Tag Archives: endophyte

Postdoc: Fungal Endophyte Genomics, U’Ren lab, U Arizona

Postdoc Position Fungal Endophyte Genomics • U’Ren lab

A postdoctoral position is available in the lab of Jana U’Ren at the University of Arizona to study the ecology and evolution of plant-endophyte symbioses. The project centers on enriching genomic, transcriptomic, and metabolomic knowledge of phylogenetically diverse endophytic fungi in collaboration with the DOE Joint Genome Institute. The start date is flexible, but anticipated to be in Fall/Winter 2018 or when the suitable candidate is identified. The position has an initial appointment for one year with a strong likelihood of extension to a second year pending performance review.

The ideal candidate will be skilled in bioinformatics, molecular biology, and microbiology with a background in plant-microbe interactions, ecology, and evolution. Minimum requirements: a PhD in ecology, evolutionary biology, microbiology, mycology, plant pathology, or a related discipline. Preference will be given to candidates with proficiency in both bioinformatics and molecular biology. Preferred candidates will have excellent communication skills, high motivation, and a strong willingness to work independently and as part of an integrative team. Potential duties include (but are not limited to) comparative genomic and transcriptomic analyses, functional trait assays, and plant inoculation experiments, with potential for the development of independent research projects related to plant-fungal interactions.

As part of the UA Ecosystem Genomics Initiative and the BIO5 Institute, the successful candidate will have extensive opportunities to collaborate across departments at UA, as well as with collaborators at other universities. This collaborative environment is conducive to development of a pathway to independence in academic research. The position also includes opportunities to mentor graduate and undergraduate researchers from diverse backgrounds.

Home to the world-class University of Arizona, Tucson is a vibrant southwestern city with a rich and distinctive heritage, fabulous access to outdoor activities, and diverse opportunities for cultural engagement. Outstanding UA benefits include health, dental, vision, and life insurance; paid vacation, sick leave, and holidays; UA/ASU/NAU tuition reduction for the employee and qualified family members; access to UA recreation and cultural activities; and more!

Applicants should submit a cover letter, CV, contact information for three references, and copies of three recent publications. All application materials should be submitted in a single email to Dr. Jana U’Ren (juren@email.arizona.edu).

PDF: Postdoc-URen-Lab-Arizona-2

Postdoc: Computational Transcriptomics. Massey University (NZ)

Postdoctoral Fellow in Computational Transcriptomics with Professor Barry Scott, Massey University, New Zealand

We are looking for a computational biologist with the necessary academic training and competency to analyse a large transcriptome data set generated from endophyte infected grass tissue. The project is collaborative with Professor Christopher Schardl at the University of Kentucky and Professor Murray Cox at Massey University. We are interested in identifying genes that are differentially expressed during the onset of stromata (sexual stage) development on the grass host. We have isolated RNA from different tissues of three different fungal-grass associations. We have gene models for the fungal components of all three associations but gene models for just one host. The post doc will be expected to develop their own hypotheses in analyzing this very large data set and work with a wider group working on the genomics, transcriptomics and functional analysis of fungal-grass associations. The analytical position requires solid quantitative and computational skills, with the ability to develop and apply new bioinformatics applications to the analyses.  At a minimum, some confidence in bioinformatics and a programming language is required. Training in fungal biology or genomics can be provided as needed, and candidates from non-standard research backgrounds with a clear fit to the position are encouraged to apply.

Funding is available for just one year from a research sub-contract with the Bioprotection Research Centre to Massey University. Salaries are competitive starting at $69,841 for step 1 of the post-doctoral scale.

The position will be based with Professor Barry Scott at Massey University in the city of Palmerston North.
Please email if you have any further questions: d.b.scott@massey.ac.nz

PDF of job ad: Post doc in computational biology

To submit an application, please provide:

  1.  A brief statement of research interests and experience, focusing on short to medium term
    career goals and your fit for this position
  2. Curriculum vitae, including qualifications and scientific publications
  3. The names and contact details of three referees willing to provide a confidential letter of recommendation upon request

Closing Date: to be readvertised

Purpose Statement: To carry out individual and team-based research on changes in gene expression associated with the onset of endophyte sexual development on grass hosts.

Responsible To: The Head of the Institute of Fundamental Sciences through Professor Barry Scott

Key Accountability Areas:
The Fellow is required to:

  • Undertake computational research on fungal transcriptomics
  • Undertake other relevant duties as specified and approved by the Principal Investigator
  • Maintain accurate and orderly records of experiments, procedures and code, and store these records and data in the laboratory group archive.
  • Report weekly to the Principal Investigator summarizing research progress and planned future research, with a focus on work towards research publications
  • Publish at least one peer-reviewed publication in an international scientific journal
  • Be familiar with Institute guidelines and rules for safety and approved practices in experimental work
  •  Maintain an organised and safe working environment
  • Be familiar with Institute guidelines and safety rules.
  • Participate fully in the academic activities of the Institute and the University
  • Provide two monthly written reports to the project leader that summarise research progress and planned future experiments with a focus on publications
  • Devote themselves full-time to University duties
  • Diligently and faithfully serve the University and use their best endeavours to promote and protect the interests of the University
  • Maintain confidentiality both during and after the appointment as Postdoctoral Fellow


Qualifications:  A PhD in bioinformatics, computational biology, or otherwise applicable field (interpreted broadly)

Miniumum Qualifications

  • Able to conduct independent cutting-edge research
  • Proven research experience, including evidence of a publication record
  • Quantitative skills, including some background in statistics and programming

Preferred Qualifications

  • Candidates will be conversant in at least one programming language (broadly defined)
  • Additional bioinformatics, computational and/or statistical experience would be an advantage
  • Candidates with a background in biology together with applied mathematics, physics or computer science are encouraged to apply
  • Some knowledge of biological systems

Attributes and Skills:

  • good quantitative skills
  • experimental and intellectual creativity
  •  initiative and enthusiasm
  • proven ability to write, and potential to take the lead on scientific publications
  • commitment to quality improvement, up-skilling and personal development
  • ability to organize and maintain quality records
  • integrity and confidentiality
  •  good time-management skills
  • ability to work as a member of a team

The superpowers of endophytes

New Scientist has an article entitled “Fungus-powered superplants may beat the heat” on how endophytic fungi from thermotollerant grass – Dichanthelium lanuginosum – can be used to improved drought-, salt-, and cold- tolerance of many other plants including rice. This symbiosis of the endophyte and grass also has additional player in the form of a mycovirus that infects the fungus which we’ve talked about before. The article doesn’t seem to reference any recently published papers but mainly the ongoing work for field trials and the application of these endophytes to speed the adaptations of the plants.

This complicated partnership is a fascinating example of the complex strategies that have evolved among these organisms as part of colonization of new niches. It is also quite likely, they are along for the ride in most plant systems and we are just now beginning to see their diversity and function.

Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

Continue reading Fungal Genetics 2007 details

Tripartate symbioses with fungi

Ants, fungi, and bacteria

I have to admit that I am fascinated by co-evolution of symbiotic and mutalistic systems. A review by Richard Robinson gives an overview. A great example is the mutalism between ants and fungi where the ants cultivate the fungi for food. There are more layers to the relationship as a fungal parasite (Escovopsis) attacks the cultivated fungi, and a bacteria. Several researchers have studied the coevolution of these studies including Ulrich Mueller and Cameron Currie. Currie and Mueller have published several great studies describing the patterns of coevolution and the nature of the cooperation.
Continue reading Tripartate symbioses with fungi