Infectious Disease ‘Omics Course

Short course 18th-20th Sept at London School of Hygiene & Tropical Medicine.

Venue

LSHTM, London

Dates

18-20th Sept 2017

More information

https://www.lshtm.ac.uk/study/cpd/pathgen.html

Infectious diseases, such as HIV-AIDS, malaria, pneumonia and tuberculosis, account for 25% of global mortality and more than half of all deaths in children under the age of five years. The genetic epidemiology of these diseases can be complex, especially as they may involve several genomes, including the host, pathogen(s) and a vector. There is also a need to look beyond the genome to consider other ‘omes, such as the transcriptome, in a more systems biology framework.

High throughput genotyping and sequencing technologies are providing insights into these genomes, metabolomes, transcriptomes and proteomes, thereby revolutionising genetic epidemiological studies and biomedical research. The use of SNP chips in large-scale genome-wide studies of association and genic selection has revolutionized the study of human disease susceptibility. Whole genome studies of pathogens using high throughput sequencing technologies is leading to the ability to track microbial evolution over time and space, as well as identify variants correlated with phenotypes such as anti-microbial resistance. Further, RNAseq methodologies are being used to measure transcript abundance and differential gene expression across isolates.

To take full advantage of new ‘omic technologies requires the ability to analyse large amounts of data using methods from bioinformatics, population genetics and statistics – the focus of this course. Specifically, this course offers hands-on experience of processing sequencing data to construct genomes, identifying genomic variants and applying downstream methods, such as phylogenetics. Further, the course covers transcriptomic and proteomic analysis in human and pathogen settings. High profile examples, including malaria, TB and MRSA, will be used to illustrate the concepts, and there is a strong emphasis on how to implement the methods in practice, with the majority of sessions computer-based.

Anaerobic protists: Integrating parasitology with mucosal microbiota and immunology

Newcastle upon Tyne, 31 August – 03 September 2017.  The central theme of the event will be: "Integrating parasitology with mucosal microbiota and immunology".

Venue

Newcastle upon Tyne, UK

Dates

31st Aug - 3rd Sept 2017

More information

The specific objectives of this EMBO Conference (ICAP VI) are to:

  1. Promote information sharing and support the advancement of research by bringing together researchers with common interests on mucosal microbial parasites, including stimulating collaborations between parasitologists and between parasitologists and mucosal microbiologists and immunologists
  2. Support outstanding junior investigators in the field and promote international communication and collaborations
  3. Promote collegial interactions, open discussion and sharing of methodologies among researchers working on mucosal parasites including parasite interactions with the microbiota and the mucosal immune system.

The central theme of the event will be: "Integrating parasitology with mucosal microbiota and immunology". Two sessions will be dedicated to this theme and complemented by additional talks from other sessions. These two sessions will cover parasites of respectively the digestive and the urogenital tracts, two important cites where health and disease states are increasingly recognised as being influenced by complex interplay between the mucosal immune system, microbial eukaryotes, bacteria and viruses.

Other sessions will cover the most recent development on mucosal parasite genomics and molecular cell biology. Upon completion of the event participants will be able to:

  • Identify major players and pathways in host responses to mucosal microbial parasites
  • Define the term "immunobiome"
  • Generate novel hypotheses for mechanisms driving parasite adaptation to the host human-microbiota environment

Considered parasites will include: Trichomonas, Giardia, Entamoeba, Dientamoeba, Microsporidia, Cryptosporidium and related species.

See: http://meetings.embo.org/event/17-anaerobic-protists

 

ICIM-4 International Congress on Invertebrate Morphology

The 4th International Congress on Invertebrate Morphology (ICIM4) will be held 18 – 23 August 2017 in Moscow, Russia.

Venue

Moscow, Russia

Dates

18th - 23rd Aug 2017

More information

ICIM 4 is devoted to actual questions and the most important achievements in the field of invertebrate morphology; to a wide range of scientific problems including the synthesis of classical morphology with advances in molecular taxonomy and phylogeny; to evolutionary developmental biology; to investigations on the structure of different groups of invertebrates; to the problem of miniaturization and the evolution of larval forms; and to modern achievements in the field of functional morphology and paleontology. Special attention will be paid to modern approaches and methods of morphological and evolutionary studies.

Congress symposia could be assigned to four major fields

(1) Recent advances in functional morphology;

(2) Special invertebrate morphology;

(3) Evolutionary theories;

(4) Advanced Microscopy and Morphology.

The congress will be hosted by Lomonosov Moscow State University (MSU), which is a perfect venue for this scientific society to gather, discuss and share ideas. The building of the Biological Department located directly on the MSU campus will open its gates to students, scientists and professors from all over the world. See website: http://www.icim4.com/

Call for papers for ‘Microbial Genomics’ journal

Microbial Genomics, a new journal published by the Microbiology Society, is seeking submissions in the area of parasitology.

