bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
Authors: Schlüter Jan-Philip , Reinkensmeier Jan , Daschkey Svenja , Evguenieva-Hackenberg Elena , Janssen Stefan , Jänicke Sebastian , Becker Jörg D , Giegerich Robert , Becker Anke 
Published: April 2010

AbstractBackgroundSmall untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacteriumSinorhizobium melilotiapplying deep sequencing of cDNAs and microarray hybridizations.ResultsA total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173), cis-encoded antisense sRNAs (117), mRNA leader transcripts (379), and sense sRNAs overlapping coding regions (456) were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus σ70promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences fromS. melilotialready known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria.ConclusionsThe screening data suggests that inS. melilotiabout 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.
The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation
Authors: Qin Qi-Long , Zhang Xi-Ying , Wang Xu-Min , Liu Gui-Ming , Chen Xiu-Lan , Xie Bin-Bin , Dang Hong-Yue , Zhou Bai-Cheng , Yu Jun , Zhang Yu-Zhong 
Published: April 2010

Abstract

Background

Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes.

Results
The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.

Conclusion
Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.
Production of enterodiol from defatted flaxseeds through biotransformation by human intestinal bacteria
Authors: Wang Cheng-Zhi , Ma Xiao-Qing , Yang Dong-Hui , Guo Zhi-Rong , Liu Gui-Rong , Zhao Ge-Xin , Tang Jie , Zhang Ya-Nan , Ma Miao , Cai Shao-Qing , Ku Bao-Shan , Liu Shu-Lin 
Published: April 2010

Abstract

Background
The effects of enterolignans, e.g., enterodiol (END) and particularly its oxidation product, enterolactone (ENL), on prevention of hormone-dependent diseases, such as osteoporosis, cardiovascular diseases, hyperlipemia, breast cancer, colon cancer, prostate cancer and menopausal syndrome, have attracted much attention. To date, the main way to obtain END and ENL is chemical synthesis, which is expensive and inevitably leads to environmental pollution. To explore a more economic and eco-friendly production method, we explored biotransformation of enterolignans from precursors contained in defatted flaxseeds by human intestinal bacteria.

Results
We cultured fecal specimens from healthy young adults in media containing defatted flaxseeds and detected END from the culture supernatant. Following selection through successive subcultures of the fecal microbiota with defatted flaxseeds as the only carbon source, we obtained a bacterial consortium, designated as END-49, which contained the smallest number of bacterial types still capable of metabolizing defatted flaxseeds to produce END. Based on analysis with pulsed field gel electrophoresis, END-49 was found to consist of five genomically distinct bacterial lineages, designated Group I-V, with Group I strains dominating the culture. None of the individual Group I-V strains produced END, demonstrating that the biotransformation of substrates in defatted flaxseeds into END is a joint work by different members of the END-49 bacterial consortium. Interestingly, Group I strains produced secoisolariciresinol, an important intermediate of END production; 16S rRNA analysis of one Group I strain established its close relatedness with Klebsiella. Genomic analysis is under way to identify all members in END-49 involved in the biotransformation and the actual pathway leading to END-production.

Conclusion
Biotransformation is a very economic, efficient and environmentally friendly way of mass-producing enterodiol from defatted flaxseeds.
Role of nitric oxide in Salmonella typhimurium-mediated cancer cell killing
Authors: Barak Yoram , Schreiber Frank , Thorne Steve H , Contag Christopher H , deBeer Dirk , Matin A 
Published: April 2010

Abstract

Background
Bacterial targeting of tumours is an important anti-cancer strategy. We previously showed that strain SL7838 of Salmonella typhimurium targets and kills cancer cells. Whether NO generation by the bacteria has a role in SL7838 lethality to cancer cells is explored. This bacterium has the mechanism for generating NO, but also for decomposing it.

