Host: Prof. Arnab Pain
 
Abstract:
In this presentation, I’ll describe some aspects of the biology of microbes that we can only discover from population genomics. I’ll start with the fission yeast Schizosaccharomyces pombe, a powerful model for molecular and cellular biology. In contrast to the budding yeast, we knew very little about the diversity, ecology or evolution of the species until very recently. I’ll introduce what little is known about the ecology of this yeast (1), and then describe three of my studies of genome diversity and function. In our initial study of genomic and phenotypic diversity, we describe population structure, date the dispersal of the species and show that genome-wide association studies are feasible in this species (2). I’ll then describe our analysis of structural variation from short read and long read sequencing data (3, 4) demonstrating that copy number variants both contribute to heritable traits and are unstable, and that quantitative traits are explained by an ancient admixture event from two populations.
I’ll then show some recent analysis from the protozoan parasite Leishmania, the causal agent of Leishmaniasis, a neglected tropical disease that is present in 98 countries. I’ll describe our genome-wide association study in Leishmania infantum, which demonstrated that drug-resistance existed in the in the Brazil population prior to the application of the drug (5). Combining data from populations in Ethiopia (6), the Indian subcontinent (7), and our unpublished data from Brazil, I’ll show that Ethiopia is by far the most genetically diverse, so is most likely the oldest population of the three. With the dense resolution of this data, we observe that all populations contain complex sub-populations, and that genetic diversity in Indian and Brazilian populations has been differentially affected by demographic change. Finally, I’ll describe our efforts to detect balancing selection in Leishmania as an indicator of host-parasite interactions.
References
1. D. C. Jeffares, The natural diversity and ecology of fission yeast. Yeast. 35, 253–260 (2017).
2. D. C. Jeffares et al., The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nature Genetics. 47, 235–241 (2015).
3. D. C. Jeffares et al., Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 8, 14061 (2017).
4. S. Tusso et al., Ancestral admixture and structural mutation define global biodiversity in fission yeast. bioRxiv, 415091 (2018).
5. J. B. T. Carniellia et al., A Leishmania infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis. EBioMedicine. 36, 83–91 (2018).
6. A. Zackay et al., Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. PLoS Genet. 14, e1007133 (2018).
7. H. Imamura et al., Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife. 5, 56 (2016).

Biography:
Daniel Jeffares began his research career with a PhD in plant molecular biology and genomics, publishing evolutionary biology articles as a hobby. After a postdoctoral research position in Copenhagen working with evolutionary genomics, he studied evolutionary and population genomics of the malaria parasite Plasmodium at the Wellcome Trust Sanger Institute. He then moved to University College London, where he initiated the study of genetic diversity and quantitative traits in the model fission yeast as a senior research fellow. He is currently a lecturer at the University of York, where he is focusing on the population genomics of the protozoan parasite Leishmania infantum, the causal agent of visceral Leishmaniasis.

Website: www.jeffareslab.org

PhD Advisor: Professor Christian Voolstra

Abstract:
Corals are cnidarian animals that build the founding structures of tropical reefs and which survival depends upon the obligate symbiotic association to photosynthetic dinoflagellate algae in the family Symbiodiniaceae. As corals are facing increasing environmental and anthropogenic stress, understanding the molecular principles governing this unique symbiotic association is crucial to predict their adaptive potential. Due to logistic, costly, and experimental difficulties of working with corals, we use the sea anemone Aiptasia (sensu Exaiptasia pallida) as a tractable model organism for the molecular study of cnidarian-algal symbiosis. A major advantage of Aiptasia is that it establishes a facultative symbiotic association with Symbiodiniaceae algae, that is, this anemone can be maintained in an aposymbiotic (symbiont-free) state, allowing for comparison of symbiotic and ‘control’ aposymbiotic processes. In this dissertation, a mass spectrometry (MS)-based phosphoproteomic approach was employed to unravel the phosphorylation-mediated protein signaling that characterizes the cnidarian-algal interaction. Given the novelty of this application in the field of coral reef biology, an extensive part of the thesis was dedicated to develop and optimize a protocol to elucidate the phosphoproteome of Aiptasia. Subsequently, protein phosphorylation across aposymbiotic and symbiotic Aiptasia was accurately quantified by DIA/SWATH-MS. More than a thousand of phosphoproteins were accurately quantified, and a distinct phosphoproteomic profile characterized symbiosis. Differential phosphorylation targeted various signaling pathways, some of which were not previously described in the context of cnidarian-algal symbiosis. Our results suggest a potentially relevant mechanism of phosphorylation-mediated control of the cnidarian-algal association.