Microbial Genomics is a new, fully open access and open data journal published by the Microbiology Society. The journal invites papers that use genomic approaches to understand parasite evolution, population genomics and phylogeography, outbreaks and epidemiological investigations, impact of climate or changing niche, metagenomic and whole transcriptome studies, and bioinformatic analysis. All article processing charges have been waived during the journal’s launch period, meaning that it is now free to publish. For more information please see the Microbial Genomicswebsite.

BSP Council member Bonnie Webster features in NHM video on schistosomiasis control

Dr Webster’s work is featured in the video: ‘Detective work to tackle debilitating disease in Zanzibar’.

In this video, Dr Bonnie Webster and Dr Anouk Gouvras explain how Natural History Museum scientists are helping to eliminate one of the most prevalent parasitic diseases in Africa: schistosomiasis.

‘It was a bit of a detective story to work out why it occurs in the north part of the island and not in the south,’ says Dr Gouvras.

The parasitic disease is carried by aquatic snails. It causes a host of devastating problems for the 250 million people affected worldwide, from painful urination and stunted growth in childhood, to irreversible damage of vital organs.

The Museum team used their taxonomic expertise to identify the culprit and treat the affected areas in a targeted way.

BSP Travel Award recipient Ciaran McCoy

A field report from Iowa, funded by a BSP International Training and Fieldwork Award

Field of Dreams

Is this heaven?... No, it's Iowa”

The primary focus of my PhD is the development of a reverse genetic platform within the model animal parasitic nematode, Ascaris suum.  Due to the emergence of drug resistance, the future prevention and treatment of animal parasitic nematode infections depend upon the development of novel control options.  RNA interference (RNAi) can facilitate the elucidation of gene function and validation of novel drug targets.

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Induction of RNAi responses in animal parasitic nematodes has proven difficult; however in adult Ascaris suum all of the genes targeted to date appear to be susceptible to RNAi.  Despite this we have not observed any crude phenotypes (motility defects or death) following statistically significant, systematic and reproducible gene knockdown, suggesting that we may have to employ a more sensitive post-RNAi assay to detect the phenotypic effects of gene knockdown.

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Ciaran with collaborators

I have been very fortunate to visit the labs of Prof. Richard Martin and Dr. Alan Robertson at Iowa State University (ISU) in the pursuit of an elusive post-RNAi phenotype.  The work completed at ISU was based largely on the employment of a highly sensitive electrophysiology-based post-RNAi assay.  As we do not have access to this specialised equipment here in Belfast, my trip to Iowa has made it possible for us to accurately quantify the responsiveness of individual nematode muscle cells to a range of nicotinic agonists following the knockdown of nicotinic acetylcholine receptor subunits.  During the three months that I spent I Iowa I also had the opportunity to dabble in a little tissue specific expression analysis and assess antihelmintic responses in Xenopus oocytes expressing nematode nicotinic acetylcholine receptor subunits.  The data associated with this study are currently being analysed and we hope to publish the results in the near future. (Fingers crossed).

Extracurricular activities included occasional in pub scientific debates, Independence Day celebrations and a (self-funded) trip to New York and Boston prior to my return home.  Despite the difficulties associated with a flooded kitchen, mangled worms, tornado warnings and vending-machine-derived dinners I feel that the trip was very productive and highly enjoyable.

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During my stay in Iowa I have learnt a range of new techniques, produced a substantial electrophysiology-based dataset, which will form the basis of a PhD thesis chapter, and made several new friends and potential future collaborators.  I would like to thanks the British Society of Parasitology for facilitating my visit to ISU and my host lab for their hospitality and good company.

Blog post by Ciaran McCoy, Queen’s University Belfast

Several BSP student members have recently benefitted from the BSP International Training and Fieldwork awards. For further details please see the linkhttp://bsp.uk.net/awards-grants/international-training-and-fieldwork-award/

BSP travel award Sabrina Lamour

Read Sabina Lamour's field report from Côte d’Ivoire, funded by a BSP International Training and Fieldwork Award

My Field Trip in Côte d’Ivoire (October 2013)

“J’ai trouvé l’amour!” (I have found love!)

Never before has my surname (Lamour) been used in so many puns as in my month-long trip to Côte d’Ivoire: from catering staff to professors, everyone seemed to enjoy shouting my name whenever I entered a room (“l’amour” literally means “the love” in French). Jokes aside though, I have thoroughly enjoyed my trip to the Ivory Coast – so different to my life in London…

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Two years into my PhD in Clinical Medicine at Imperial College London, my work so far has been based on laboratory research on experimental models of tropical parasitic infections, accompanied by heavy amounts of statistical analyses. I often joke that the most “exotic” travels for my PhD so far have been my brief trips to Cardiff where I was working on mouse poop! Whilst my project work has been highly rewarding, I had yet to experience the clinical side of the disease areas I work in and longed for the chance to engage and help patients face-to-face. As luck would have it, an excellent opportunity presented itself through long-standing collaborators of my supervisor at the “Swiss Tropical and Public Health Institute” (Swiss TPH), to visit the “Centre Suisse de Recherches Scientifiques en Côte d’Ivoire” (CSRS) and help out in nearby hospitals. So off I went!

