bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria
Authors: Valencia Estela Y , Braz Vânia S , Guzzo Cristiane , Marques Marilis V 
Published: April 2013

Abstract

Background
Heavy metal Resistance-Nodulation-Division (HME-RND) efflux systems help Gram-negative bacteria to keep the intracellular homeostasis under high metal concentrations. These proteins constitute the cytoplasmic membrane channel of the tripartite RND transport systems. Caulobacter crescentus NA1000 possess two HME-RND proteins, and the aim of this work was to determine their involvement in the response to cadmium, zinc, cobalt and nickel, and to analyze the phylogenetic distribution and characteristic signatures of orthologs of these two proteins.

Results
Expression assays of the czrCBA operon showed significant induction in the presence of cadmium and zinc, and moderate induction by cobalt and nickel. The nczCBA operon is highly induced in the presence of nickel and cobalt, moderately induced by zinc and not induced by cadmium. Analysis of the resistance phenotype of mutant strains showed that the ΔczrA strain is highly sensitive to cadmium, zinc and cobalt, but resistant to nickel. The ΔnczA strain and the double mutant strain showed reduced growth in the presence of all metals tested. Phylogenetic analysis of the C. crescentus HME-RND proteins showed that CzrA-like proteins, in contrast to those similar to NczA, are almost exclusively found in the Alphaproteobacteria group, and the characteristic protein signatures of each group were highlighted.

Conclusions
The czrCBA efflux system is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt. The nczCBA efflux system is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. CzrA belongs to the HME2 subfamily, which is almost exclusively found in the Alphaproteobacteria group, as shown by phylogenetic analysis. NczA belongs to the HME1 subfamily which is more widespread among diverse Proteobacteria groups. Each of these subfamilies present distinctive amino acid signatures.
The effect of ‘Candidatus Liberibacter asiaticus’ infection on the proteomic profiles and nutritional status of pre-symptomatic and symptomatic grapefruit (Citrus paradisi) plants
Authors: Nwugo Chika C , Lin Hong , Duan Yongping , Civerolo Edwin L 
Published: April 2013

Abstract

Background
Huanglongbing (HLB) is a highly destructive citrus disease which threatens citrus production worldwide and ‘Candidatus Liberibacter asiaticus’ (Las), a non-culturable phloem-limited bacterium, is an associated causal agent of the disease. To better understand the physiological and molecular processes involved in host responses to Las, 2-DE and mass spectrometry analyses, as well as ICP spectroscopy analysis were employed to elucidate the global protein expression profiles and nutrient concentrations in leaves of Las-infected grapefruit plants at pre-symptomatic or symptomatic stages for HLB.

Results
This study identified 123 protein spots out of 191 spots that showed significant changes in the leaves of grapefruit plants in response to Las infection and all identified spots matched to 69 unique proteins/peptides. A down-regulation of 56 proteins including those associated with photosynthesis, protein synthesis, and metabolism was correlated with significant reductions in the concentrations of Ca, Mg, Fe, Zn, Mn, and Cu in leaves of grapefruit plants in response to Las infection, particularly in symptomatic plants. Oxygen-evolving enhancer (OEE) proteins, a PSI 9 kDa protein, and a Btf3-like protein were among a small group of proteins that were down-regulated in both pre-symptomatic and symptomatic plants in response to Las infection. Furthermore, a Las-mediated up-regulation of 13 grapefruit proteins was detected, which included Cu/Zn superoxide dismutase, chitinases, lectin-related proteins, miraculin-like proteins, peroxiredoxins and a CAP 160 protein. Interestingly, a Las-mediated up-regulation of granule-bound starch synthase was correlated with an increase in the K concentrations of pre-symptomatic and symptomatic plants.

Conclusions
This study constitutes the first attempt to characterize the interrelationships between protein expression and nutritional status of Las-infected pre-symptomatic or symptomatic grapefruit plants and sheds light on the physiological and molecular mechanisms associated with HLB disease development.
Comparative analysis of oral treponemes associated with periodontal health and disease
Authors: You Meng , Mo Sisu , Leung W Keung , Watt Rory M 
Published: April 2013

Abstract

Background
Periodontal diseases, such as periodontitis, are chronic inflammatory infections affecting the gingivae (gums), underlying connective tissues and bone that support the teeth. Oral treponemes (genus Treponema) are widely-considered to play important roles in periodontal disease etiology and pathogenesis; however, precise relationships remain to be fully established.

