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Graduate School of Life Sciences

Cancer, stem cells & developmental biology, research area.

Fundamental developmental processes are frequently affected in human disease. Many of the important genes and mechanisms controlling development also regulate adult physiology, and deregulation of these processes may result in pathological conditions. Our understanding of the genome (all genes) and the proteome (all proteins) is rapidly increasing, but the regulatory processes that shape our bodies and, when affected, cause diseases such as cancer, are still poorly understood and require fundamental research. Genomic and proteomic technologies have shaped a new area of research enabling us to monitor the expression of some 20,000 genes simultaneously and to monitor the presence and modifications of proteins. Bioinformatics has become a major aspect of modern biomedical research. In addition, microscopic analysis has witnessed a true revolution in the past few years.

The PhD programme Cancer, Stem Cells & Developmental Biology focuses on understanding processes underlying cancer and developmental biology using techniques and applications of post-genomic research, including genomics and transcriptomics (through next generation sequencing), proteomics, metabolomics and advanced microscopy techniques. PhD candidates in this programme explore research questions concerning embryonic growth, stem cells, signalling pathways, gene regulation, evolution and development in relation to health and disease using various model systems.

Associated research groups

All information regarding our researchers and research groups can be found at our website .

Profile of prospective PhD candidates

Prospective PhD candidates should have a Dutch or equivalent foreign MSc degree in life sciences (e.g. medicine, biomedical sciences, biology, chemistry). We expect PhD candidates to be highly motivated, talented and capable of working independently as well as in groups.

Mission of the training programme

The programme offers training programmes at both the Master’s and PhD level, which are frequently combined in joint courses and other activities so as to offer students a truly integrated research and educational programme with a natural progression from the Master’s to the PhD level. The aim of the programme is to offer research, training and education that builds on novel methodology in genomics, proteomics, metabolomics and bioinformatics technology applied to biomedical and developmental systems and processes. PhD candidates participate in the research lines of the participating groups, collaborating with their fellow PhD candidates and postdocs yet at the same time developing their own research project and expertise within the group that should lead to a series of articles and a PhD thesis to be defended in public before an expert committee. PhD candidates are encouraged to seek collaborations outside Utrecht and The Netherlands and to attend international workshops and meetings in addition to the course and seminar programme offered by the CS&D PhD programme.

Master’s students seeking a PhD position within CS&D are expected to be highly motivated to perform their thesis research in this field, as the programme aims to attract the most talented and motivated students in the life sciences from the Netherlands and abroad.

Training programme

Seminar series.

Every Thursday at 16.00 pm an invited (international) speaker presents a seminar on a topic relevant to the programme’s research programme. PhD candidates are expected to attend the seminars and engage in the discussion sessions. A seminar committee is responsible for the selection of high quality speakers. Both group leaders and PhD candidates are asked to send suggestions for speakers to the committee’s chairs.

Introductory course

All first-year PhD candidates participate in a one-day course aimed at introducing them to each other and the school’s research programme and organisation. The course consists of a theoretical part and visits at the organizing departments as an introduction to the practical aspects of the research performed by the affiliated research groups.

Specialized courses

Several specialized 1-10 day courses are organized every year or biannually on topics related to cancer, stem cells and developmental biology, but also on bioinformatics and various technologies.

Master class

Every year, a 2-day Master class is organized for all PhD candidates at a conference centre away from the lab. International leaders in the field of cancer, stem cells and developmental biology are invited to present their latest research and actively participate in workshops with the PhD students. The PhD award for the best publication of the year is announced during this Master class.

PhD candidate retreat

This 3-day meeting is organized yearly entirely by and for the PhD candidates. The programme’s PhD committee composes a programme consisting of seminars by the senior PhD candidates and poster presentations by the junior PhD candidates that are discussed between themselves without any interference from supervisors.

You can find the training programme including frecuencies and credits here  (pdf).

Programme organization

Programme director .

Prof. Boudewijn Burgering, PhD [email protected]

Programme coordinator

Eric Kalkhoven, PhD [email protected]

More information about this programme:

Mail to  [email protected]    Or visit www.csnd.nl

Utrecht University Heidelberglaan 8 3584 CS Utrecht The Netherlands Tel. +31 (0)30 253 35 50

Faculty of Science: Graduate Schools

Master's programmes, majors and minors, scholarships, cookie consent.