Methods
Mechanism underlying Salmonella typhimurium tumour therapy was investigated through in vitro and in vivo studies. NO measurements were conducted either by chemical assays (in vitro) or using Biosensors (in vivo). Cancer cells cytotoxic assay were done by using MTS. Bacterial cell survival and tumour burden were determined using molecular imaging techniques.

Results
SL7838 generated nitric oxide (NO) in anaerobic cell suspensions, inside infected cancer cells in vitro and in implanted 4T1 tumours in live mice, the last, as measured using microsensors. Thus, under these conditions, the NO generating pathway is more active than the decomposition pathway. The latter was eliminated, in strain SL7842, by the deletion of hmp- and norV genes, making SL7842 more proficient at generating NO than SL7838. SL7842 killed cancer cells more effectively than SL7838 in vitro, and this was dependent on nitrate availability. This strain was also ca. 100% more effective in treating implanted 4T1 mouse tumours than SL7838.

Conclusions
NO generation capability is important in the killing of cancer cells by Salmonella strains.
Docosahexaenoic acid has influence on action potentials and transient outward potassium currents of ventricular myocytes
Authors: Wang Ru-xing , Li Xiao-rong , Guo Tao , Sun Li-ping , Guo Su-xia , Yang Zhen-Yu , Yang Xiang-Jun , Jiang Wen-ping 
Published: April 2010

AbstractBackgroundThere are many reports about the anti-arrhythmic effects of ω-3 polyunsaturated fatty acids, however, the mechanisms are still not completely delineated. The purpose of this study was to investigate the characteristics of action potentials and transient outward potassium currents (Ito) of Sprague-Dawley rat ventricular myocytes and the effects of docosahexaenoic acid (DHA) on action potentials and Ito.MethodsThe calcium-tolerant rat ventricular myocytes were isolated by enzyme digestion. Action potentials and Itoof epicardial, mid-cardial and endocardial ventricular myocytes were recorded by whole-cell patch clamp technique.Results1.Action potential durations (APDs) were prolonged from epicardial to endocardial ventricular myocytes (P< 0.05).2.Itocurrent densities were decreased from epicardial to endocardial ventricular myocytes, which were 59.50 ± 15.99 pA/pF, 29.15 ± 5.53 pA/pF, and 12.29 ± 3.62 pA/pF, respectively at +70 mV test potential (P< 0.05).3.APDs were gradually prolonged with the increase of DHA concentrations from 1 μmol/L to 100 μmol/L, however, APDs changes were not significant as DHA concentrations were in the range of 0 μmol/L to 1 μmol/L.4.Itocurrents were gradually reduced with the increase of DHA concentrations from 1 μmol/L to 100 μmol/L, and its half-inhibited concentration was 5.3 μmol/L. The results showed that there were regional differences in the distribution of action potentials and Itoin rat epicardial, mid-cardial and endocardial ventricular myocytes. APDs were prolonged and Itocurrent densities were gradually reduced with the increase of DHA concentrations.ConclusionThe anti-arrhythmia mechanisms of DHA are complex, however, the effects of DHA on action potentials and Itomay be one of the important causes.
Functioning and health in patients with cancer on home-parenteral nutrition: a qualitative study
Authors: Mueller Martin , Lohmann Stefanie , Thul Paul , Weimann Arved , Grill Eva 
Published: April 2010

Abstract

Background
Malnutrition is a common problem in patients with cancer. One possible strategy to prevent malnutrition and further deterioration is to administer home-parenteral nutrition (HPN). While the effect on survival is still not clear, HPN presumably improves functioning and quality of life. Thus, patients' experiences concerning functioning and quality of life need to be considered when deciding on the provision of HPN. Currently used quality of life measures hardly reflect patients' perspectives and experiences. The objective of our study was to investigate the perspectives of patients with cancer on their experience of functioning and health in relation to HPN in order to get an item pool to develop a comprehensive measure to assess the impact of HPN in this population.

