This post highlights the approach and finding of a new research article published by Disease Models and Mechanisms (DMM). This feature is written by Lacey Kennedy as apart of a seminar at The University of Alabama (taught by DMM Editorial Board member, Prof. Guy Caldwell) on current topics related to use of animal and cellular model systems in studies of human disease.
Lacey Kennedy
Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
Pansarasa O.1, Bordoni M.1,2, Dufruca L.1, Diamanti L.2,3, Sproviero D.1, Trotti R. 4, Bernuzzi S.5, La Salvia S.1, Gagliardi S.1, Ceroni M.2,3, Cereda C.1
Genomic and post-Genomic Center, “C. Mondino” National Neurological Institute, Pavia, Italy.
Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
General Neurology Unit, “C. Mondino” National Neurological Institute, Pavia, Italy.
Department of Neurodiagnostics and Services, Laboratory of Clinicals and Chemicals Analysis (SMeL), , “C. Mondino” National Neurological Institute, Pavia, Italy.
Department of “Medicina Diagnostica e dei Servizi”, IRCCS Policlinico San Matteo Foundation, Pavia, Italy.
Pansarasa, O., Bordoni, M., Dufruca, L., Diamanti, L., Sproviero, D., Trotti, R., Bernuzzi, S., La Salvia S., Gagliardi, S., Cereda, C.(2018). ALS lymphoblastoid cell lines as a considerable model to understand disease mechanisms. Disease Models & Mechanisms, (January), dmm.031625. https://doi.org/10.1242/dmm.031625
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons (Hardiman et al. 2017). Although a rare disease, affecting approximately 15,000 Americans between the ages of 55-75 years old, it is one of the many ageing-related diseases growing in prevalence as global lifespan increases (https://www.ninds.nih.gov/Disorders/Patient-Caregiver-Education/Fact-Sheets/Amyotrophic-Lateral-Sclerosis-ALS-Fact-Sheet). ALS is a multi-factorial disease that causes muscle weakness, spasticity, cognitive impairment, and ultimately ends in a premature death within five years after the diagnosis (http://www.alsa.com/about-als/facts-you-should-know.html). While many causes are still unknown, there are three main genes thought to play a role in the pathogenesis of ALS: Copper zinc superoxide dismutase (SOD1), TAR DNA Binding Protein 43 (TDP-43), and RNA binding protein FUS. SOD1 is a highly conserved enzyme that scavenges for superoxide radicals, but in its mutated form is very unstable and has been found to unfold even at physiological pH and temperature (Lee, S., & Kim, H. 2015). This mutation can lead to an aggressive form of the disease; in fact, ALS can be characterized by an increase of SOD1 expression in peripheral blood mononuclear cells, as well as neurons (Cereda, C. et al., 2013). Furthermore, TDP-43 and FUS, which are both involved with RNA regulation and transcription, appear to be functionally related in ALS pathology (Lee, S., & Kim, H. 2015). FUS mutations appear to play a role in young-onset of the disease and are characterized by predominate degeneration of the lower motor neurons, although a direct mechanism is not well understood (Blokhuis, A. M, etal. 2013).
While serving different functions, when any of these three genes are mutated in ALS patients, mitochondrial function becomes abnormal, which affects neurons, as well as surrounding tissues. Due to the increasing realization that the molecular mechanisms of ALS are not isolated to the nervous system, Pansarasa et al.identified the need for an alternative model for ALS research in a recent Disease Models and Mechanismsarticle. In this study, they sought to identify biologically relevant molecular hallmarks of ALS in lymphoblastic cell lines (LCLs) isolated directly from human ALS patients, with the hope of establishing a new, more effective model for ALS research (Pansarasa, O. et al., 2018). To do this, they looked at the two known pathogenic mechanisms of ALS: protein aggregate accumulation and mitochondrial dysfunction.
Evidence has indicated that mislocalization of SOD1, TDP-43, and FUS could explain many irregularities in ALS signaling(Ido, A., et al,2011). Using western blot,Pansarasa et al. show that SOD1 expression levels decrease in the nucleus of LCLs from patients with sporadic ALS (sALS), SOD1, and TDP-43 mutations as compared to LCLs from healthy patients. They did not see such a change in cytoplasmic SOD1 levels, suggesting that there is a failure to relocate from the cytoplasm to the nucleus. Supporting this idea through immunostaining, the authors found an abnormal presence of protein aggregates in the cytoplasm of SOD1 and TDP-43 mutated LCLs, which further supports the idea of protein mislocalization in ALS patients (Pansarasa, O. et al., 2018). SOD1 and TDP-43 aggregate in certain forms of ALS (Blokhuis, A. M., et al 2013). Therefore, demonstrating the presence of protein aggregates marks an important first step in the establishment of LCLs as a model for ALS as these aggregates are a known hallmark of the disease.
