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[PMID]: 29211796 [Au] Autor: Saison-Ridinger M; DelGiorno KE; Zhang T; Kraus A; French R; Jaquish D; Tsui C; Erikson G; Spike BT; Shokhirev MN; Liddle C; Yu RT; Downes M; Evans RM; Saghatelian A; Lowy AM; Wahl GM [Ad] Endereço: Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America. [Ti] Título: Reprogramming pancreatic stellate cells via p53 activation: A putative target for pancreatic cancer therapy. [So] Source: PLoS One;12(12):e0189051, 2017. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extremely dense fibrotic stroma, which contributes to tumor growth, metastasis, and drug resistance. During tumorigenesis, quiescent pancreatic stellate cells (PSCs) are activated and become major contributors to fibrosis, by increasing growth factor signaling and extracellular matrix deposition. The p53 tumor suppressor is known to restrict tumor initiation and progression through cell autonomous mechanisms including apoptosis, cell cycle arrest, and senescence. There is growing evidence that stromal p53 also exerts anti-tumor activity by paracrine mechanisms, though a role for stromal p53 in PDAC has not yet been described. Here, we demonstrate that activation of stromal p53 exerts anti-tumor effects in PDAC. We show that primary cancer-associated PSCs (caPSCs) isolated from human PDAC express wild-type p53, which can be activated by the Mdm2 antagonist Nutlin-3a. Our work reveals that p53 acts as a major regulator of PSC activation and as a modulator of PDAC fibrosis. In vitro, p53 activation by Nutlin-3a induces profound transcriptional changes, which reprogram activated PSCs to quiescence. Using immunofluorescence and lipidomics, we have also found that p53 activation induces lipid droplet accumulation in both normal and tumor-associated fibroblasts, revealing a previously undescribed role for p53 in lipid storage. In vivo, treatment of tumor-bearing mice with the clinical form of Nutlin-3a induces stromal p53 activation, reverses caPSCs activation, and decreases fibrosis. All together our work uncovers new functions for stromal p53 in PDAC. [Mh] Termos MeSH primário: Carcinoma Ductal Pancreático/terapia Reprogramação Celular Genes p53 Neoplasias Pancreáticas/terapia Células Estreladas do Pâncreas/metabolismo [Mh] Termos MeSH secundário: Animais Carcinoma Ductal Pancreático/metabolismo Carcinoma Ductal Pancreático/patologia Ésteres do Colesterol/metabolismo Seres Humanos Masculino Camundongos Camundongos Endogâmicos C57BL Camundongos Knockout Neoplasias Pancreáticas/metabolismo Neoplasias Pancreáticas/patologia Transcrição Genética Triglicerídeos/metabolismo Células Tumorais Cultivadas [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Cholesterol Esters); 0 (Triglycerides) [Em] Mês de entrada: 1712 [Cu] Atualização por classe: 180311 [Lr] Data última revisão: 180311 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171207 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0189051

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[PMID]: 29175453 [Au] Autor: Zhang Y; Lickteig AJ; Csanaky IL; Klaassen CD [Ad] Endereço: School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China. Electronic address: youcai.zhang@tju.edu.cn. [Ti] Título: Activation of PPARα decreases bile acids in livers of female mice while maintaining bile flow and biliary bile acid excretion. [So] Source: Toxicol Appl Pharmacol;338:112-123, 2018 01 01. [Is] ISSN: 1096-0333 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Fibrates are hypolipidemic drugs that act as activators of peroxisome proliferator-activated receptor α (PPARα). In both humans and rodents, females were reported to be less responsive to fibrates than males. Previous studies on fibrates and PPARα usually involved male mice, but little has been done in females. The present study aimed to provide the first comprehensive analysis of the effects of clofibrate (CLOF) and PPARα on bile acid (BA) homeostasis in female mice. Study in WT male mice showed that a 4-day CLOF treatment increased liver weight, bile flow, and biliary BA excretion, but decreased total BAs in both serum and liver. In contrast, WT female mice were less susceptible