Methods
A 16S rRNA clone library-based approach was used to comprehensively characterize and compare the diversity of treponeme taxa present in subgingival plaque sampled from periodontitis patients (n = 10) versus periodontitis-free controls (n = 10). 16S rRNA gene sequences were assigned to operational taxonomic units (OTUs) using a 99% identity cut-off A variety of taxonomy (OTU) and phylogeny-based statistical approaches were used to compare populations of treponeme OTUs present in both subject groups.

Results
A total of 615 plasmid clones containing ca. 1500 bp Treponema 16S rRNA gene sequences were obtained; 365 from periodontitis subjects, 250 from periodontitis-free controls. These were assigned to 110 treponeme OTUs. 93 OTUs were detected in the periodontitis subjects (mean 9.3 ± 5.2 OTUs per subject; range 9–26), and 43 OTUs were detected in controls (mean 4.3 ± 5.9 OTUs per subject; range 3–20). OTUs belonging to oral treponeme phylogroups 1–7 were detected in both subject sets. Phylogroup 1 treponemes had the highest levels of OTU richness (diversity) and clonal abundance within both subject groups. Levels of OTU richness and clonal abundance of phylogroup 2 treponemes were significantly higher in the periodontitis subjects (Mann Whitney U-test, p < 0.001). Both OTU-based and phylogeny-based analyses clearly indicated that there were significant differences in the composition of treponeme communities present in periodontitis versus control subjects. The detection frequency of five OTUs showed a statistically-significant correlation with disease status. The OTU (8P47) that corresponded to the type strain of Treponema denticola had the strongest association with periodontitis (p < 0.01).

Conclusions
Higher levels of treponeme taxon richness and clonal abundance were associated with periodontitis. However, our results clearly indicated that subjects free from clinical symptoms of periodontal disease also contained highly diverse populations of treponeme bacteria within their subgingival microbiota. Our data supports the hypothesis that specific treponeme taxa are associated with periodontal disease.
Analysis of motivations that lead women to participate (or not) in a newborn cohort study
Authors: Vecchi Brumatti Liza , Montico Marcella , Russian Stefano , Tognin Veronica , Bin Maura , Barbone Fabio , Volpi Patrizia , Ronfani Luca 
Published: April 2013

AbstractBackgroundLittle is known about reasons that influence parents’ decision to participate in studies enrolling healthy children. The aim of this observational study was to verify the reasons that lead pregnant women to give their consent or to refuse participation to a newborn cohort study with a long follow up time.MethodsTo prospectively investigate the reasons that lead women to participate, to refuse the participation or to withdraw from a newborn cohort study, three different questionnaires were administered to pregnant women contacted or enrolled in the Phime cohort study, carried out in an Italian Hospital from 2007 to 2010.ResultsPhime study participation was refused by 304 women and 145 withdrew their consent during the follow up. All these women filled in the related questionnaires. Within 632 mothers in follow up at 18 months, 430 filled in the questionnaire on motivation to participate: 97% stated that the main reason was to contribute to research; 96% and 90% stated that they wanted to benefit future babies’ and mothers’ health. Ninety-six percent of women would appreciate to know the results of analysis carried out on biological samples collected and of the overall study results. One third of the mothers (37%) wanted to be involved in the definition of future similar studies, bringing their experience and their views. Within the 304 women who refused participation, 56% stated that the study was too demanding, 26% was not interested in participating and 18% was concerned about the need to collect biological samples and to be submitted to neurocognitive tests. Fifty-two percent of 145 women who withdrew after enrollment stated that the study was too demanding (52%), and 6% was concerned about the biological samples collection.ConclusionsThe altruistic reason appears to be the main reported by women to decide to participate in a newborn cohort study. The fact that the study was too demanding and the need to collect biological samples are important reasons that lead women to refuse participation or to withdraw from the study. An adequate communication on these aspects should minimize difficulties in enrolment and losses to follow up.
Bioluminescence imaging for IL-1β expression in experimental colitis
Authors: Li Limei , Liu Zhenzhe , Yang Xinyu , Yan Huimin , Bao Shisan , Fei Jian 
Published: April 2013

Abstract

Background
Interleukin 1 beta (IL-1β) contributes to the development of inflammatory bowel disease (IBD) and is correlated with the severity of intestinal inflammation. However, the precise source of IL-1β producing cells in DSS colitis is currently not known.