Next, the authors investigated changes in mitochondrial morphology and function. Through TEM microscopy, they confirmed that patients with SOD1, TDP-43, and FUS mutations harbored morphological signs of degeneration in the mitochondria, such as a smaller, rounder size and increased number of vacuoles. After examining the mitochondria, Pansarasa et al. looked at the protein expression levels of proteins regulating the fission and fusion processes. Notably, in patients with a TDP-43 mutation there was a significant increase in expression levels of proteins regulating the fusion process (Pansarasa O. et al, 2018). This increased fusion corresponds to the same increase found in the neurons of ALS patients with TDP-43 mutations.
Finally, the authors investigated the functional changes in mitochondria through the examination of respiration and glycolytic flux. Using the Seahorse Bioanalyzer, Pansarasa et al found that mitochondrial oxygen consumption significantly increased in sALS patients as compared to the controls. Additionally, they found that Spare Respiratory Capacity, the ability of mitochondria to produce energy in conditions of high energy demand, was greatly diminished. The results also suggested a down-regulation of glycolytic flux in SOD1 mutated patients. These changes in mitochondrial activity correspond to a failure of ALS mitochondria to adequately respond to increased energy demands (Pansarasa et al. 2018).
With this, the authors have established a variety of physiological hallmarks of cells affected by ALS. This is of the utmost importance in ALS research as the field changes from the perspective that ALS is just a neurological disease to the view that it is a multifaceted disorder that impacts the entire body. It should be noted, however, that there are some disadvantages to LCLs as a model. Due to the nature of in vitro culturing, LCLs lack environmental factors that affect behavior. For example, Pansarasa et al demonstrated that while some LCL mutations facilitated protein aggregation, there was a lack of aggregation in LCLs from sALS patients, which the authors theorized could be due to a lack of elements regulating nuclear import and export pathways. In addition, there was little significant change in protein aggregation of LCLs with mutated FUS, suggesting that this is not an effective representation of the FUS mutation in ALS patients due to the role of this protein in lymphoblastic cells (Pansarasa O. et al. 2018). Despite this fact, using human LCLs offers a solution to many of the limitations presented with current ALS models.
Before this paper, Peripheral Blood Mononuclear Cells (PBCMs) was the new model growing in popularity for ALS research. While this method shows promise for a potential diagnostic tool, there are major disadvantages to their use in basic research (Nardo, G., et al2011). First, they cannot be maintained long-term because they will lack important environmental stimuli present in the body. Second, although they are part of the immune system, they are not representative of the immune system cells outside of the blood niche. What occurs in PBMCs does not necessarily recapitulate the response of the immune cells from other parts of the body, for example the central nervous system. Finally, researchers are not able to generalize the implications of any one result due to the fact that the immune system health of the donors impacts the response of these cells, resulting in very limited inter-experimental reproducibility (Kleiveland C.R., et al 2015).
The use of LCLs addresses many of these problems, because they can be immortalized and grown in culture. This prospective model represents the potential of a non-nervous system method to study the molecular mechanisms of ALS. Pansarasa et al. have already successfully identified morphological indicators of ALS and have shown that, with the establishment of LCLs as a model, we might be able to one day understand the causes and biological effects of ALS and find ways to do more for patients than simply slow down its progression.