to these CLOF-mediated responses observed in males. In WT female mice, CLOF decreased total BAs in the liver, but had little effect on the mRNAs of hepatic BA-related genes. Next, a comparative analysis between WT and PPARα-null female mice showed that lack of PPARα in female mice decreased total BAs in serum, but had little effect on total BAs in liver or bile. However, lack of PPARα in female mice increased mRNAs of BA synthetic enzymes (Cyp7a1, Cyp8b1, Cyp27a1, and Cyp7b1) and transporters (Ntcp, Oatp1a1, Oatp1b2, and Mrp3). Furthermore, the increase of Cyp7a1 in PPARα-null female mice was associated with an increase in liver Fxr-Shp-Lrh-1 signaling. In conclusion, female mice are resistant to CLOF-mediated effects on BA metabolism observed in males, which could be attributed to PPARα-mediated suppression in females on genes involved in BA synthesis and transport. [Mh] Termos MeSH primário: Ácidos e Sais Biliares/metabolismo Bile/metabolismo Fígado/metabolismo PPAR alfa/fisiologia [Mh] Termos MeSH secundário: Animais Colesterol/metabolismo Colesterol 7-alfa-Hidroxilase/genética Clofibrato/farmacologia Feminino Íleo/metabolismo Camundongos Camundongos Endogâmicos C57BL [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, N.I.H., EXTRAMURAL [Nm] Nome de substância: 0 (Bile Acids and Salts); 0 (PPAR alpha); 97C5T2UQ7J (Cholesterol); EC 1.14.14.23 (Cholesterol 7-alpha-Hydroxylase); EC 1.14.14.23 (Cyp7a1 protein, mouse); HPN91K7FU3 (Clofibrate) [Em] Mês de entrada: 1801 [Cu] Atualização por classe: 180311 [Lr] Data última revisão: 180311 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171128 [St] Status: MEDLINE

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[PMID]: 29499665 [Au] Autor: Zhu Z; Zhang H; Yue J; Liu S; Li Z; Wang L [Ad] Endereço: People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, 450003, China. [Ti] Título: Antimicrobial efficacy of corneal cross-linking in vitro and in vivo for Fusarium solani: a potential new treatment for fungal keratitis. [So] Source: BMC Ophthalmol;18(1):65, 2018 Mar 02. [Is] ISSN: 1471-2415 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: BACKGROUND: Fungal keratitis is one of the major causes of visual impairment worldwide. However, the effectiveness of corneal collagen cross-linking (CXL) for fungal keratitis remains controversial. In this study, we developed an in vitro and an in vivo models to assess the efficacy of CXL for Fusarium keratitis. METHODS: The effect of in vitro CXL fungicidal was evaluated on the cultures of Fusarium solani which were exposed to irradiation for different durations. Viability of fungal was appraised under four conditions: no treatment (control); CXL: UVA (365 nm)/riboflavin; riboflavin and UVA (365 nm). Each batch of sterile plate culture was irradiated for different CXL durations. The in vivo Therapeutic effect was studied on a mouse keratitis model. The animals were divided randomly into three groups: group A with no treatment (control); Group B with CXL treatment for two minutes and group C with CXL treatment for three minutes. The CXL procedure was performed 24 h post inoculation in each group. All mice with corneal involvement were scored daily for 7 days and 10 days after infection. Corneals were extracted at various time points for quantitative fungal recovery. Histological evaluations were conducted to calculate the number of polymorphonuclear cells. RESULTS: Viability of fungal decreased significantly in CXL group with 30-min irradiation compared with that in control, riboflavin and UVA groups (P < 0.01). The colony-forming units (CFUs) of fungal solutions in culture significantly decreased with CXL treatment (P < 0.05). Clinical scores, corneal lesion, corneal opacity, neovascularization and the depth of ulceration scores in group B and group C were remarkably lower than that in group A (P < 0.05, P = 0.001, P = 0.001, P = 0.034 and P = 0.025 respectively). Scores of group C were much lower than that in group B. Histological revealed that destruction of corneal collagen fibers and infiltration of inflammatory cells into corneal tissue in group B and group C were much lower than that in group A. CONCLUSIONS: We believe that