Methods
To determine IL-1β activity during intestinal inflammation in real time, an IL-1β transgenic mouse has been generated by incorporating the firefly luciferase gene driven by a 4.5-kb fragment of human IL-1β gene promoter (named cHS4I-hIL-1βP-Luc transgenic mice). Dextran sodium sulfate (DSS) induced colitis was confirmed with clinical presentation and histopathology.

Results
A substantial increase in luciferase activity (reflecting IL-1β production) in the region of inflamed colon was observed in a time dependent manner, followed by additional activity in the region of the mesenteric lymph node. The up-regulated luciferase activity was suppressed by dexamethasone (steroids) during DSS challenge, consistent with reduced severity of colitis, confirming the specificity of luciferase activity.

Conclusions
Our data suggests that bioluminescence is an interesting technology, which may be used to evaluate transcription of various genes in real time in experimental colitis.
Evaluation of H.264/AVC over IEEE 802.11p vehicular networks
Authors: Rozas-Ramallal Ismael , Fernández-Caramés Tiago M , Dapena Adriana , García-Naya José Antonio 
Published: April 2013

Abstract
The capacity of vehicular networks to offer non-safety services, like infotainment applications or the exchange of multimedia information between vehicles, have attracted a great deal of attention to the field of Intelligent Transport Systems (ITS). In particular, in this article we focus our attention on IEEE 802.11p which defines enhancements to IEEE 802.11 required to support ITS applications. We present an FPGA-based testbed developed to evaluate H.264/AVC (Advanced Video Coding) video transmission over vehicular networks. The testbed covers some of the most common situations in vehicle-to-vehicle and roadside-to-vehicle communications and it is highly flexible, allowing the performance evaluation of different vehicular standard configurations. We also show several experimental results to illustrate the quality obtained when H.264/AVC encoded video is transmitted over IEEE 802.11p networks. The quality is measured considering two important parameters: the percentage of recovered group of pictures and the frame quality. In order to improve performance, we propose to substitute the convolutional channel encoder used in IEEE 802.11p for a low-density parity-check code encoder. In addition, we suggest a simple strategy to decide the optimum number of iterations needed to decode each packet received.
LKB1 tumor suppressor and salt-inducible kinases negatively regulate human T-cell leukemia virus type 1 transcription
Authors: Tang Hei-Man Vincent , Gao Wei-Wei , Chan Ching-Ping , Siu Yeung-Tung , Wong Chi-Ming , Kok Kin-Hang , Ching Yick-Pang , Takemori Hiroshi , Jin Dong-Yan 
Published: April 2013

Abstract

Background
Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL). Treatment options are limited and prophylactic agents are not available. We have previously demonstrated an essential role for CREB-regulating transcriptional coactivators (CRTCs) in HTLV-1 transcription.

Results
In this study we report on the negative regulatory role of LKB1 tumor suppressor and salt-inducible kinases (SIKs) in the activation of HTLV-1 long terminal repeats (LTR) by the oncoprotein Tax. Activation of LKB1 and SIKs effectively blunted Tax activity in a phosphorylation-dependent manner, whereas compromising these kinases, but not AMP-dependent protein kinases, augmented Tax function. Activated LKB1 and SIKs associated with Tax and suppressed Tax-induced LTR activation by counteracting CRTCs and CREB. Enforced expression of LKB1 or SIK1 in cells transfected with HTLV-1 molecular clone pX1MT repressed proviral transcription. On the contrary, depletion of LKB1 in pX1MT-transfected cells and in HTLV-1-transformed T cells boosted the expression of Tax. Treatment of HTLV-1 transformed cells with metformin led to LKB1/SIK1 activation, reduction in Tax expression, and inhibition of cell proliferation.