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Molecular genetic laboratory

DNA/RNA isolation

Every Sample, from plant and animal species to soil and water, requires a specific and optimized DNA/RNA isolation protocol. The same applies for tissue types and sample storage conditions. We not only use the popular DNA or RNA isolation kits but also the more “old school” protocols like 2%CTAB, TES buffers or hot phenol, that we can optimize and tweak for the highest quality of DNA/RNA possible.

For the cell lysis steps we use the Precellys24 or the Qiagen TissueLyser II. Furthermore, the lab is equipped with different centrifuges, cooled and non-cooled, swing-out and fixed-angle rotors, for the centrifugation of all size reactions vails and tubes.

To measure the DNA/RNA quantity and quality we use a wide variety of gel electrophoresis equipment plus two dedicated gel photo-documentation systems, the Syngene GeneGenius and VWR Imager2.  For the more precise measurements we have the Nanodrop-1000, Qubit and Implen NanoPhotometer N60 Touch.

Downstream analysis

For downstream analysis we have 4 Bio-Rad T100 Thermal cyclers. They are used for all possible PCR applications, from amplification of genomic regions of interest to cDNA synthesis and other enzymatic incubations. For gene expression experiment we have several systems

• two Quantitative Real-Time PCR Systems (qPCR)

• the ABI 7500 and the Bio-Rad CFX Connect

We also implemented new techniques like DNA sequencing from Oxford Nanopore Technologies for whole genome and microbiome sequencing, but also genetic modification techniques like CRISPR-Cas.

For CRISPR-cas9 experiments we have an Eppendorf Femtojet-4i that allows us to inject guide RNA in insect eggs. With this technique individual genes can be manipulated to study their effects on physiology and behaviour. There are 2 Biological Safety Cabinets and a large amount of climate chambers, climate cabinets and stoves for our genetic transformation and cell cultures

In the molecular biology we also have a Pamas SVSS-c, a Standard laboratory particle counter and a Partec Ploidy analyser for DAPI based DNA fluorescence used for plant cell ploidy measurements.

Organization

Three technicians are dedicated to molecular genetic analyses: Peter Kuperus, Betsie Voetdijk and Lin Dong. They assist in conducting molecular-genetic experiments using established protocols together with (and provided by) IBED PhD candidates, Postdoc researchers and staff members. Moreover, they regularly assist in a wide range of projects and courses of Bachelor and Master students.

Contact information

Please contact us if you are a permanent IBED staff member and you or your students are planning to undertake a project for which you need help on conducting molecular genetics: [email protected]

Lab Manager

[email protected] +31 (0)20 525 8357

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Wildlife, Fish and Conservation Biology

This concentration leads to both Master of Science (MS) and Doctor of Philosophy (PhD) degrees in Environmental Conservation (ECo) and is designed for students who want scientific training in the multi-disciplinary field of wildlife, fish and conservation biology. The focus of this concentration is broadly on animal ecology and conservation biology but encompasses specialized training in fields such as conservation genetics, population ecology and landscape ecology. The prime impetus for this concentration is the need for an adequate science base and professional training for decision-making regarding wildlife and fish resources.

Coursework and more detailed information  (pdf)

Concentration Description:

 Faculty affiliated with this concentration (see below) have expertise in vertebrate population ecology; endangered, threatened, and overabundant species; wetland and forest ecology; animal behavior and physiology; geographic information systems and remote sensing; aquatic toxicology; population dynamics and demographic modeling; and landscape and ecosystems ecology. A major strength of our program is the unique convergence of Universities, federal and state agencies in Amherst, unmatched in the Northeast. A series of cooperative agreements, memoranda of research understanding and sole-source vendor relationships with state and federal agencies provide a strong base of research funding. These agreements also provide important teaching and research relationships between our program and state and federal natural resource agencies. Wildlife research focuses on wetlands, biodiversity, animal habitat associations, landscape and systems ecology, remote sensing, human-wildlife conflicts, forest-wildlife relationships, and international conservation. Fisheries research focuses on marine, estuarine, and inland resources and specifically on population dynamics, relationship of ecosystem structure and production, the effect of organic and inorganic contamination on aquatic ecosystem function, and anadromous fish behavior, ecology and physiology. There are approximately 70 graduate students in the Wildlife, Fish and Conservation Biology Concentration. Through their research projects, graduate students often employ or provide volunteer opportunities for interested undergraduates (about 150 in the Wildlife and Fisheries Conservation concentration within the Natural Resources Conservation major). Graduate students are encouraged to participate in projects and activities of their colleagues to broaden their experience and to provide and receive ideas and suggestions for improvements.