CXL treatment may be applied to fungal keratitis, therapeutic efficacy will improve with longer treatment duration. [Mh] Termos MeSH primário: Anti-Infecciosos/uso terapêutico Substância Própria/metabolismo Úlcera da Córnea/tratamento farmacológico Reagentes para Ligações Cruzadas Infecções Oculares Fúngicas/tratamento farmacológico Fusariose/tratamento farmacológico Fusarium/efeitos dos fármacos [Mh] Termos MeSH secundário: Animais Colágeno/metabolismo Contagem de Colônia Microbiana Úlcera da Córnea/metabolismo Úlcera da Córnea/microbiologia Modelos Animais de Doenças Infecções Oculares Fúngicas/metabolismo Infecções Oculares Fúngicas/microbiologia Fusariose/metabolismo Fusariose/microbiologia Fusarium/isolamento & purificação Masculino Camundongos Camundongos Endogâmicos C57BL Fármacos Fotossensibilizantes/uso terapêutico Riboflavina/uso terapêutico Raios Ultravioleta [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Anti-Infective Agents); 0 (Cross-Linking Reagents); 0 (Photosensitizing Agents); 9007-34-5 (Collagen); TLM2976OFR (Riboflavin) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180304 [St] Status: MEDLINE [do] DOI: 10.1186/s12886-018-0727-0

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[PMID]: 29484750 [Au] Autor: Saraswati S; Alhaider AA; Abdelgadir AM [Ad] Endereço: Camel Biomedical Research Unit, College of Pharmacy and Medicine, King Saud University, Riyadh, Saudi Arabia. [Ti] Título: Costunolide suppresses an inflammatory angiogenic response in a subcutaneous murine sponge model. [So] Source: APMIS;126(3):257-266, 2018 Mar. [Is] ISSN: 1600-0463 [Cp] País de publicação: Denmark [La] Idioma: eng [Ab] Resumo: Costunolide is known to possess anti-inflammatory and antitumor activity, but its role in tumor angiogenesis, the key step involved in tumor growth and metastasis, and the involved molecular mechanism is still unknown. We aimed to investigate the effects of costunolide on key components of inflammatory angiogenesis in the murine cannulated sponge implant angiogenesis model. Polyester-polyurethane sponges, used as a framework for fibrovascular tissue growth, were implanted in Swiss albino mice and costunolide (5, 10 and 20 mg/kg/day) was administered for 14 days through installed cannula. The implants collected at day 14 post-implantation were processed for the assessment of hemoglobin (Hb), myeloperoxidase (MPO), N-acetylglucosaminidase (NAG) and collagen, which were used as indices for angiogenesis, neutrophil and macrophage accumulation, and extracellular matrix deposition, respectively. Relevant inflammatory, angiogenic and fibrogenic cytokines were also determined. Costunolide treatment attenuated the main components of the fibrovascular tissue, wet weight, vascularization (Hb content), macrophage recruitment (NAG activity), collagen deposition, and the levels of vascular endothelial growth factor (VEGF), interleukin (IL)-1ß, IL-6, IL-17, tumor necrosis factor (TNF)-α and transforming growth factor (TGF-ß). Regulatory function of costunolide on multiple parameters of the main components of inflammatory angiogenesis has been revealed giving insight into the potential therapeutic benefit underlying the anti-angiogenic actions of costunolide. [Mh] Termos MeSH primário: Inibidores da Angiogênese/farmacologia Macrófagos/imunologia Neovascularização Patológica/imunologia Neutrófilos/imunologia Poliésteres/efeitos adversos Poliuretanos/efeitos adversos Sesquiterpenos/farmacologia [Mh] Termos MeSH secundário: Acetilglucosaminidase/metabolismo Animais Colágeno/metabolismo Citocinas/metabolismo Modelos Animais de Doenças Hemoglobinas/metabolismo Masculino Camundongos Peroxidase/metabolismo [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Angiogenesis Inhibitors); 0 (Cytokines); 0 (Hemoglobins); 0 (Polyesters); 0 (Polyurethanes); 0 (Sesquiterpenes); 4IK578SA7Z (costunolide); 9007-34-5 (Collagen); EC 1.11.1.7 (Peroxidase); EC 3.2.1.52 (Acetylglucosaminidase) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180228 [St] Status: MEDLINE [do] DOI: 10.1111/apm.12808