References
Blokhuis, A. M., Groen, E. J. N., Koppers, M., Van Den Berg, L. H., & Pasterkamp, R. J.(2013). Protein aggregation in amyotrophic lateral sclerosis. Acta Neuropathologica, 125(6), 777–794. https://doi.org/10.1007/s00401-013-1125-6
Cereda, C., Leoni, E., Milani, P., Pansarasa, O., Mazzini, G., Guareschi, S., Alivisi, E., Ghiroldi, A., Diamanti, L., Bernuzzi, S., Ceroni, Mauro., Cova, E.(2013). Altered Intracellular Localization of SOD1 in Leukocytes from Patients with Sporadic Amyotrophic Lateral Sclerosis. PLoS ONE, 8(10).https://doi.org/10.1371/journal.pone.0075916
Hardiman, O., Al-chalabi, A., Chio, A., Corr, E. M., Robberecht, W., Shaw, P. J., & Simmons, Z.(n.d.). Amyotrophic lateral sclerosis. https://doi.org/10.1038/nrdp.2017.71
Ido, A., Fukuyama, H. and Urushitani, M.(2011). Protein misdirection inside and outside motor neurons in Amyotrophic Lateral Sclerosis (ALS): a possible clue for therapeutic strategies. Int J Mol Sci. 12(10), 6980- 7003.
Ju Gao1, Luwen Wang1, Mikayla L. Huntley1, G. P. and X. W.(2018). Pathomechanisms of TDP-43 in neurodegeneration Accepted. Journal of Neurochemistry. https://doi.org/10.1111/jnc.14327
Kleiveland C.R.(2015) Peripheral Blood Mononuclear Cells. In: Verhoeckx K. et al. (eds) The Impact of Food Bioactives on Health. Springer International Publishing, https://doi.org/1007/978-3-319-16104-4
Lee, S., & Kim, H. (2015). Prion-like Mechanism in Amyotrophic Lateral Sclerosis: Are Protein Aggregates the Key. Exp Neurobiol., 24(1), 1–7.
Mackenzie, I. R. A., Bigio, E. H., Ince, P. G., Geser, F., Neumann, M., Cairns, N. J., Kwong, L. K., Forman, M. S., Ravits, J., Steward, H., et al (2007). Pathological TDP-43 Distinguishes Sporadic Amyotrophic Lateral Sclerosis from Amyotrophic Lateral Sclerosis with SOD1 Mutations. 4, 427–434. https://doi.org/10.1002/ana.21147
Nardo, G., Pozzi, S., Pignataro, M., Lauranzano, E., Spano, G., Garbelli, S., Mantovani, S., Marinou, K., Papetti, L., Monteforte, M., Torri, V., Paris, L., Bazzoni, G., Lunetta, C., Corbo, M., Mora, G., Bendotti, C. and Bonetto, V. (2011). Amyotrophic lateral sclerosis multiprotein biomarkers in peripheral blood mononuclear cells. PLoS One.6(10),e25545.
Pansarasa, O., Bordoni, M., Dufruca, L., Diamanti, L., Sproviero, D., Trotti, R., Bernuzzi, S., La Salvia S., Gagliardi, S., Cereda, C.(2018). ALS lymphoblastoid cell lines as a considerable model to understand disease mechanisms. Disease Models & Mechanisms, (January), dmm.031625. https://doi.org/10.1242/dmm.031625
This post highlights the approach and findings of a new research article published in Disease Models and Mechanisms (DMM). This feature was written by J. Brucker Nourse Jr. as part of a graduate level seminar at The University of Alabama (taught by DMM Editorial Board member, Prof. Guy Caldwell) on current topics related to use of animal and cellular model systems in studies of human disease.
J. Brucker Nourse Jr.
Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
1. National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
2. The John Hopkins University/National Institutes of Health Graduate Partnership Program, National Institutes of Health, Bethesda, Maryland
3. National Institute on Aging, National Institutes of Health, Bethesda, Maryland
Developments in modern medicine have allowed humans to reach life expectancies that surpass prior generations (Mills et al., 2016). The tradeoff for increased longevity in most populations has led to greater occurrences of neurodegenerative diseases (NDD), such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Amyotrophic Lateral Sclerosis (ALS). One commonality among NDD is that age is the greatest risk factor (Savica et al., 2013; Nho et al., 2016; Valdez et al., 2012). The bridge between age and NDD incidence remains a mystery, which is why investigation into this link is necessary in order to identify potential therapeutic targets. The majority of NDD cases are associated with individuals over the age of 50. However, there are rare early-onset diagnoses of NDD suggesting that the physiological age of a person may supersede their chronological age, in terms of disease development.