Conclusions
Our findings revealed a new function of LKB1 and SIKs as negative regulators of HTLV-1 transcription. Pharmaceutical activation of LKB1 and SIKs might be considered as a new strategy in anti-HTLV-1 and anti-ATL therapy.
One century later: the folk botanical knowledge of the last remaining Albanians of the upper Reka Valley, Mount Korab, Western Macedonia
Authors: Pieroni Andrea , Rexhepi Besnik , Nedelcheva Anely , Hajdari Avni , Mustafa Behxhet , Kolosova Valeria , Cianfaglione Kevin , Quave Cassandra L 
Published: April 2013

Abstract
Background
Ethnobotanical surveys of the Western Balkans are important for the cross-cultural study of local plant knowledge and also for obtaining baseline data, which is crucial for fostering future rural development and eco-tourism initiatives in the region. The current ethnobotanical field study was conducted among the last remaining Albanians inhabiting the upper Reka Valley at the base of Mount Korab in the Mavrovo National Park of the Republic of Macedonia.
The aims of the study were threefold: 1) to document local knowledge pertaining to plants; 2) to compare these findings with those of an ethnographic account written one century ago and focused on the same territory; and 3) to compare these findings with those of similar field studies previously conducted in other areas of the Balkans.

Methods
Field research was conducted with all inhabitants of the last four inhabited villages of the upper Reka Valley (n=17). Semi-structured and open interviews were conducted regarding the perception and use of the local flora and cultivated plants.

Results and conclusion
The uses of ninety-two plant and fungal taxa were recorded; among the most uncommon uses, the contemporary use of young cooked potato (Solanum tuberosum) leaves and Rumex patientia as a filling for savory pies was documented. Comparison of the data with an ethnographic study conducted one century ago in the same area shows a remarkable resilience of original local plant knowledge, with the only exception of rye, which has today disappeared from the local foodscape. Medicinal plant use reports show important similarities with the ethnobotanical data collected in other Albanian areas, which are largely influenced by South-Slavic cultures.
Suppression of STIM1 inhibits human glioblastoma cell proliferation and induces G0/G1 phase arrest
Authors: Li Guilin , Zhang Zhenxing , Wang Renzhi , Ma Wenbin , Yang Ying , Wei Junji , Wei Yanping 
Published: April 2013

Abstract

Background
Depletion of calcium (Ca2+) from the endoplasmic reticulum (ER) activates the ubiquitous store-operated Ca2+ entry (SOCE) pathway which sustains long-term Ca2+ signals and is critical for cellular functions. Stromal interacting molecule 1 (STIM1) serves a dual role as an ER Ca2+ sensor and activator of SOCE. Aberrant expression of STIM1 could be observed in several human cancer cells. However, the role of STIM1 in regulating tumorigenesis of human glioblastoma still remains unclear.

Methods
Expression of STIM1 protein in a panel of human glioblastoma cell lines (U251, U87 and U373) in different transformation level were evaluated by Western blot method. STIM1 loss of function was performed on U251 cells, derived from grade IV astrocytomas-glioblastoma multiforme with a lentvirus-mediated short harpin RNA (shRNA) method. The biological impacts after knock down of STIM1 on glioblastoma cells were investigated in vitro and in vivo.

Results
We discovered that STIM1 protein was expressed in U251, U87 and U373 cells, and especially higher in U251 cells. RNA interference efficiently downregulated the expression of STIM1 in U251 cells at both mRNA and protein levels. Specific downregulation of STIM1 inhibited U251 cell proliferation by inducing cell cycle arrest in G0/G1 phase through regulation of cell cycle-related genes, such as p21Waf1/Cip1
, cyclin D1 and cyclin-dependent kinase 4 (CDK4), and the antiproliferative effect of STIM1 silencing was also observed in U251 glioma xenograft tumor model.

Conclusion
Our findings confirm STIM1 as a rational therapeutic target in human glioblastoma, and also indicate that lentivirus-mediated STIM1 silencing is a promising therapeutic strategy for human glioblastoma.
Arthritis augments breast cancer metastasis: role of mast cells and SCF/c-Kit signaling
Authors: Roy Lopamudra Das , Curry Jennifer M , Sahraei Mahnaz , Besmer Dahlia M , Kidiyoor Amritha , Gruber Helen E , Mukherjee Pinku 
Published: April 2013

Abstract
Introduction
Breast cancer remains the second leading cause of cancer-related deaths for women in the United States. Metastasis is regulated not only by intrinsic genetic changes in malignant cells, but also by the microenvironment, especially those associated with chronic inflammation. We recently reported that mice with autoimmune arthritis have significantly increased incidence of bone and lung metastasis and decreased survival associated with breast cancer. In this study, we evaluated the mechanism underlying the increased metastasis.