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[PMID]: 29431329 [Au] Autor: Belyaeva NN; Sycheva LP [Ti] Título: [Morphological comparative assessment of in vivo 2-week oral exposure of silver nanoparticles and silver sulfate on the mice liver]. [So] Source: Gig Sanit;95(9):899-902, 2016. [Is] ISSN: 0016-9900 [Cp] País de publicação: Russia (Federation) [La] Idioma: rus [Ab] Resumo: Currently the problem of the impact of nanoparticles and nanomaterials on human health remains to be poorly understood. As in our studies of the impact of silver nanoparticles on rats liver as well in works of other researchers there were investigated morphofunctional indices under peroral exposure. Although all researchers took different sizes, doses and concentrations of silver nanoparticles, various exposure time and different stabilizers, the same effects had been obtained, which, however, were occurred under both different doses and time of exposure. However, it was interesting to compare the impact of silver nanoparticles with reference substance - silver sulfate on the mice liver with the previously evaluated effect produced on the rats ' liver. By ourselves there was executed the morphological comparative evaluation of in vivo oral 2-weeks exposure of 4 concentrations (0.1; 5; 50 and 500 mg/l) of silver nanoparticles with size of 14 nm, stable arabian gum 1:7 by weight, and of 4 similar concentrations of silver sulfate on the liver of male mice СВÐ�хС57Ð’1/6 weighing 25-35g. 2 groups were considered as control: intact mice and mice received gum in water. Results of the exposure were assessed according to 10 morphological and functional indices. The impact of nanosilver was shown to initiate from its concentration of 50 mg/l and to express in the gain of the index of alteration of the cytoplasm of hepatocytes with the increasing in both severity of steatosis and the number of micronecroses, persisting at the same level at concentrations of 500 mg/l and with the elevation of the index of alteration of nuclei of hepatocytes, while the similar effect develops under the influence of silver sulfate at a concentration of 500 mg/l only. The remaining investigated morphofunctional indices did not differ significantly in all groups of mice. Unlike previously executed studies on rats, mice appeared to be sensitive to the effects of nano-silver more than to silver sulfate. [Mh] Termos MeSH primário: Doença Hepática Induzida por Substâncias e Drogas Fígado Gorduroso Fígado Nanoestruturas Compostos de Prata [Mh] Termos MeSH secundário: Administração Oral Animais Doença Hepática Induzida por Substâncias e Drogas/diagnóstico Doença Hepática Induzida por Substâncias e Drogas/etiologia Modelos Animais de Doenças Fígado Gorduroso/induzido quimicamente Fígado Gorduroso/patologia Células Hep G2 Seres Humanos Fígado/efeitos dos fármacos Fígado/patologia Camundongos Nanoestruturas/química Nanoestruturas/toxicidade Necrose Compostos de Prata/química Compostos de Prata/toxicidade Testes de Toxicidade/métodos [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Silver Compounds) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180213 [St] Status: MEDLINE

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[PMID]: 29414979 [Au] Autor: Takahashi H; Kozhuharova A; Sharma H; Hirose M; Ohyama T; Fasolo F; Yamazaki T; Cotella D; Santoro C; Zucchelli S; Gustincich S; Carninci P [Ad] Endereço: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan. [Ti] Título: Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation. [So] Source: PLoS One;13(2):e0183229, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest. [Mh] Termos MeSH primário: Biossíntese de Proteínas/genética Proteínas/genética RNA Longo não Codificante/genética [Mh] Termos MeSH secundário: Animais Linhagem Celular Tumoral Células HEK293 Seres Humanos Camundongos Fosforilação [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Proteins); 0 (RNA, Long Noncoding) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180208 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0183229