Bio:
Fabia is a molecular biologist with 5+ years of experience in protein research applied to different fields of Life Sciences, ranging from medical to environmental research. Fabia holds a B.Sc. degree in biology & biochemistry and a M.Sc. degree in human biology from the University of Zurich (UZH), Switzerland. Her M.Sc. thesis aimed to define the interaction between the Leucine-rich repeat kinase 2 (LRRK2), a kinase mutated in patients with late onset Parkinson’s disease, the intestinal phosphate transporter NaPi2b, and the regulation of the vitamin D3 signaling. Given her passion for marine life, Fabia pursued a Ph.D. in Biosciences at the Red Sea Research Center in KAUST, where she applied her knowledge in molecular biology to the study of coral reefs, and particularly to investigate the vital interaction that corals maintain with their algal endosymbiotic partners. To this end, Fabia employed a mass spectrometry-based phosphoproteomic approach to unravel the phosphorylation-mediated protein signaling that characterizes the coral-algal interaction.

​Advisor: Professor Takashi Gojobori
 
Abstract:
Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the energy industries around the world because it causes a huge economic loss due to not only frequent replacements of the parts of pipelines and tanks but also potential damage of the entire fields of crude oil. Current studies have revealed that corrosions are generated mainly by microbial activities and they are now called as Microbial Influenced Corrosion (MIC) or simply bio-corrosion. Bacterial species actually causing bio-corrosion is crucial information for the suppression of the corrosion.
To diagnose and give proper treatment to pipelines in industrial plants, it is essential to identify the bacterial species responsible for bio-corrosions. For this aim, I conducted an analysis of the microbial community at the corrosion sites in pipelines of oil plants, using the comparative metagenomic analysis along with bioinformatics and statistics. 
In this study, I examined two types of oil fields, one uses seawater as an injection water, and the other uses ground water. Both fields are suffering from bio-corrosions.
First, I collected samples from the seawater pipelines that are essential in the oil fields to maintain seawater injection system (field#1), and then I conducted the metagenomic analysis of these samples. The metagenomes obtained revealed that samples in both sites contain a wide range of bacterial taxa.  However, the comparative analysis of the microbial community with statistics between corrosion-happning and corrosion-not-happning sites revealed the presence of   microorganisms whose abundances were significantly higher in sites with corrosion . Some of these microbes can be sulfate reducers and sulfur oxidizers of which are considered to be casual agents in recent bio-corrosion models. 
In addition to the seawater pipelines, I also collect samples from corrosion sites in oil pipelines at Field #1. My metagenomic analysis combined with statistics showed that several microorganisms are speculated to be very active at the corrosion sites in the oil pipeline. Although biological mechanisms of forming bio-corrosion in the oil pipelines still remain unclear, these microbial species are suggested to be some of the responsible bacteria for bio-corrosion in the oil pipelines.
Besides seawater injection systems, groundwater injection systems are often used, especially in inland oil fields. Therefore, more detailed understanding of bio-corrosion in the groundwater injection system is also required in oil industries. In the present studies, I then analyzed the microbial communities in pipelines in the oil field where groundwater is used as injection water (field #2). I collected samples from six different facilities in the field #2. Metagenome analysis revealed that microbial community structures were largely different even among samples from the same facility. Treatments such as biocide and demineralization at each location in the pipeline may affect the microbial communities independently. The results indicated that microbial inspection throughout the pipeline network is important to protect industrial plants from bio-corrosions.  
Identifying the bacterial species responsible to bio-corrosion, this study provides us with information on bacterial indicators that will be available to classify and diagnose bio-corrosions.  Furthermore, these species may be available as biomarkers to detect the events of bio-corrosion at an early stage. Then, any appropriate care such as the appropriate choice of biocides can be taken immediately and appropriately.  Thus, my study will provide a platform for obtaining microbial information related to bio-corrosion that enables us to obtain a practical approach to protect them from bio-corrosion.
 

​Host: Prof. Arnab Pain  
 
Abstract:
The Scherf laboratory has made several seminal discoveries that contribute to the complex process of antigenic variation (monoallelic expression of the multigene varfamily encoding surface adhesive antigens). This includes the identification a long ncRNA gene family (GC-rich ncRNA) that acts as a trans-activator of the monoallelic var expression site in the nuclear periphery. We discovered histone H3 N-terminal clipping by a nuclear protease that targets 5’UTR of DNA replication genes. Furthermore, we discovered a new DNA modification called 5’hydroxymethylcytosine (5’hmC) and show that 5hmC is the dominant DNA modification in P. falciparum. We reveal that the P. falciparum epi-transcriptome is methylated at unprecedented high levels and show it’s implication in the mRNA half-life. We also discovered the role of a nuclear chromatin-associated RNase II in gene regulation of var genes as a novel type of posttranscriptional regulator.
 
