A mutagenicity and cytotoxicity study on Limonium effusum aqueous extracts by Allıum, ames and MTT tests

Nowadays plants or plant extracts have become very important for alternative medicine. Plants and their extracts have many therapeutical advantages but some of them are potentially toxic, mutagenic, carcinogenic and teratogenic. Root, stem and leaf parts of Limonium effusum were used in this study and this species is an endemic species for Turkey. Mutagenic and cytotoxic effects of root, stem and leaf aqueous extracts were observed with Allium, Ames and MTT tests. Allium root growth inhibition test and mitotic index studies showed that aqueous extracts have dose-dependent toxic effects. Chromosome aberration studies indicated that especially sticky chromosome, anaphase-telophase disorder and laggard chromosome anomalies were highly observed. Ames test performed with Limonium effusum root aqueous extracts, showed weak mutagenic effects in Salmonella typhimurium TA98 strain with S9. MTT test based on mitochondrial activity indicated that most of the aqueous extracts have cytotoxic effects. This study aimed to determine the possible mutagenic and cytotoxic effects of L. effusum aqueous extracts by using bacterial, plant and mammalian cells. This research showed that some low concentrations of the L. effusum extracts have inhibited cytotoxic effects but high concentrations have induced cytotoxicity. On the other hand only a weak mutagenic activity was identified by Ames test with TA98 S9(+).В настоящее время растения или экстракты растений стали очень важными для альтернативной медицины. Растения и их экстракты имеют много терапевтических преимуществ, однако некоторые из них являются потенциально токсичными, мутагенными, канцерогенными и тератогенными. Корни, стебли и листья Limonium effusum, эндемичного вида Турции, были изучены в этой работе. Мутагенные и цитотоксические эффекты водных экс-трактов корней, стеблей и листьев Limonium effusum были изучены с помощью Allium-теста, теста Эймса и МТТ-теста. Тест на ингибирование роста корней лука и определение митотического индекса показали, что водные экстракты имеют дозозависимый токсичный эффект. При изучении хромосомных аберраций обнаружено большое количество таких аномалий, как слипшиеся хромосомы, нарушения анафазы-телофазы и отставшие хромосомы. Тест Эймса, проведенный на водных экстрактах корней Limonium effusum, показал слабо выраженный мутагенный эффект по отношению к Salmonella typhimurium, штамм TA98 с S9. МТТ-тест, основанный на митохондриальной активности, показал, что большинство экстрактов имели цитотоксические эффекты. Цель этого исследования изучить возможные мутагенные и цитотоксические эффекты водных экстрактов L. effusum с использованием бактериальных, растительных клеток и клеток млекопитающих. Определенные низкие концентрации экстрактов L. effusum ингибировали цитотоксические эффекты, а высокие концентрации индуцировали цитотоксичность. Слабая мутагенная активность была определена только при помощи теста Эймса с TA98 S9(+)

DRISEE overestimates errors in metagenomic sequencing data

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.]

Gut microbes contribute to variation in solid organ transplant outcomes in mice

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 6 (2018): 96, doi:10.1186/s40168-018-0474-8.Solid organ transplant recipients show heterogeneity in the occurrence and timing of acute rejection episodes. Understanding the factors responsible for such variability in patient outcomes may lead to improved diagnostic and therapeutic approaches. Rejection kinetics of transplanted organs mainly depends on the extent of genetic disparities between donor and recipient, but a role for environmental factors is emerging. We have recently shown that major alterations of the microbiota following broad-spectrum antibiotics, or use of germ-free animals, promoted longer skin graft survival in mice. Here, we tested whether spontaneous differences in microbial colonization between genetically similar individuals can contribute to variability in graft rejection kinetics. We compared rejection kinetics of minor mismatched skin grafts in C57BL/6 mice from Jackson Laboratory (Jax) and Taconic Farms (Tac), genetically similar animals colonized by different commensal microbes. Female Tac mice rejected skin grafts from vendor-matched males more quickly than Jax mice. We observed prolonged graft survival in Tac mice when they were exposed to Jax mice microbiome through co-housing or fecal microbiota transplantation (FMT) by gastric gavage. In contrast, exposure to Tac mice did not change graft rejection kinetics in Jax mice, suggesting a dominant suppressive effect of Jax microbiota. High-throughput sequencing of 16S rRNA gene amplicons from Jax and Tac mice fecal samples confirmed a convergence of microbiota composition after cohousing or fecal transfer. Our analysis of amplicon data associated members of a single bacterial genus, Alistipes, with prolonged graft survival. Consistent with this finding, members of the genus Alistipes were absent in a separate Tac cohort, in which fecal transfer from Jax mice failed to prolong graft survival. These results demonstrate that differences in resident microbiome in healthy individuals may translate into distinct kinetics of graft rejection, and contribute to interpersonal variability in graft outcomes. The association between Alistipes and prolonged skin graft survival in mice suggests that members of this genus might affect host physiology, including at sites distal to the gastrointestinal tract. Overall, these findings allude to a potential therapeutic role for specific gut microbes to promote graft survival through the administration of probiotics, or FMT.This work was supported by NIH/NIAID R01 AI115716 to MLA