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[PMID]: 29412476 [Au] Autor: Bakela K; Dimakopoulou M; Batsou P; Manidakis N; Athanassakis I [Ad] Endereço: Laboratory of Immunology, Department of Biology, University of Crete, Heraklion, Crete, Greece. [Ti] Título: Soluble MHC class II-driven therapy for a systemic lupus erythematosus murine experimental in vitro and in vivo model. [So] Source: Scand J Immunol;87(3), 2018 Mar. [Is] ISSN: 1365-3083 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Taking into consideration the multiparametric nature of systemic lupus erythematosus (SLE), the severity and variability of symptoms and the lack of effective therapeutic approaches, this study took advantage of the recently described role of soluble major histocompatibility complex class II (sMHCII) molecules in maintaining tolerance to the organism and attempted to apply sMHCII proteins as a treatment to murine SLE experimental models in vitro as well as in vivo. After breaking tolerance to DNA in vitro, which was accompanied by development of specific anti-dsDNA antibodies, syngeneic or allogeneic sMHCII molecules, purified from healthy mouse serum, could significantly reduce the specific antibody levels and drive the system towards immunosuppression, as assessed by specific marker analysis on T cells and cytokine production by flow cytometry and ELISA, respectively. The in vivo experimental model consisted of pristane-induced SLE symptoms to BALB/c mice, which developed maximal levels of anti-dsDNA 2 months after pristane inoculation. Syngeneic or allogeneic sMHCII administration could alleviate pristane-induced symptoms, significantly decrease specific anti-dsDNA antibody production and develop immunosuppression to the host, as manifested by increase of CD4 + CTLA-4 +  and CD4 + CD25 +  cell populations in the spleen. Thus, the results presented in this study introduced the ability of sMHCII proteins to suppress specific autoantigen response, opening new areas of research and offering novel therapeutic approaches to SLE with expanding features to other autoimmune diseases. [Mh] Termos MeSH primário: Anticorpos Antinucleares/imunologia Autoantígenos/imunologia Antígenos de Histocompatibilidade Classe II/imunologia Tolerância Imunológica/imunologia Imunoterapia/métodos Lúpus Eritematoso Sistêmico/imunologia Lúpus Eritematoso Sistêmico/terapia Linfócitos T/imunologia [Mh] Termos MeSH secundário: Animais Antígenos CD4/metabolismo Antígeno CTLA-4/metabolismo Células Cultivadas DNA/imunologia Modelos Animais de Doenças Imunossupressão Subunidade alfa de Receptor de Interleucina-2/metabolismo Lúpus Eritematoso Sistêmico/induzido quimicamente Camundongos Camundongos Endogâmicos BALB C Baço/citologia Baço/imunologia Terpenos/efeitos adversos [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Antibodies, Antinuclear); 0 (Autoantigens); 0 (CD4 Antigens); 0 (CTLA-4 Antigen); 0 (Histocompatibility Antigens Class II); 0 (Il2ra protein, mouse); 0 (Interleukin-2 Receptor alpha Subunit); 0 (Terpenes); 26HZV48DT1 (pristane); 9007-49-2 (DNA) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180208 [St] Status: MEDLINE [do] DOI: 10.1111/sji.12644

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[PMID]: 29408856 [Au] Autor: Kimura-Suda H; Takahata M; Ito T; Shimizu T; Kanazawa K; Ota M; Iwasaki N [Ad] Endereço: Graduate School of Photonics Science, Chitose Institute of Science and Technology, Chitose, Hokkaido, Japan. [Ti] Título: Quick and easy sample preparation without resin embedding for the bone quality assessment of fresh calcified bone using fourier transform infrared imaging. [So] Source: PLoS One;13(2):e0189650, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Fourier transform infrared (FTIR) imaging is a powerful tool for the assessment of bone quality; however, it requires the preparation of thin bone sections. Conventional poly(methyl methacrylate) (PMMA) embedding for the preparation of sections takes more than two weeks and causes denaturation of the bone. Development of a quick and easy sample preparation technique without denaturation is needed for accurate clinical evaluation of fresh calcified bone using FTIR imaging. Frozen sectioning allows the quick and easy preparation of thin sections without denaturation, but it requires a substrate with good chemical resistance and improved heat shock resistance. Polypropylene (PP) film afforded both good chemical resistance and greater heat