At the MS level, students have the option of pursuing either a professional degree or thesis degree. The thesis/dissertation degree leads to the MS or PhD degree and centers around the completion of a major independent research project in addition to a modest coursework requirement. The professional degree leads to the MS degree and centers around a professional paper based on an internship/practicum in addition to a more substantial coursework requirement. Both degree options provide students a strong foundation in three core topic areas: environmental science (biology, ecology, conservation and environmental building systems), 2) quantitative science (statistics, GIS and modeling), and 3) human dimensions (environmental policies, economics, politics, administration, management and values). The MS thesis degree is intended to prepare students for the option of pursuing a PhD or a career in conservation science. The MS professional degree is meant to be a terminal degree for students seeking graduate-level training in a particular field of study and a career as a professional conservation scientist. Overall, the academic requirements of this concentration in combination with the research/practicum experience provide students the professional training for conservation science positions within academia, state and federal resource management agencies, nongovernmental conservation organizations, and private industry (e.g., environmental consulting firms). In addition, MS thesis degree students completing this program are well prepared to meet the challenges of any PhD program.

Course Offerings

The following courses are offered for partial fulfillment of the degree requirements (see below). Note, all courses ending in 90 and 97 have an additional letter designation (e.g., 697A) not specified below because it is subject to change; Please check the SPIRE online and department’s course offering sheet ( https://tinyurl.com/y7pz3uu2 )for the current course number listing.

1. Core Courses for the MS Thesis degree

• ECO 601 Research concepts (fall, 3cr)
• ECO 697 Analysis of environmental data - lecture (fall, 3cr)
• ECO 691A* Current research in env. conservation seminar (1cr)

2. Core Topic Areas for the MS degree

a. Environmental Science

• NRC 564 Wildlife habitat management (fall, 4cr)
• NRC 565 Wildlife population dynamics & management (fall, 4cr)
• NRC 570 Fish ecology (fall odd yrs, 4cr)
• NRC 571 Fisheries science & management (spr odd yrs, 4cr)
• NRC 581 Wetlands Assessment (spr odd yrs, 3cr)
• NRC 590AE Aquatic ecology (fall even yrs, 4 cr)
• NRC 590 Global change ecology (fall odd yrs, 3cr)
• NRC 590 Invasion ecology (fall even yrs, 3 cr)
• NRC 590 Restoration ecology (spring, 3cr)
• ECO 621 Landscape ecology (spr even yrs, 4cr)
• ECO 622 Conservation biology (spr odd yrs, 3cr)
• ECO 624 Diadromous fisheries ecology & conservation (fall, 3cr)
• ECO 697 Recreational fisheries science and management (fall odd yrs, 2cr)
• ECO 697 Urban wildlife ecology and management (spr even yrs, 4cr)
• ECO 757 Advanced fisheries management (spr odd yrs, 3cr)
• ECO 758 Advanced wildlife conservation (fall even yrs, 3 cr)
• ECO 768 Wetland ecology & conserv. (fall even yrs, 3cr)
• ECO 777 Advanced systems ecology (spr odd yrs, 3cr)

b. Quantitative Science

• NRC 577 Ecosystem modeling & simulation (fall even yrs, 3cr)
• NRC 585 Introduction to GIS (both, 4cr)
• NRC 587 Digital remote sensing (spr even yrs, 3cr)
• NRC 597 WebGIS (spr, 3 cr)
• ECO 632 Multivariate statistics for environmental cons. (spr odd yrs, 4cr)
• ECO 634 Analysis of environmental data - lab (fall, 2cr)
• ECO 697 Advanced topics in GIS (fall even yrs, 3cr)
• ECO 697 Applied biostatistics (spr, 4cr)
• ECO 697 Advanced statistics for env conservation (fall even yrs, 4cr)
• GEOG 668 GIS and Spatial Analysis (spr, 3 cr)
• PLSOIL 661 Intermediate biometry (fall, 3 cr)

