Domestication-driven metaorganism evolution in wheat

Plants are not standalone entities but colonized by an immense diversity of eukaryotic and prokaryotic microbes, collectively called the “plant microbiota”. In my PhD thesis, I studied the impact of domestication on the vertically-transmitted (i.e. seedborne) and environmentally-acquired microbial community assembly in the bread wheat Triticum aestivum and its wild progenitors. Furthermore, I disentangled factors shaping seedborne microbial variation in domesticated wheat. In my study, I improved and optimized techniques to increase the accuracy and resolution of amplicon-based sequencing of wheat seeds based on 16S rRNA and ITS marker loci for bacterial and fungal profiling, respectively. Using these techniques, I revealed that: i) Domestication may has conferred a strong role of stochastic processes in the assembly of vertical transmitting microbes, ii) Domestication has not affected the ability of the plant to assemble soil-derived microbial diversity in leaves and roots, iii) Intra- and inter-plant variation is comparable in seedborne microbial communities. This study is, to the best of my knowledge, the most comprehensive study analyzing wheat microbial communities spanning a wide collection of genotypes in details

Determining the origin of synchronous multifocal bladder cancer by exome sequencing

BACKGROUND: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours. METHODS: To better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients. RESULTS: Phylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC* dinucleotides (Fisher’s exact test p < 10(−41)), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC* type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10(−4)) suggesting that TpC* mutations largely occurred early in the development of the tumour. CONCLUSIONS: These results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-015-1859-8) contains supplementary material, which is available to authorized users

Ekzom dizileme yoluyla mesane kanseri evriminin araştırılması.

New genome sequencing technologies today allow the study of cancer evolution within individual tissues. In bladder cancer, it is commonly observed that multiple tumours co-occur in a tissue. However, whether these tumours are related (clonal hypothesis) or develop independently but synchronously (field effect hypothesis), was yet unknown. In this study, exome sequencing data was utilized to reveal the origin of multifocal tumours. The data was generated in an experiment where samples from bladder tumour (3 tumour samples per patient) and neighbouring normal mucosa (1 normal sample per patient) from 3 patients were collected and sequenced. The tumour samples were composed of apex and base sections of the tumours. Thousands of single nucleotide variants (SNV) were called in each patient. The phylogenetic trees constructed by SNV datasets of the 2 patients showed a topology consistent with clonal origin hypothesis, with a long shared tumour branch, indicating that the tumours derive from the same origin. The third patient's samples were suspected to be contaminated with neoplastic material, and thus not included in the rest of the analysis. An analysis of SNV types with respect to sequence context revealed that TpC* mutations were particularly enriched on the shared tumour branch, indicative of activity of APOBEC enzymes (single stranded DNA/RNA editing proteins) causing accumulation of TpC* mutations. Thus, it is hypothesized that a period of APOBEC activity led to accumulation of TpC* mutations, some of which included driver mutations that led to tumour formation, and subsequent separation of the tumours in 2 patients.M.S. - Master of Scienc

- Dinamik Ortamlarda Gerçek Zamanlı Görüntü Kullanarak Çoklu Robot Konum ve Bakış Açısı Belirleme

Yapay zeka ve robotik alanlarının birleştirilmesiyle ortaya çıkan RoboCup son yıllarda dünyada en çok ilgi çeken alanlardan biri olmuştur. Gerçek zamanlı ve doğru pozisyon tespiti, dinamik bir ortama sahip RoboCup için en önemli konuların başında gelmektedir.&nbsp; Bu projede, robot lokalizasyonu için derin öğrenme ve görüntü işleme yaklaşımının kullanımını araştırılmaktadır. Konvolüsyonel Sinir Ağları(CNN) ve obje tanımlama algoritmaları kullanılarak robotların pozisyon ve açı bilgilerine ulaşmayı amaçlanmaktadır. Çalışmanın ilk aşamasında görüntü işleme algoritmaları kullanılarak oyun sahası içindeki, farklı renklerdeki her bir robot ve topun pozisyon bilgilerine ulaşılacaktır. Ayrıca, farklı açı ve pozisyonlardaki robotların görüntüleri alınarak MATLAB ortamında derin öğrenme algoritmaları kullanılarak konvolüsyonel sinir ağı eğitilerek robot bakış açısı belirlenecektir. Bu çalışma oyun sırasında robotların yerini ve açısını futbol sahası üzerindeki bir kameradan olabildiğince hızlı ve doğru şekilde bulmayı amaçlamaktadır.&nbsp; RoboCup, which emerged by combining the fields of artificial intelligence and robotics, has been one of the most interesting areas in the world in recent years. Real-time and accurate position detection is one of the most important issues for RoboCup, which operates in a dynamic environment. This project explores the utilization of deep learning and image processing approaches for robot localization. It is aimed to determine the position and angle information of the robots by using Convolutional Neural Networks (CNN) and object detection algorithms. In the first stage of the study, the position information of each robot and ball, represented by different colors on the playing field will be obtained by using image processing algorithms. In addition, the robot perspective will be determined by capturing images of the robots from different angles and positions, and then training the CNN using deep learning algorithms in the MATLAB environment. This study aims to find the location and angle of the robots during the game from a camera on the football field as quickly and accurately as possible.</p

Enterosignatures define common bacterial guilds in the human gut microbiome

International audienceThe human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures.Temporal analysis implies that the Bacteroides-associated ES is “core” in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease

Yeni nesil moleküler veri analizi yoluyla genom ve transkriptom evriminin incelenmesi

Tüm genom dizileme verisi, genom çapında veya ekzom çapında polimorfizm verisi, mikrodizin ve RNA-dizileme verisi, GC-MS metabolit verisi gibi geniş çaplı moleküler veri setlerinin hesaplamalı analizi yoluyla uzun zamandır biyologları meşgul eden çok sayıda sorunun cevaplanması bugün mümkün hale gelmiştir. Araştırma grubumuzda genom ve transkriptom evrimi üzerine şu soruları gelecek yıl içinde cevaplayamaya çalışacağız:- Primatlar arasında testis transkriptomu niye ve nasıl evrilmektedir? - Türler arasında transkriptom farkları arasında en anlamlı olanlar nasıl tespit edilir?- Genom çapında kısa nükleotit homopolimerleri oluşturan mutasyonların insan popülasyonu içinde hızlı yayılmasının sebepleri nelerdir? - Yaşlanma sırasında metabolit ve gen ifadesi değişimlerinin sebepleri nedir?- Anadolu insan popülasyonunda Neandertal karışımı başka popülasyonlardan farklı olabilir mi?- Anadolu’da geçmiş göç örüntüleri nelerdir?- Mesane kanserinde görülen senkronize tümörler akraba mıdır

L'Écho : grand quotidien d'information du Centre Ouest

25 septembre 19261926/09/25 (A55).Appartient à l’ensemble documentaire : PoitouCh