shock resistance, and the 4-µm-thick PP film coated with glue was thin enough for the IR beam to pass through it, while the optical anisotropy of infrared bands overlapping with PO43- band was negligible. The bone quality of femoral thin sections prepared by the conventional PMMA embedding and sectioning procedure (RESIN-S) or the newly developed frozen sectioning procedure (FROZEN-S) was evaluated by FTIR imaging. The mineral-to-matrix ratio and crystallinity in the RESIN-S sections were higher than those in the FROZEN-S sections, whereas the carbonate-to-phosphate ratio in the RESIN-S sections was lower than that in the FROZEN-S sections. In RESIN-S, the increased mineral-to-matrix ratio could be caused by dehydration, and the increased crystallinity and decreased carbonate-to-phosphate ratio might be consequence of dissolution of bone mineral during PMMA embedding. Therefore, the combined use of PP film coated with glue and the frozen sectioning procedure without denaturation appears well suited to the assessment of the bone quality of fresh calcified bone using FTIR imaging. [Mh] Termos MeSH primário: Osso e Ossos/diagnóstico por imagem Calcificação Fisiológica Espectroscopia de Infravermelho com Transformada de Fourier/métodos [Mh] Termos MeSH secundário: Alcenos Animais Camundongos Camundongos Endogâmicos BALB C Polimetil Metacrilato [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Alkenes); 9011-14-7 (Polymethyl Methacrylate); AUG1H506LY (propylene) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180207 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0189650

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[PMID]: 29391275 [Au] Autor: Yang X; Wang J; Bing G; Bie P; De Y; Lyu Y; Wu Q [Ad] Endereço: Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China. [Ti] Título: Ortholog-based screening and identification of genes related to intracellular survival. [So] Source: Gene;651:134-142, 2018 Apr 20. [Is] ISSN: 1879-0038 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival. Only 19 clusters were present in facultative intracellular pathogens, and not all were present in extracellular pathogens. Construction of a phylogenetic tree selected 18 of these 19 clusters. Comparisons with the DEG database and previous research revealed that seven other clusters are considered essential gene clusters and that seven other clusters are associated with intracellular survival. Moreover, this study confirmed that clusters screened by orthologs with similar function could be replaced with an approved uvrY gene and its orthologs, and the results revealed that the usg gene is associated with intracellular survival. The study improves the current understanding of intracellular pathogens characteristics and allows further exploration of the intracellular survival-related gene modules in these pathogens. [Mh] Termos MeSH primário: Bactérias/genética Fenômenos Fisiológicos Bacterianos Células/microbiologia Genes Bacterianos [Mh] Termos MeSH secundário: Animais Proteínas de Bactérias/genética Proteínas de Bactérias/fisiologia Células Cultivadas Genes Essenciais Interações Hospedeiro-Patógeno Camundongos Família Multigênica Filogenia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (Bacterial Proteins) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180203 [St] Status: MEDLINE

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[PMID]: 29389989 [Au] Autor: Almutairy M; Torng E [Ad] Endereço: Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America. [Ti] Título: Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches. [So] Source: PLoS One;13(2):e0189960, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. [Mh] Termos MeSH primário: Biologia Computacional [Mh] Termos MeSH secundário: Animais Genoma Humano Sequenciamento de Nucleotídeos em Larga Escala Seres Humanos Camundongos Modelos Teóricos [Pt] Tipo de publicação: COMPARATIVE STUDY; JOURNAL ARTICLE [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180309 [Lr] Data última revisão: 180309 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180202 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0189960

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