Pairwise Compatibility Graphs: A Survey

International audienceA graph $G=(V,E)$ is a pairwise compatibility graph (PCG) if there exists an edge-weighted tree $T$ and two nonnegative real numbers $d_{min}$ and $d_{max}$ such that each leaf $u$ of $T$ is a node of $V$ and there is an edge $(u,v) \in E$ if and only if $d_{min} \leq d_T (u, v) \leq d_{max}$, where $d_T (u, v)$ is the sum of weights of the edges on the unique path from $u$ to $v$ in $T$. In this article, we survey the state of the art concerning this class of graphs and some of its subclasses

The PHOENIX Exoplanet Retrieval Algorithm and Using H−^{-} Opacity as a Probe in Ultra-hot Jupiters

Atmospheric retrievals are now a standard tool to analyze observations of exoplanet atmospheres. This data-driven approach quantitatively compares atmospheric models to observations in order to estimate atmospheric properties and their uncertainties. In this paper, we introduce a new retrieval package, the PHOENIX Exoplanet Retrieval Analysis (PETRA). PETRA places the PHOENIX atmosphere model in a retrieval framework, allowing us to combine the strengths of a well-tested and widely-used atmosphere model with the advantages of retrieval algorithms. We validate PETRA by retrieving on simulated data for which the true atmospheric state is known. We also show that PETRA can successfully reproduce results from previously published retrievals of WASP-43b and HD 209458b. For the WASP-43b results, we show the effect that different line lists and line profile treatments have on the retrieved atmospheric properties. Lastly, we describe a novel technique for retrieving the temperature structure and $e^{-}$ density in ultra-hot Jupiters using H$^{-}$ opacity, allowing us to probe atmospheres devoid of most molecular features with JWST.Comment: 17 pages, 18 figures. Accepted for publication in A

CHIP_QC, COMPUTATIONAL PLATFORM FOR MULTIVARIATE EPIGENETIC STUDIES AND ITS APPLICATION IN UNCOVERING ROLE OF POLYCOMB DEPENDENT METHYLATIONS STATES

ABSTRACT During my PhD tenure, I have been involved in developing a user-friendly cross-platform system capable of analyzing epigenomic data and further use it in understanding the role of the Polycomb Repressive Complex 2 (PRC2) in genome regulation. From current trending in epigenetics research, we can sense increasing ease of high throughput sequencing and greater interest towards genome wide epigenomic studies. As a result of which we experience an exponential flooding of epigenetic related data such as Chromatin immunoprecipitation followed by sequencing (ChIP-seq), and RNA sequencing (RNA-seq) in public domain. This creates an opportunity for crowd sourcing and exploring data outside the boundaries of specific query centered studies. Such data has to undergo standard primary analysis, which with the aid of multiple programs has been stabilized courtesy to the scientific community. Further downstream, out of many, genome wide comparative, correlative and quantitative studies have proven to be critical and helpful in deciphering key biological features. For such studies we lack platforms, which can be capable of handling, analyzing and linking multiple interdisciplinary (ChIP-seq/RNA-seq) datasets with efficient analytical methods. With this aim we developed ChIP_QC, a user-friendly standalone computational program with an ability to support numerous datasets with high/moderate sequencing depth for performing genome wide analysis. First, using ENCODE project (Consortium, 2012) data, we illustrated few applications of the program by posing different biological scenarios and showed the comfort with which some known observations can be verified and also how it can be helpful in deducing some other novel observations. Second, we were interested in understanding the functionality of the products generated through catalytic activity of PRC2. It is known that Lysine 27 of histone H3 (H3K27) undergoes posttranslational modification (PTM) and methylation is one such dominant PTM. Methylation on H3K27 can be either mono/di/tri-methylation form. Out of all three forms, it is very well demonstrated that trimethylation of H3K27 (H3K27me3) is PRC2 dependent and at the same time its role in gene repression is well characterized, but functional roles of other forms of methylation on H3K27 are still poorly characterized. For understanding this, we used mouse embryonic stem cells (mESC) as model system of our study and we were able to provide an extensive characterization of other forms of methylation, highlighting their differential deposition along the genome, their fundamental role in transcriptional regulation, and their indispensability during differentiation program. Using ChIP_QC and with other computational methods along with experimental evidences, our data demonstrated that the monomethylation of Lys27 (H3K27me1) is required for correct transcription of genes and positively correlates with trimethylated Lys36 (H3K36me3); on the other hand dimethylated Lys27 (H3K27me2), that we identified to be the principal activity of PRC2, prevents firing of non cell type specific enhancers

Evolutionary genetics and human assisted movement of a globally invasive pest (Russian wheat aphid : Diuraphis noxia)

This PhD study has examined the population genetics of the Russian wheat aphid (RWA, Diuraphis noxia), one of the world’s most invasive agricultural pests, throughout its native and introduced global range. Firstly, this study investigated the geographic distribution of genetic diversity within and among RWA populations in western China. Analysis of mitochondrial data from 18 sites provided evidence for the long-term existence and expansion of RWAs in western China. The results refute the hypothesis that RWA is an exotic species only present in China since 1975. The estimated date of RWA expansion throughout western China coincides with the debut of wheat domestication and cultivation practices in western Asia in the Holocene. It is concluded that western China represents the limit of the far eastern native range of this species. Analysis of microsatellite data indicated high contemporary gene flow among northern populations in western China, while clear geographic isolation between northern and southern populations was identified across the Tianshan mountain range and extensive desert regions. Secondly, this study analyzed the worldwide pathway of invasion using both microsatellite and endosymbiont genetic data. Individual RWAs were obtained from native populations in Central Asia and the Middle East and invasive populations in Africa and the Americas. Results indicated two pathways of RWA invasion from 1) Syria in the Middle East to North Africa and 2) Turkey to South Africa, Mexico and then North and South America. Very little clone diversity was identified among invasive populations suggesting that a limited founder event occurred together with predominantly asexual reproduction and rapid population expansion. The most likely explanation for the rapid spread (within two years) from South Africa to the New World is by human movement, probably as a result of the transfer of wheat breeding material. Furthermore, the mitochondrial data revealed the presence of a universal haplotype and it is proposed that this haplotype is representative of a wheat associated super-clone that has gained dominance worldwide as a result of the widespread planting of domesticated wheat. Finally, this study examined salivary gland gene diversity to determine whether a functional basis for RWA invasiveness could be identified. Peroxidase DNA sequence data were obtained for a selection of worldwide RWA samples. Results demonstrated that most native populations were polymorphic while invasive populations were monomorphic, supporting previous conclusions relating to demographic founder effects in invasive populations. Purifying selection most likely explains the existence of a universal allele present in Middle Eastern populations, while balancing selection was evident in East Asian populations. Selection acting on the peroxidase gene may provide an allele-dependent advantage linked to the successful establishment of RWAs on wheat, and ultimately their invasion potential. In conclusion, this study is the most comprehensive molecular genetic investigation of RWA population genetics undertaken to date and provides significant insights into the source and pathway of global invasion and the potential existence of a wheat-adapted genotype that has colonised major wheat growing countries worldwide except for Australia. This research has major biosecurity implications for Australia’s grain industry