c. Human Dimensions

• NRC 576 Water resources management & policy (fall, 3 cr)
• NRC 579 Cree culture, natural resources and sustainability (spr, 3 cr)
• NRC 590 Adapt. to climate change: theories, policy ... (spr even yrs, 3cr)
• ECO 690 Environmental conflict & collaborative policy (spr even yrs, 3cr)
• ECO 690 Public engagement and communication (spr even, 3cr)
• ECO 697 Federal environmental law & regulation (fall, 3 cr)
• ECO 697SV Design, Implementation, Analysis of Surveys of People (spr 3cr)
• REGIONPL 553 Resource policy & planning (spr even yrs, 3 cr)
• REGIONPL 575 Environmental law & resource management (spr, 3 cr)
• RES-ECON 720 Environmental & resource economics (fall even yrs, 3 cr)
• RES-ECON 721 Advanced natural resource economics (fall, 3 cr)
• GEO-SCI 666 Water resource policy (spr, 4 cr)
• POLSCI 784 Environmental policy (tbd, 3 cr)

The MS Professional Degree

Prerequisites.

Candidates for an MS professional degree in this concentration will be admitted on the basis of their academic training, work experience, and letters of recommendation. At a minimum, candidates will be expected to possess a Bachelor’s degree in:

• a natural resources field or environmental sciences; or
• the biological sciences with an emphasis in ecology; or
• any field with strong background in mathematics and the biological and physical sciences, and professional experience working as a natural resources professional.

Note, prerequisites exist for many of the required courses. Students are expected to have satisfied these prerequisites prior to commencing the program.

Requirements

Students in this concentration are expected to meet all the requirements for a MS degree in ECo, as outlined in the student handbook, including the following:

• Complete one semester of ECO 691A Current research in env. conservation seminar (1cr)
• A minimum of 30 credits is required, 29 of which must be in the major (defined broadly), 12 of which must be at the 600 level or above; up to 6 graduate credits can be transferred from previous course work from UMass or another university;
• Successful completion of a comprehensive exam based upon the student’s academic training in environmental conservation, encompassing three “core” topic areas (environmental science, quantitative science, and human dimensions) in addition to the required ECo core courses; and
• Successful final exam conducted by the committee.

The MS Thesis Degree

Prerequisites .

Candidates for an MS thesis degree in this concentration will be admitted on the basis of their academic training, work experience, and letters of recommendation. At a minimum, candidates will be expected to possess a Bachelor’s degree in:

MS thesis degree students in this concentration are expected to meet all of the requirements for an MS degree in ECo, as outlined in the student handbook, including the following:

• Core courses (see above): 7 credits.
• Core topic area courses: 17 credits in the major field (defined broadly), 8 of which must be at the 600 level or above, including a minimum of one 500-level or above 3- 4 credit course in each core topic area (see above). Note, students may take courses other than those listed above to fulfill the core topic area requirements, such as special topics courses that are offered irregularly, if they are approved by the students advisory committee. Note, up to 6 graduate credits can be transferred from previous course work from UMass or another university to fulfill these requirements.
• Thesis: 6 credits. All students in the MS thesis degree option are required to complete a thesis based on independent research as approved by the student's advisory committee.
• Successful completion of a comprehensive exam based upon the student’s academic training in environmental conservation, encompassing three “core” topic areas (core science, quantitative science, and human dimensions) in addition to the required ECo core courses.
• Successful final defense of the thesis.
• A minimum of one publishable-quality scientific paper resulting from the thesis research project.

The PhD Degree

Candidates for a PhD degree in this concentration will be admitted on the basis of their academic training, work experience, and letters of recommendation as evaluated by the faculty sponsor. At a minimum, candidates will be expected to possess:

• a Bachelor’s degree in:
• a natural resources field or environmental sciences; or 
• mathematics, statistics, or policy with some coursework in biological and physical sciences, or experience working as a natural resource professional.

*Note, students wishing to pursue a PhD with only a BS degree can choose to obtain a MS degree on the way to completion of Ph.D. degree requirements. MS is not a requirement.

Students in this concentration are expected to meet all of the requirements for a PhD degree in ECo, as outlined in the student handbook, including the following:

• A minimum of 10 dissertation credits is required, based on a research project specific to this concentration and approved by the student's advisory committee; no other course credits are required other than those determined by the student’s advisory committee.
• Complete two consecutive, full time semester residency
• Successful completion of a comprehensive exam based on the three “core” topic areas (environmental science, quantitative science, and human dimensions).
• Successful final defense of the dissertation.
• A minimum of three publication-quality dissertation chapters.