Cyclin-dependent kinase 5 (Cdk5) and its regulation have become a key area of interest for researchers, as the activation of Cdk5 can result in the hyper-phosphorylation of tau and increased amyloid beta aggregation in the brains of AD patients (Wilkanie et al., 2016). Additionally, Cdk5 and one of its activators, p35, were recently found in the Lewy Bodies of the brains of PD patients (Wilkanie et al., 2016). Numerous studies have also demonstrated that abnormalities in Cdk5 expression, both increases and decreases, are associated with multiple types of NDD (Wilkanie et al., 2016). Cdk5 obviously merits researchers’ exploration. A recent article by Spurrier et al. (Spurrier et al., 2018) sought out to observe how manipulating Cdk5α, the Drosophila p35 homologue, would impact NDD and aging in vivo.
Understanding the impacts of alterations to the expression levels of Cdk5αin vivo is a crucial stepping stone into uncovering its role in the aging process. Spurrier and colleagues measured the number of GFP-expressing gamma motor neurons present in the mushroom body (MB) of Drosophila that either had wild-type (WT), overexpression (OE), or knockout (KO) levels of Cdk5α in the motor neurons. Wild-type flies showed a steady, gradual decline of gamma motor neurons over time; however, the Cdk5α-OE and Cdk5α-KO flies had a steep decline with significance appearing at 30- and 45-days old (figure 1B in Spurrier et al., 2018). The associated loss of motor neurons with fluctuations in Cdk5α expression was validated through a motor function assay. Flies with either Cdk5α-OE or Cdk5α-KO demonstrated significant defects in climbing ability from 10- to 45-days old (figure 1D in Spurrier et al., 2018). Flies were also subjected to a lifespan assay that resulted in Cdk5α-OE and Cdk5α-KO flies having a decrease in longevity compared to wild-type animals (figure 1C in Spurrier et al., 2018). It is noteworthy that Cdk5α-OE yielded more severe phenotypes in the neuronal loss and lifespan assays. Collectively, these findings suggest that dysregulation of Cdk5α is involved in accelerating the aging process.
In order to confirm that Cdk5α-induced neuronal loss occurs in a degenerative manner, Spurrier and colleagues measured neurodegenerative phenotypes in Cdk5α-OE and Cdk5α-KO flies. Dysregulation in autophagy is implicated in the pathogenesis of NDD (Menzies et al., 2015). To follow autophagy in vivo, Spurrier et al. used the two autophagy markers: autophagy-related protein 8 (Atg8), a required component of the autophagosomal membrane, and Ref(2)P, a homologue of nucleoporin p62. Wild-type Drosophila steadily expressed both autophagic proteins, with a slight increase in protein levels as the animals aged (figures 2A-D in Spurrier et al., 2018). Cdk5α-KO flies had a significant increase in autophagic markers; however, Cdk5α-OE flies showed a greater fold change (figures 2A-D in Spurrier et al., 2018). Together, these findings suggest a dysregulation of autophagy. This observation corroborates with previous studies that suggest an increase in autophagy protects against NDD (Menzies et al., 2015). The researchers’ observation of an impairment in autophagy fits the narrative that Cdk5 is involved in the pathogenesis of NDD.
In addition to autophagy, researchers used the flies’ sensitivity to oxidative stress to measure aging (Uttara et al., 2009). Flies of different ages, ranging between 3- and 45-days old, were treated with hydrogen peroxide (H2O2) and paraquat, then tested for viability. Cdk5α-OE and Cdk5α-KO flies were significantly less tolerant for oxidative stress when compared to wild-type for both treatments (figures 6A-B in Spurrier et al., 2018). Young Cdk5α-OE and Cdk5α-KO flies had a stress tolerance that was more similar to older wild-type flies. This further supports the notion that modified activation of Cdk5 fast-tracks the aging process.
A major gap in the field of neuropathology is understanding how aging enhances disease susceptibility. Spurrier and colleagues have approached this question by developing an elegant method to identify the physiological age of flies. They compared the expression levels of the genes typically involved in basic biological processes (e.g. metabolism, mitochondrial homeostasis, immunity) in wild-type flies as they aged to establish a standard curve of gene expression, adjusted over time. They then compared the expression levels of these genes to flies with either Cdk5α-OE or Cdk5α-KO genotypes. Both increasing and abolishing expression of Cdk5α led to accelerated physiological aging (figures 3B, E & 5D-E in Spurrier et al., 2018). Spurrier et al. also revealed an overlap of genes that were affected by Cdk5α levels (figures 4B, D in Spurrier et al., 2018). Even though the expression of Cdk5α is limited to neurons, genes affected by the alteration of its expression showed an accelerated aging trend in both the head and thorax of Drosophila (figures 5D-E in Spurrier et al., 2018). The researchers noted that the results from the thorax were unexpected, but this demonstrates that neuronal Cdk5α can cause systemic changes that alter the lifespan of the organism.