Methods
We conducted a series of qualitative semi-structured interviews. The interviews were analysed to identify categories of the International Classification of Functioning, Disability and Health (ICF) addressed by patients' statements. Patients were consecutively included in the study until an additional patient did not yield any new information.

Results
We extracted 94 different ICF-categories from 16 interviews representing patient-relevant aspects of functioning and health (32 categories from the ICF component 'Body Functions', 10 from 'Body Structures', 32 from 'Activities & Participation', 18 from 'Environmental Factors'). About 8% of the concepts derived from the interviews could not be linked to specific ICF categories because they were either too general, disease-specific or pertained to 'Personal Factors'. Patients referred to 22 different aspects of functioning improving due to HPN; mainly activities of daily living, mobility, sleep and emotional functions.

Conclusions
The ICF proved to be a satisfactory framework to standardize the response of patients with cancer on HPN. For most aspects reported by the patients, a matching concept and ICF category could be found. The development of categories of the component 'Personal Factors' should be promoted to close the existing gap when analyzing interviews using the ICF. The identification and standardization of concepts derived from individual interviews was the first step towards creating new measures based on patients' preferences and experiences which both catch the most relevant aspects of functioning and are sensitive enough to monitor change associated to an intervention such as HPN in a vulnerable population with cancer.
Advanced moderately differentiated neuroendocrine carcinoma of the rectum with favorable prognosis by postoperative chemoradiation
Authors: Nojima Hiroyuki , Seike Kazuhiro , Kosugi Chihiro , Shida Takashi , Koda Keiji , Oda Kenji , Kamata Shigeyuki , Ishikura Hiroshi , Miyazaki Masaru 
Published: April 2010

Abstract
Rectal neuroendocrine carcinoma is rare with poor prognosis. We report herein a case of advanced moderately differentiated neuroendocrine carcinoma of the rectum with relatively favorable prognosis treated by postoperative adjuvant chemoradiation therapy. A 58-year-old Japanese female was referred and colonofiberscopy revealed an easy-bleeding irregular tumor in the lower rectum, which was pathologically diagnosed as a neuroendocrine carcinoma. Surgical treatment consisted of abdominoperineal resection and lymph node dissection. The tumor invaded deeply into perirectal tissues, and 9 of 11 lymph node metastases were observed. Immunohistochemically, chromogranin A showed diffuse and strong staining, and the MIB-1 labeling index was 18.3 ± 5.6, supporting the high proliferation of the tumor. Some nucleus of the tumor showed positive staining for p21/WAF1. A total dose of 46 Gy of radiotherapy was delivered with 800 mg of daily oral doxifluridine. At 5 years post-surgery, the patient demonstrated no clinical evidence of intrapelvic recurrence or distant metastases.
Postmastectomy locoregional recurrence and recurrence-free survival in breast cancer patients
Authors: Kheradmand Ali Arab , Ranjbarnovin Neda , Khazaeipour Zahra 
Published: April 2010

Abstract

Background
One essential outcome after breast cancer treatment is recurrence of the disease. Treatment decision is based on assessment of prognostic factors of breast cancer recurrence. This study was to investigate the prognostic factors for postmastectomy locoregional recurrence (LRR) and survival in those patients.

Methods
114 patients undergoing mastectomy and adjuvant radiotherapy in Cancer Institute of Tehran University of Medical Sciences were retrospectively reviewed between 1996 and 2008. All cases were followed up after initial treatment of patients with breast cancer via regular visit (annually) for discovering the LRR. Cumulative recurrence free survival (RFS) was determined using the Kaplan-Meier method, with univariate comparisons between groups through the log-rank test. The Cox proportional hazards model was used for multivariate analysis.

Result
The median follow up time was 84 months (range 2-140). Twenty-three (20.2%) patients developed LRR. Cumulative RFS rate at 2.5 years and 5 years were 86% (95%CI, 81-91) and 82.5% (95%CI, 77-87) respectively. Mean RFS was 116.50 ± 4.43 months (range, 107.82 - 125.12 months, 95%CI). At univariate and multivariate analysis, factors had not any influence on the LRR.