Resources & Facilities

Two University forests (totaling 2,000 acres), the 800-acre Swift River Wildlife Management Area of the Massachusetts Division of Fisheries and Wildlife, and the 81,000-acre Quabbin Reservation of the Massachusetts Department of Conservation and Recreation offer unique field study areas close to campus. The University of Massachusetts also maintains the Nantucket Field Station and the Marine Station at Gloucester. The Conte Anadromous Fish Research Center in Turners Falls offers excellent, modern facilities for both lab and field study of migratory fish behavior, ecology and physiology. Cooperation with the National Marine Fisheries Service allows graduate students to participate in research cruises in the Northwest Atlantic, as well as use facilities at the NMFS Woods Hole Laboratory. As members of the Five College School of Marine Science Program, students have access to research laboratories at Woods Hole and Waquoit Bay on Cape Cod. Further, concentration faculty conduct research in a variety of sites outside Massachusetts, including overseas.

Matriculation & Financial Aid

This program typically takes a full-time MS professional degree student 2-4 semesters to complete, a full-time MS thesis degree student 3-5 semesters to complete, and a full-time PhD student 8-10 semesters to complete, including the completion of a practicum/thesis/dissertation. However, some students may be able to complete the degree in less time and some take longer depending on their academic preparedness and the dictates of the practicum or thesis/dissertation research project.

Funding opportunities are limited, yet financial assistance is provided to our MS thesis and PhD students through teaching or research assistantships (at Graduate Employee Organization bargained wage rates), University fellowships, or hourly wages. Tuition is waived during semesters in which at least a 10-hour assistantship or fellowship is awarded, but the student is responsible for most fees. Research assistantships are available through faculty members who have grant-supported research, and many faculty only accept students if they are able to provide grant-supported assistantships. Limited University and Departmental fellowships are awarded by the Graduate School or ECo Graduate Program in open competition.

Funding opportunities are more limited for students in the MS professional degree option. Some teaching assistantships and University fellowships may be available, or internship institutions may be able to provide some assistance, but most professional degree students are self-funded. Again, tuition is waived during semesters in which at least a 10-hour assistantship or fellowship is awarded (or the equivalent from an internship employer), but the student is responsible for most fees.

Concentration Coordinator & Faculty Affiliates

The following on-campus faculty (both regular and adjuncts) and professional staff, including the Graduate Concentration Coordinator, are principally affiliated with this concentration and regularly serve in the role of the student’s advisory committee chair or member and instructor for core courses; other faculty and staff are occasionally involved in this concentration. See Departmental website for information about the faculty and staff ( http://eco.umass.edu/index.php/people/ ).

Graduate Concentration Coordinator:

Timothy Randhir Dept. of Environmental Conservation 160 Holdsworth Way Amherst, MA 01003-4210 Tel: 413-545-3969 Email: [email protected]

Principal Faculty Affiliates:

• Ann Averill ([email protected])
• Bethany Bradley ([email protected])
• Brett Butler ([email protected])
• Brian Cheng ([email protected])
• Andy Danylchuk ([email protected])
• Stephen DeStefano ([email protected])
• Joe Elkinton ([email protected])
• John Finn ([email protected])
• Todd Fuller ([email protected])
• Evan Grant ([email protected])
• Curt Griffin ([email protected])
• Alexander Haro ([email protected])
• Scott Jackson ([email protected])
• Adrian Jordaan ([email protected])
• Katherine Kahl ([email protected])
• David King ([email protected])
• Lisa Komoroske ([email protected])
• Boyd Kynard ([email protected])
• Susannah Lerman ([email protected])
• Ben Letcher ([email protected])
• Steven McCormick ([email protected])
• Kevin McGarigal ([email protected])
• Toni Lyn Morelli  ([email protected])
• Keith Nislow ([email protected])
• Timothy Randhir ([email protected])
• Allison Roy ([email protected])
• Ahmed A. H. Siddig ([email protected])
• Paul Sievert ([email protected])
• Michelle Staudinger ([email protected])
• Roy Van Driesche ([email protected])
• Paige Warren ([email protected])

University of Massachusetts 160 Holdsworth Way Amherst, MA 01003-9285 Map

1 (413) 545-2665

• University of Amsterdam
• Department of Molecular Cell Biology
• Jaap van Buul

Jaap van Buul University of Amsterdam | UVA  ·  Department of Molecular Cell Biology

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