Methods
We used two mouse models; one that develops spontaneous autoimmune arthritis (SKG mice) injected with metastatic breast cancer cells (4T1), and another that develops spontaneous breast cancer (MMTV-PyV MT mice) injected with type II collagen to induce autoimmune arthritis. Mast cell levels and metastasis were monitored.

Results
First, we confirmed that breast tumor-bearing arthritic mice have a significantly higher incidence of bone and lung metastasis than do their nonarthritic counterparts. Next, we showed increased recruitment of mast cells within the primary tumor of arthritic mice, which facilitates metastasis. Next, we report that arthritic mice without any tumors have higher numbers of mast cells in the bones and lungs, which may be the underlying cause for the enhanced lung and bone metastases observed in the arthritic mice. Next, we showed that once the tumor cells populate the metastatic niches (bones and lungs), they further increase the mast cell population within the niche and assist in enhancing metastasis. This may primarily be due to the interaction of c-Kit receptor present on mast cells and stem cell factor (SCF, the ligand for ckit) expressed on tumor cells. Finally, we showed that targeting the SCF/cKit interaction with an anti-ckit antibody reduces the differentiation of mast cells and consequently reduces metastasis.

Conclusion
This is the first report to show that mast cells may play a critical role in remodeling not only the tumor microenvironment but also the metastatic niche to facilitate efficient metastasis through SCF/cKit interaction in breast cancer with arthritis.
Identification of p63+ keratinocyte progenitor cells in circulation and their matrix-directed differentiation to epithelial cells
Authors: Nair Renjith P , Krishnan Lissy K 
Published: April 2013

Abstract
Introduction
In the event of chronic diabetes or burn wounds, accomplishing skin regeneration is a major concern. Autologous skin grafting is the most effective remedy, but the tissue harvest may create more nonhealing wounds. Currently available skin substitutes have a limited clinical outcome because of immune reactions arising from the xenobiotic scaffold or allogenous cells. Autologous stem cells that can be collected without an additional injury may be a viable option for skin-tissue engineering. Presence of a low number of keratinocyte progenitor cells (KPCs) within the peripheral blood mononuclear cell (PBMNC) population has been indicated. Identification, isolation, expansion, and differentiation of KPCs is necessary before they are considered for skin regeneration, which is the focus of this study.

Methods
Culture of isolated human PBMNCs on a cell-specific matrix was carried out to induce differentiation of KPCs. Flow cytometry and reverse transcriptase polymerase chain reaction were done for epithelial stem cell marker p63 and lineage markers cytokeratin 5 and cytokeratin 14, to track differentiation. Proliferation was confirmed by quantifying the proliferating cell nuclear antigen-expressing cells. Immunostaining with epithelial cell markers, involucrin and filaggrin, was carried out to establish terminal differentiation. Microscopic analysis confirmed growth and survival of KPCs on the dermal fibroblast monolayer and on a transplantable fibrin sheet.

Results
We demonstrated that KPCs are p63+ and CD34-. The specifically designed composition of the extracellular matrix was found to support selective adhesion, proliferation, and differentiation of p63+ KPCs. The PBMNC culture for 12 days under controlled conditions resulted in a homogenous population that expressed cytokeratins, and >90% of the cells were found to proliferate. Subculture for 5 days resulted in expression of filaggrin and involucrin, suggesting terminal differentiation. Transfer of matrix-selected KPCs to a dermal fibroblast monolayer or fibrin supported cell proliferation and showed typical hexagonal morphology of keratinocytes within 15 days.

Conclusions
Circulating KPCs were identified with p63, which differentiated into keratinocytes with expression of the cytokeratins, involucrin and filaggrin. Components of the specifically designed matrix favored KPC attachment, directed differentiation, and may turn out to be a potential vehicle for cell transplantation.