Determination of the cold storage conditions of some apple cultivars

Bu araştırma 2000 2002 yıllan arasında Eğirdir Bahçe Kültürleri Araştırma Enstitüsü ve Süleyman Demirel Üniversitesi Ziraat Fakültesi Bahçe Bitkileri Bölümü Derim Sonrası Fizyoloji Laboratuvarında yürütülmüştür. Çalışmada M9 anacı üzerine aşılı Granny Smith, Imparatore ve Idared elma çeşitlerinin soğukta depolanma koşulları incelenmiştir. Uygun depolama koşulunu belirlemek için iki farklı zamanda derilen elmalar ilk yıl 0 oC ve % 90-95 nispi nem , ikinci yıl -1, 0 ve +2 oC sıcaklık ve yine % 90-95 nispi nem koşullarına sahip üç farklı soğuk odada 6 ay süreyle depolanmışlardır. Depolama boyunca birer ay aralıklarla depodan çıkartılan örneklerde ağırlık kaybı, meyve eti sertliği, suda çözünebilir kuru madde, titre edilebilir asitlik ve renk değerleriyle beraber fizyolojik ve patojen kaynaklı bozulmalar incelenmiştir. Deneme sonuçlarına göre Eğirdir ekolojisinde M9 anacı üzerinde yetiştirilen Granny Smith, Imparatore ve Idared elma çeşitlerinin 0 oC sıcaklık ve % 90-95 nispi nem koşullarında 5-6 ay depolanabileceği saptanmıştır.This research was carried out at Horticulture Research Institute of Egirdir and Postharvest Physiology Lab. of Department of Horticulture, Faculty of Agriculture, University of Süleyman Demirel between 2000 and 20002. Storage conditions of apple varieties Granny Smith, Imparatore and Idared grafted on M9 rootstock were investigated. In order to determine the optimum storage condition, these varieties harvested two different stage were stored at 0 Ctemperature and 90-95%relative humidity in the first year, and at -1, 0 and +2 Cand 90-95% RHin the second year for 6 months. During the storage period, weight loss, fruit flesh firmness, total solible solid, titretable acidity, colorimeter values (L*, a*, b*) and physiological disorders of apples taken from storage by montly intervals were examined.According to the storage results, it is determined that Granny Smith, Imparatore and Idared apple varieties can be stored at 0 Ctemperature and 90-95%relative humidity for 5-6 months

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change

Componential coding in the condition monitoring of electrical machines Part 2: application to a conventional machine and a novel machine

This paper (Part 2) presents the practical application of componential coding, the principles of which were described in the accompanying Part 1 paper. Four major issues are addressed, including optimization of the neural network, assessment of the anomaly detection results, development of diagnostic approaches (based on the reconstruction error) and also benchmarking of componential coding with other techniques (including waveform measures, Fourier-based signal reconstruction and principal component analysis). This is achieved by applying componential coding to the data monitored from both a conventional induction motor and from a novel transverse flux motor. The results reveal that machine condition monitoring using componential coding is not only capable of detecting and then diagnosing anomalies but it also outperforms other conventional techniques in that it is able to separate very small and localized anomalies

Environment-Induced Changes in Selective Constraints on Social Learning During the Peopling of the Americas

The weaponry technology associated with Clovis and related Early Paleoindians represents the earliest well-defined evidence of humans in Pleistocene North America. We assess the technological diversity of these fluted stone points found at archaeological sites in the western and eastern halves of North America by employing statistical tools used in the quantification of ecological biodiversity. Our results demonstrate that the earliest hunters in the environmentally heterogeneous East used a more diverse set of points than those in the environmentally homogenous West. This and other evidence shows that environmental heterogeneity in the East promoted the relaxation of selective constraints on social learning and increased experimentation with point designs

A20 Prevents Inflammasome-Dependent Arthritis by Inhibiting Macrophage Necroptosis Through Its ZnF7 Ubiquitin-Binding Domain

Deficiency in the deubiquitinating enzyme A20 causes severe inflammation in mice, and impaired A20 function is associated with human inflammatory diseases. A20 has been implicated in negatively regulating NF-κB signalling, cell death and inflammasome activation; however, the mechanisms by which A20 inhibits inflammation in vivo remain poorly understood. Genetic studies in mice revealed that its deubiquitinase activity is not essential for A20 anti-inflammatory function. Here we show that A20 prevents inflammasome-dependent arthritis by inhibiting macrophage necroptosis and that this function depends on its zinc finger 7 (ZnF7). We provide genetic evidence that RIPK1 kinase-dependent, RIPK3-MLKL-mediated necroptosis drives inflammasome activation in A20-deficient macrophages and causes inflammatory arthritis in mice. Single-cell imaging revealed that RIPK3-dependent death caused inflammasome-dependent IL-1β release from lipopolysaccharide-stimulated A20-deficient macrophages. Importantly, mutation of the A20 ZnF7 ubiquitin binding domain caused arthritis in mice, arguing that ZnF7-dependent inhibition of necroptosis is critical for A20 anti-inflammatory function in vivo