Biography:
Prof. Artur Scherf received a PhD at the University of Cologne, Institut für Genetik (1987) and moved to the Institut Pasteur in Paris to study malaria parasites. He is an international leader in malaria parasite epigenetics in the Department of Parasite and Insect Vectors (https://research.pasteur.fr/fr/team/biology-of-host-parasite-interactions/). He has made seminal contributions to monoallelic expression of virulence genes in the human malaria parasite Plasmodium falciparum and has pioneered the CRISPR Cas9 system for this pathogen, an essential genome editing tool for introducing point mutations and gene inactivation. He has coordinated a European Network of Excellence in Malaria (45 teams) and is the Scientific Director of a French National Parasitology LabEx Consortium on parasitology (http://www.labex-parafrap.fr/en/). The research activities of the different teams in his laboratory are based on the red blood cell stage of P. falciparum life cycle that is responsible for all clinical symptoms and for the transmission of the disease via the Anopheles mosquito. The team has established skills in Molecular Biology, Cell Biology, Pharmacology and humanized mouse models to develop exciting fundamental research projects and develop translational aspects to combat this pathogen

​Host: Professor Arnab Pain

Abstract:

One aspect of malaria biology that has been associated with severity of disease has been the ability of erythrocytes infected with Plasmodium falciparum to adhere to the endothelial cells lining the small blood vessels (and also within the placenta).  Several endothelial receptors are able to mediate this binding, but studies on patient isolates have identified a subset of these are being important in the field.  Our research has focussed on one of the major receptors, intercellular adhesion molecule 1 (ICAM-1) and uses live endothelium as a model of the interactions taking place in vivo, as recent studies have indicated that disease severity may be linked to the ability of parasites to adhere to multiple receptors.  The group's work has extended into an analysis of post-adhesive effects on both the parasite and the host endothelium.
As well as wishing to understand the molecular processes underpinning sequestration in malaria, we are also carrying out work on clinical correlation of specific types of adhesion with severe disease and the differential distribution of variant populations of parasites in the body due to receptor tropism.  Our main goal is an understanding of the pathology of adhesion-based pathology in malaria and, thereby, the development of novel anti-disease therapeutics.

Biography:

Alister Craig graduated in Genetics from Edinburgh University in 1981 and obtained his PhD in Molecular Biology from Leicester University in 1984.  He spent the next two years as an EMBO Fellow at EMBL in Heidelberg followed by two years as an ICRF Fellow in London working on developing techniques for genome analysis.  He subsequently worked for ten years at the Institute of Molecular Medicine in Oxford on malaria before joining the Liverpool School of Tropical Medicine (LSTM) in 1999. Prof. Craig is a former member of the Wellcome Trust Funding Panel/ Expert Review Group (Pathogen Biology and Disease Transmission) and Scientific Advisory Committee for the European Vaccine Initiative. Currently, he serves as the Dean of Biological Sciences in LSTM.

​Host: Professor Daniele G. Daffonchio

Abstract:
Hot deserts cover around a fifth of the Earth's terrestrial surface and models predict their overall expansion with climate change. In these extreme environments, where the presence of plants and animals is limited, microbial communities are essentials as they dominate and drive most of nutrient biogeochemical cycling. Using the Namib Desert of south western Africa as a model hot desert ecosystem, this presentation will (i) give an overview on the state of desert microbial ecology research, (ii) illustrate how we employed various meta-omics approaches (-genomics, -transcriptomics and -proteomics) to challenge long-lasting microbial ecology paradigms and (iii) show how drones can be used in desert microbial ecology studies.
 
Bio:
Dr. Jean-Baptiste Ramond obtained his PhD in 2008 from the Université de Rouen in France. He has since been working in South Africa: as a post-doctoral research fellow from 2009 til 2012 at the Institute for Microbial Biotechnology and Metagenomics of the University of the Western Cape and since 2013 as a research fellow at the Centre for Microbial Ecology and Genomics of the University of Pretoria. Using ‘omics’ technologies, he is interested in better understanding the adaptation of microbial communities to extreme environmental conditions and climate change; particularly in hot deserts.