Conclusion
Despite use of adjuvant therapies during the study, we found a LRR rate after mastectomy of 20.2%. Therefore, for patients with LRR without evidence of distant disease, aggressive multimodality therapy is warranted.
Case-control study of disease determinants for non-typhoidal Salmonella infections among Michigan children
Authors: Younus Muhammad , Wilkins Melinda J , Davies Herbert D , Rahbar Mohammad H , Funk Julie , Nguyen Chau , Siddiqi Azfar-E A , Cho Seongbeom , Saeed Mahdi 
Published: April 2010

AbstractBackgroundInfections withSalmonellaserotypes continue to be a significant global public health problem. In addition to contaminated foods, several other sources contribute to infections withSalmonellaserotypes. We have assessed the role of socioeconomic factors, exposure to food, and environmental sources in the etiology of non-typhoidalSalmonellainfections in Michigan children.FindingsA case-control study among Michigan children aged ≤ 10 years was conducted. A total of 123 cases of children with laboratory-confirmedSalmonellainfections and 139 control children, who had not experienced symptoms of gastrointestinal illness during the month prior to the interviews, were enrolled. The cases and controls were matched on age-category (<1 year, 2-<6 years and 6-10 years). Data on socioeconomic status, food intake, and environmental exposures, were collected on the queried case and control subjects. After adjusting for race and household-income the final regression multivariable model revealed thatSalmonellainfections were significantly associated with attendance of a daycare center (adjusted matched odds ratio = 5.00, 95% CI: 1.51 - 16.58), contact with cats (MOR = 2.53, 95% CI: 1.14 - 5.88), and contact with reptiles (MOR = 7.90, 95% CI: 1.52 - 41.01), during the 3 days prior to the onset of child's illness.ConclusionsStudy results suggest that exposure to environmental sources may play an important role in sporadic infections withSalmonellaserotypes in children. Additional efforts are needed to educate parents and caretakers about the risk ofSalmonellatransmission to children from these sources.
The role of calcium signaling in phagocytosis
Authors: Nunes Paula , Demaurex Nicolas 
Published: April 2010

Abstract
This review focuses on the sequence of cellular events leading to calcium signals critical for phagosome maturation.
Immune cells kill microbes by engulfing them in a membrane-enclosed compartment, the phagosome. Phagocytosis is initiated when foreign particles bind to receptors on the membrane of phagocytes. The best-studied phagocytic receptors, those for Igs (FcγR) and for complement proteins (CR), activate PLC and PLD, resulting in the intracellular production of the Ca2+-mobilizing second messengers InsP3 and S1P, respectively. The ensuing release of Ca2+ from the ER activates SOCE channels in the plasma and/or phagosomal membrane, leading to sustained or oscillatory elevations in cytosolic Ca2+ concentration. Cytosolic Ca2+ elevations are required for efficient ingestion of foreign particles by some, but not all, phagocytic receptors and stringently control the subsequent steps involved in the maturation of phagosomes. Ca2+ is required for the solubilization of the actin meshwork that surrounds nascent phagosomes, for the fusion of phagosomes with granules containing lytic enzymes, and for the assembly and activation of the superoxide-generating NADPH oxidase complex. Furthermore, Ca2+ entry only occurs at physiological voltages and therefore, requires the activity of proton channels that counteract the depolarizing action of the phagocytic oxidase. The molecules that mediate Ca2+ ion flux across the phagosomal membrane are still unknown but likely include the ubiquitous SOCE channels and possibly other types of Ca2+ channels such as LGCC and VGCC. Understanding the molecular basis of the Ca2+ signals that control phagocytosis might provide new, therapeutic tools against pathogens that subvert phagocytic killing.
The myeloid 7/4-antigen defines recently generated inflammatory macrophages and is synonymous with Ly-6B
Authors: Rosas Marcela , Thomas Benjamin , Stacey Martin , Gordon Siamon , Taylor Philip R 
Published: April 2010

