

SummaryCervical cytobrush sampling is a relatively non‐invasive method for obtaining mucosal cells from the female genital tract. To define mucosal immune cells sampled by cervical cytobrushing and to validate this approach for local immunity studies, we investigated the impact of human immunodeficiency virus (HIV) status and inflammation on the yield and composition of cervical cytobrush specimens. Cervical cytobrush samples were obtained from 89 chronically HIV‐infected and 46 HIV‐negative women. The HIV‐infected women had significantly higher yields of CD3+, CD45+, CD19+, CD14+, Langerin+ and CD24+ cells than the uninfected women. While cytobrush‐derived T cells from uninfected women were predominantly CD4+ (4·2 CD4 : 1 CD8), CD8+ T cells were predominant in HIV‐infected women (0·6 CD4 : 1 CD8). The majority of CD4+ and CD8+ T cells from HIV‐infected and uninfected women were of the effector memory (CD45RA− CCR7− CD27−) phenotype. HIV‐infected women had significantly elevated levels of interleukin (IL)‐1β, IL‐6 and IL‐8 in cervical supernatants compared with uninfected women. We observed a significant positive correlation between T‐cell counts and IL‐1β, tumour necrosis factor (TNF)‐α and IL‐12 concentrations. Neutrophil counts correlated significantly with cervical concentrations of IL‐1β, TNF‐α, IL‐8, IL‐6 and IL‐10. Antigen‐presenting cell numbers correlated significantly with TNF‐α and IL‐12 concentrations. HIV‐infected women on antiretroviral therapy had similar levels of cervical lymphocyte infiltration and inflammation to women naïve to therapy. In conclusion, we suggest that inflammation at the cervix and HIV infection are likely to be key determinants in the absolute number of mucosal immune cells recovered by cervical cytobrushing.
Peptidoglycan from lactobacilli inhibits interleukin‐12 production by macrophages induced by Lactobacillus casei through Toll‐like receptor 2‐dependent and independent mechanisms
Authors: Shida Kan , Kiyoshima‐Shibata Junko , Kaji Rumi , Nagaoka Masato , Nanno Masanobu 
Published: March 2009

SummaryWe previously showed that Lactobacillus strains having a rigid cell wall resistant to intracellular digestion can stimulate macrophages to induce large a quantity of interleukin‐12 (IL‐12). In this study, we examined the influence of lactobacilli and bacterial cell wall components on IL‐12 production by macrophages that was induced by Lactobacillus casei, which has a rigid cell wall. Easily digestible lactobacilli such as Lactobacillus johnsonii and Lactobacillus plantarum or their intact cell walls (ICWs) weakly or very weakly induced IL‐12 production by macrophages, and inhibitedL. casei‐induced IL‐12 production. While the ICW of L. casei was resistant to intracellular digestion and did not inhibit L. casei‐induced IL‐12 production, its polysaccharide‐depleted ICW, i.e. intact peptidoglycan, was sensitive to intracellular digestion and inhibited L. casei‐induced IL‐12 production. Furthermore, the peptidoglycans of L. johnsonii, L. plantarum and Staphylococcus aureus also inhibited L. casei‐induced IL‐12 production. Peptidoglycans from lactobacilli suppressed L. casei‐induced expression of IL‐12p40 but not IL‐12p35 mRNA. Inhibition of IL‐12 production by peptidoglycan was mitigated in Toll‐like receptor 2 (TLR2)‐deficient macrophages compared with the inhibition in wild‐type macrophages. A derivative of the minimal structural unit of peptidoglycan (6‐O‐stearoyl‐muramyl dipeptide) recognized by nucleotide‐binding oligomerization domain 2 (NOD2) could also suppress L. casei‐induced IL‐12 production. These findings demonstrate that easily digestible bacteria and peptidoglycan suppress IL‐12 production through pattern recognition receptors such as TLR2 and NOD2. IL‐12 production in the gut may be negatively regulated by the simultaneous inhibitory actions of various resident bacteria that are susceptible to intracellular digestion.
Coadministration of the fungal immunomodulatory protein FIP‐Fve and a tumour‐associated antigen enhanced antitumour immunity
Authors: Ding Ying , Seow See Voon , Huang Chiung Hui , Liew Lee Mei , Lim Yaw Chyn , Kuo I. Chun , Chua Kaw Yan 
Published: March 2009

SummaryFve is a fungal protein isolated from the golden needle mushroom Flammulina velutipes and has previously been reported to trigger immunological responses in both mouse and human lymphocytes. In this study, we evaluated the potential application of Fve as an adjuvant for tumour immunotherapy and examined the underlying mechanism(s). When the human papillomavirus (HPV)‐16 E7 oncoprotein was used as a model antigen, mice coimmunized with HPV‐16 E7 and Fve showed enhanced production of HPV‐16 E7‐specific antibodies as well as expansion of HPV‐16 E7‐specific interferon (IFN)‐γ‐producing CD4+ and CD8+ T cells as compared with mice immunized with HPV‐16 E7 alone. Tumour protection assays showed that 60% of mice coimmunized with HPV‐16 E7 plus Fve, as compared with 20% of those immunized only with HPV‐16 E7, remained tumour‐free for up to 167 days after challenge with the tumour cells. Tumour therapeutic assays showed that HPV‐16 E7 plus Fve treatment significantly prolonged the survival of tumour‐bearing mice as compared with those treated only with HPV‐16 E7. In vivo cell depletion and adoptive T‐cell transfer assays showed that CD4+ and CD8+ T cells and IFN‐γ played critical roles in conferring the antitumour effects. Interestingly, Fve could stimulate the maturation of splenic dendritic cells in vivo and induce antigen‐specific CD8+ T‐cell immune responses. In summary, Fve has potent adjuvant properties that enhance T helper type 1 antigen‐specific humoral and cellular immune responses which confer strong antitumour effects. The use of Fve as an adjuvant could be an attractive alternative to the current vaccination strategy for cancer immunotherapy.