Following minor hiccups on the first few days of my stay (including multiple flight delays and “digestive adjustments” to the local food), I spent the first week participating at the “EcoHealth Africa 2013 Conference” in Grand Bassam, organised by CSRS. I was intrigued and interested at the different perspectives and approaches presented by African researchers. Research here appeared to be strongly driven by local public’s concerns, often directly engaging with communities, health workers and sanitation engineers, during project planning and implementation of interventions. There was a strong focus on working collectively across different disciplines in order to ultimately ameliorate human health as well as that of animals and the environment – highlighted in their conference declaration (which I helped translate into English), available online at : http://www.csrs.ch/actualites.php?id=113

Furthermore, there was a great interest in using endogenous public knowledge, especially with regards to medical plants and herbs, in the quest to find alternative treatments for infectious diseases of people as well as of livestock.

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Professor Adou Yao and I, announcing the Declaration of the EcoHealth Conference Africa 2013,
Grand Bassam, Côte d’Ivoire

After briefly visiting the research facilities at the CSRS in Adipo Doume (outside of Abidjan city), I spent the majority of my stay working at the Methodist Hospital of Dabou town, around 40 minutes drive west from the CSRS. Following introductory visits to the different departments, I assisted staff at the clinical laboratory where I performed multiple diagnostic tests, including microscopic examination of stool samples for gastro-intestinal parasitic cysts, eggs and worm detection, various biochemical analyses (e.g. measuring fasting glucose levels in serum) and performing immunological tests, e.g. testing for presence of anti-Salmonella typhi antibodies for typhoid fever diagnosis. Although the laboratory had malaria rapid diagnostic test strips available, the workers preferred relying on blood smear tests (which I spent a lot of my time doing whilst working there, shown in photo) as they thought this method was more reliable, was able to give a measure of parasitic burden (as opposed to simply presence/absence of Plasmodia infection), and was much cheaper (especially as they could re-use glass slides). I also performed HIV tests, full blood counts and tested patient blood types (as well as my own which I never knew until then!). This was the first time that I was able to experience the day-to-day activity of what goes on in a hospital lab that deals with patients having tropical diseases – notably HIV, malaria, TB, and typhoid which represented the large bulk of infectious diseases – that I’ve learnt much about at university but never got to see face-to-face: it was a highly rewarding experience.

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Dabou Clinical Lab: Staining blood smear slides with Giemsa dye for microscopic detection of Plasmodia

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Dabou Clinical Lab: Determining my own blood type via blood antibody-antigen agglutination tests

In addition to working in a town hospital, I was able to visit and assist in a more rural setting, in the clinical lab of Taabo General Hospital (about 2 hours drive further inland from Abidjan city). Here I was immediately struck by the much more limited resources of both the hospital and the local community, which consisted of the small town of Taabo surrounded by neighbouring villages. Poverty and illiteracy were serious issues that limited many of the locals to access health care services. The clinical tests available at Taabo laboratory were similar to that of Dabou hopsital, though on a much smaller scale. Furthermore, the few patients that arrived at the hospital often presented with serious inflictions (e.g. systemic organ problems linked to malnourishment) which to me appeared completely novel but unfortunately for the hospital staff, were in fact quite common. Taabo was definitely much more of an eye-opener to the many problems faced by rural communities in low-income countries such as Côte d’Ivoire.

Upon my return, I have since written a short observational report on clinical diagnostics in Côte d’Ivoire, using both Dabou and Taabo hospitals as case studies. This is now publicly available on my Imperial College Blog site at:http://wwwf.imperial.ac.uk/blog/sabrinalamour/2013/11/11/clinical-diagnostics-report/

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Me and clinical staff at Taabo Hospital Clinical Laboratory

When I wasn’t cooped up working in the labs or at the conference I did my best to explore the area, e.g. travelling in crammed mini-buses with locals, shopping at the vibrant markets, eating street-food (whilst trying my best to turn a blind-eye to some of the sanitary conditions of the food preparation), visiting some of the nearby beaches on the weekends (absolutely beautiful!), and conversing with fellow students about life in Ivory Coast, under the trees with random lizards and goats passing by…

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Local market in Adiopo Doume, near the CSRS

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Abidjan City (Plateau district) and Slums just outside Abidjan

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Fellow workers at Dabou hospital lab teaching me how to carry a bucket of water on my head

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Local mini-bus (with goats on the roof!)

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Weekend trip to beautiful Assinie Mafia Beach and Scenery around Taabo river dam

I would take this opportunity to give great thanks to both the British Society for Parasitology (BSP) and the Medical Research Council (MRC) for sponsoring this field trip where I have learnt so much – both professionally and personally. Thank you for all your support, I’m so grateful for being given such an opportunity to have a truly valuable experience. I would do it again and recommend anyone else interested to visit Africa to go see the Ivory Coast.

- Sabrina

 

Sabrina Lamour

Postgraduate student, Section of Computational and Systems Medicine, Department of Surgery & Cancer, Imperial College London

http://www.imperial.ac.uk/people/sabrina.lamour10

 

More than 9 BSP student members have recently benefitted from the BSP International Training and Fieldwork awards. For further details please see the link