115 research outputs found
Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics.
No full textThe growth of all microorganisms is limited to a specific temperature range. However, it has not previously been determined to what extent global protein profiles change in response to temperatures that incrementally span the complete growth temperature range of a microorganism. As a result it has remained unclear to what extent cellular processes (inferred from protein abundance profiles) are affected by growth temperature and which, in particular, constrain growth at upper and lower temperature limits. To evaluate this, 8-plex iTRAQ proteomics was performed on the Antarctic microorganism, Methanococcoides burtonii. Methanococcoides burtonii was chosen due to its importance as a model psychrophilic (cold-adapted) member of the Archaea, and the fact that proteomic methods, including subcellular fractionation procedures, have been well developed. Differential abundance patterns were obtained for cells grown at seven different growth temperatures (-2°C, 1°C, 4°C, 10°C, 16°C, 23°C, 28°C) and a principal component analysis (PCA) was performed to identify trends in protein abundances. The multiplex analysis enabled three largely distinct physiological states to be described: cold stress (-2°C), cold adaptation (1°C, 4°C, 10°C and 16°C), and heat stress (23°C and 28°C). A particular feature of the thermal extremes was the synthesis of heat- and cold-specific stress proteins, reflecting the important, yet distinct ways in which temperature-induced stress manifests in the cell. This is the first quantitative proteomic investigation to simultaneously assess the response of a microorganism to numerous growth temperatures, including the upper and lower growth temperatures limits, and has revealed a new level of understanding about cellular adaptive responses
Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part II: the effect of different methylated growth substrates
No full textMethanococcoides burtonii is a cold-adapted methanogenic archaeon from Ace Lake in Antarctica. Methanol and methylamines are the only substrates it can use for carbon and energy. We carried out quantitative proteomics using iTRAQ of M. burtonii cells grown on different substrates (methanol in defined media or trimethylamine in complex media), using techniques that enriched for secreted and membrane proteins in addition to cytoplasmic proteins. By integrating proteomic data with the complete, manually annotated genome sequence of M. burtonii, we were able to gain new insight into methylotrophic metabolism and the effects of methanol on the cell. Metabolic processing of methanol and methylamines is initiated by methyltransferases specific for each substrate, with multiple paralogs for each of the methyltransferases (similar to other members of the Methanosarcinaceae). In M. burtonii, most methyltransferases appear to have distinct roles in the metabolism of methylated substrates, although two methylamine methyltransferases appear to be nonfunctional. One set of methyltransferases for trimethylamine catabolism appears to be membrane associated, potentially providing a mechanism to directly couple trimethylamine uptake to demethylation. Important roles were highlighted for citrate synthase, glutamine synthetase, acetyl-CoA decarbonylase/synthase, and pyruvate synthase in carbon and nitrogen metabolism during growth on methanol. M. burtonii had only a marginal response to the provision of exogenous amino acids (from yeast extract), indicating that it is predisposed to the endogenous synthesis of amino acids. Growth on methanol appeared to cause oxidative stress in the cell, possibly through the formation of reactive nonoxygen species and formaldehyde, and the oxidative inactivation of corrinoid proteins, with the cell responding by elevating the synthesis of universal stress (Usp) proteins, several nucleic acid binding proteins, and a serpin. In addition, changes in levels of cell envelope proteins were linked to counteracting the disruptive solvent effects of methanol on cell membranes. This is the first global proteomic study to examine the effects of different carbon sources on the growth of an obligately methylotrophic methanogen
Domuz Gribi: Durum Kuş Gribinden Tehlikeli
No full textİnfluenza A virüslerinin evriminde korkulan gerçekleşiyor mu
Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation
Full text link© 2016 Jugder, Ertan, Bohl, Lee, Marquis and Manefield.Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed
Patolojik tanısı belirsiz sitoloji olan tiroit nodüllerinde yeni nesil dizi analizi tabanlı hedefe yönelik somatik mutasyon analizi
Full text linkTıp Fakültesi, Tıbbi Genetik A.B.D. Araştırma ProjesiAraştırma Projesi elektronik ortamda bulunmaktadır.Amaç: Tiroit nodülleri toplumda yaygın görülen bir sorunu temsil eder. Saptanan tiroit nodüllerine yaklaşımda en önemli aşama malignite riskinin tespitidir. Bunun için hastaya ait risk faktörleri, fizik muayene, ultrasonografi gibi nodüle ait ipuçlarının toplanması gereklidir. İİAB, nodüllerin sitopatolojik incelemesine olanak sağlar. Sitopatolojik olarak belirsiz grupta kalan nodüllere yaklaşım klinik pratikteki önemli zorluklardan birini oluşturur. Bu örneklerin moleküler profillemesi son dönemde öne çıkan seçeneklerdendir. Çalışmamızda belirsiz sitolojiye sahip nodüllerin moleküler analizi yapılarak; klinik pratikte malign-benign ayrımına katkı sağlaması ve klinik yönetime yardımcı olacak belirteçlerin araştırılması hedeflenmiştir. Gereç ve Yöntem: Çalışmamıza 20 adet belirsiz sitolojiye sahip tiroit nodül aspirasyon örneği dahil edildi. Örnekler ameliyat kararı verilmiş hastalara aitti ve cerrahi patoloji sonucu mevcuttu. Örneklerin moleküler profillemesinde, 67 geni içeren bir yeni nesil dizileme paneli kullanıldı. Analiz sonuçları cerrahi patolojik veriler altın standart kabul edilerek kıyaslandı. Kullanılan yöntemin sensitivite, spesivite, PPV ve NPV değerleri belirlendi. Bulgular: Analiz sonucunda 20 örnekten 10 tanesinde 6 farklı gene (BRAF, NRAS, PTEN, TERT, PIK3CA, TP53) ait Tier 1 veya Tier 2 varyant saptandı. Çalışmaya dahil edilen 15 örneğin cerrahi patoloji sonucu malign, 5 örneğin ise benigndi. Malign patolojiye sahip örneklerin 10 tanesi tiroidin papiller karsinomu, 5 tanesi ise tiroidin papiller mikrokarsinomu idi. Bir hastaya lenf nodu metastazı eşlik etmekteydi (Evre IVA), bir hastanın tümör çapı 4 cm'den büyüktü (Evre III) ve bir hastanın ise 2.2 cm idi (Evre II). Varyant saptanan 9 hastanın patoloji sonucu malign, bir hastanın ise benigndi. Varyant saptanan hastaların yaş ortalaması 56 iken, varyant saptanmayan grubun 46 idi. Testte NPV: %40, PPV: %90, Spesivite: %60, Sensitivite: %80 olarak hesaplanmıştır. Sonuç: Tüm örneklere ait aspirasyon materyalinden elde edilen DNA çalışma için yeterli olmuştur. Elde edilen moleküler belirteçler ile en az 9 hastada İİAB girişimi tekrarı gerekmeden yönetim doğru şekilde yapılabilirdi. Çalışmada kullanılan test dahil etme testi (rule-in) olarak, özellikle 45 yaş üstü hastalarda, yararlı olabilir. Çalışma belirsiz sitolojiye sahip nodüllerin yönetiminde giderek geçerlilik kazanan moleküler testlerin, klinik pratikteki faydasının altını çizmektedir. Ülkemizdeki ilk çalışma olarak sonraki çalışmalara öncülük etmesi hedeflenmiştir.;İİAB; Tiroit Nodülü; Tiroit Kanseri; NGS.;FNAB; Thyroid nodules; Thyroid cancer, NGS
Thermostabilization of penicillin G acylase obtained from a mutant of Escherichia coli ATCC 11105 by bisimidoesters as homobifunctional cross-linking agents
No full textWe investigated the effects of three different bisimidoesters as homobifunctional cross-linking agents on the thermostabilization of penicillin G acylase (PGA) obtained from a mutant of Escherichia coli ATCC 11105. Cross-linkers were dimethyladipimidate (DMA), dimethylsuberimidate (DMS), and dimethyl-3,3'-dithiobispropionimidate (DTBP). The thermal inactivation mechanisms of the native and cross-linked PGA were both considered to obey first-order inactivation kinetics during prolonged heat treatment, forming fully active, susceptible transient stares. The efficacy of the cross-linkers on the thermostabilization of PGA was estimated to be DMA > DMS > DTBP. Optimal concentrations of DMA, DMS, and DTBP for cross-linking of PGA were found to be 0.5, 0.4, and 0.3% (w/v), respectively. The greatest enhancement of the thermostabilities was observed during DMA cross-linking, as a nearly 15-fold increase at temperatures above 50 degrees C. Cross-linking by DMA did not cause much change in the parameters V-m, K-m, and the optimal temperature values of PGA, but the activation energy of the enzyme was slightly decreased and k(cat) value slightly increased after cross-linking
Author Correction: Multiperiod Multi Traveling Salesmen Problem Considering Time Window Constraints with an Application to a Real World Case
No full textWOS: 000473179100002
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