Abstract
The murine Ly-6B (7/4) alloantigen is differentially expressed by macrophages during the resolution phase of the inflammatory response and is a marker of macrophage turn-over.
This study aimed to identify the inflammation-associated 7/4-antigen, which is highly expressed on neutrophils, inflammatory monocytes, some activated macrophages, as well as on bone marrow myeloid-restricted progenitors. The high expression on inflammatory cells is suggestive of a role in inflammation and makes the 7/4-antigen a potential target for the manipulation of inflammatory cells. Consistent with this, the 7/4-antibody mediates specific depletion of 7/4-expressing neutrophils and monocytes. We have identified the 7/4-antigen as a 25- to 30-kDa GPI-anchored glycoprotein synonymous with the Ly-6B.2 alloantigen. We characterized the expression of Ly-6B during the inflammatory reaction induced by zymosan. During the later stages of an experimental, acute, self-resolving inflammatory response, we found that Ly-6B is differentially expressed on macrophages. Ly-6B-expressing macrophages also express more MHCII, CIITA, CCR2, Ly-6C, and CD62L than the Ly-6B-negative macrophages, which in turn, express more of the resident tissue macrophage marker SIGN-R1 and higher CD11b and F4/80. Ly-6B-expressing macrophages incorporate more BrdU than their Ly-6B-negative contemporaries when fed during the resolution phase of the acute inflammatory response. Thus, Ly-6B expression on mature macrophages defines a subset of recently generated inflammatory macrophages that retain monocytic markers and is hence a surrogate marker of macrophage turnover in inflammatory lesions. The definition of the 7/4:Ly-6B antigen will allow further characterization and specific modulation of Ly-6B-expressing cells in vivo.
Functional heterogeneity and differential priming of circulating neutrophils in human experimental endotoxemia
Authors: Pillay Janesh , Ramakers Bart P , Kamp Vera M , Loi Adele Lo Tam , Lam Siu W , Hietbrink Falco , Leenen Luke P , Tool Anton T , Pickkers Peter , Koenderman Leo 
Published: April 2010

Abstract
Systemic inflammation results in release of refractory neutrophils which can cause susceptibility to infections and activates differentiated neutrophils, which can mediate tissue damage.
Neutrophils play an important role in host defense. However, deregulation of neutrophils contributes to tissue damage in severe systemic inflammation. In contrast to complications mediated by an overactive neutrophil compartment, severe systemic inflammation is a risk factor for development of immune suppression and as a result, infectious complications. The role of neutrophils in this clinical paradox is poorly understood, and in this study, we tested whether this paradox could be explained by distinct neutrophil subsets and their functionality. We studied the circulating neutrophil compartment immediately after induction of systemic inflammation by administering 2 ng/kg Escherichia coli LPS i.v. to healthy volunteers. Neutrophils were phenotyped by expression of membrane receptors visualized by flow cytometry, capacity to interact with fluorescently labeled microbes, and activation of the NADPH-oxidase by oxidation of Amplex Red and dihydrorhodamine. After induction of systemic inflammation, expression of membrane receptors on neutrophils, such as CXCR1 and -2 (IL-8Rs), C5aR, FcγRII, and TLR4, was decreased. Neutrophils were also refractory to fMLF-induced up-regulation of membrane receptors, and suppression of antimicrobial function was shown by decreased interaction with Staphylococcus epidermis. Simultaneously, activation of circulating neutrophils was demonstrated by a threefold increase in release of ROS. The paradoxical phenotype can be explained by the selective priming of the respiratory burst. In contrast, newly released, CD16dim banded neutrophils display decreased antimicrobial function. We conclude that systemic inflammation leads to a functionally heterogeneous neutrophil compartment, in which newly released refractory neutrophils can cause susceptibility to infections, and activated, differentiated neutrophils can mediate tissue damage.