Together, the in vivo assays and bioinformatics analyses in Drosophila suggest that altering the activation of Cdk5 by manipulating Cdk5α expression can lead to accelerated aging and enhanced neurodegenerative phenotypes. While both the overexpression and null mutations were deleterious, the Cdk5α-OE flies presented exaggerated phenotypes in the majority of the assays, which is consistent with previous findings (Wilkanie et al., 2016). Spurrier and colleagues have superbly devised an unbiased way to determine physiological aging through genome-wide expression profiling. Establishing physiological age is a tremendous tool that can be implemented in future NDD studies to validate that physiological aging supersedes chronological aging. The next question to address in this field is identifying potential genetic targets and exogenous factors that manipulate the physiological aging process. The aging-related genes in the present study offer a potential starting point to provide a fuller picture of the aging process and its link to the genesis of diseases.
References
1. Menzies, Fiona M., Angeleen Fleming, and David C. Rubinsztein. “Compromised autophagy and neurodegenerative diseases.” Nature Reviews Neuroscience 16, no. 6 (2015): 345.
2. Mills, Kathryn F., Shohei Yoshida, Liana R. Stein, Alessia Grozio, Shunsuke Kubota, Yo Sasaki, Philip Redpath et al. “Long-term administration of nicotinamide mononucleotide mitigates age-associated physiological decline in mice.” Cell Metabolism 24, no. 6 (2016): 795-806.
3. Nho, Kwangsik, Andrew J. Saykin, and Peter T. Nelson. “Hippocampal sclerosis of aging, a common Alzheimer’s disease ‘Mimic’: risk genotypes are associated with brain atrophy outside the temporal lobe.” Journal of Alzheimer’s Disease 52, no. 1 (2016): 373-383.
4. Savica, Rodolfo, Brandon R. Grossardt, James H. Bower, Bradley F. Boeve, J. Eric Ahlskog, and Walter A. Rocca. “Incidence of dementia with Lewy bodies and Parkinson disease dementia.” JAMA Neurology 70, no. 11 (2013): 1396-1402.
5. Spurrier, Shukla, McLinden, Johnson, Giniger. “Altered expression of the Cdk5 activator-like protein, Cdk5α, causes neurodegeneration in part by accelerating the rate of aging.” Disease Models & Mechanisms. no.11 (2018): 1-14.
6. Uttara, Bayani, Ajay V. Singh, Paolo Zamboni, and R. T. Mahajan. “Oxidative stress and neurodegenerative diseases: a review of upstream and downstream antioxidant therapeutic options.” Current Neuropharmacology 7, no. 1 (2009): 65-74.
7. Valdez, Gregorio, Juan C. Tapia, Jeff W. Lichtman, Michael A. Fox, and Joshua R. Sanes. “Shared resistance to aging and ALS in neuromuscular junctions of specific muscles.” PloS One 7, no. 4 (2012): e34640.
8. Wilkaniec, Anna, Grzegorz A. Czapski, and Agata Adamczyk. “Cdk5 at crossroads of protein oligomerization in neurodegenerative diseases: facts and hypotheses.” Journal of Neurochemistry 136, no. 2 (2016): 222-233.
An engineer position in molecular and cellular biology is available starting in summer 2018 in the group of Pierre-François Lenne and in collaboration with Rosanna Dono at the Developmental Biology Institute of Marseille (IBDM), France. The initial appointment will be made for 1 year, with a possible extension to up to 2 years.
We are seeking a highly-motivated candidate, who will support an interdisciplinary project on cell dynamics and tissue morphogenesis.
The main tasks of the engineer will be the preparation of cell aggregates from mouse embryonic stem cells (“embryonic organoids”), and the development of cell lines expressing fluorescent reporter proteins to monitor gene expression dynamics through imaging. Specifically, the job requires expert knowledge in cell biology (cell cultures, immuno-staining), imaging (e.g. confocal microscopy) and molecular biology (cloning of large DNA fragments, routine and advanced PCR technology). Expertise in stem-cell biologyis desirable.
The working language in the laboratory is English. Candidates are expected to be fluent in English.
A letter of motivation, a CV and the names of two referees should be sent to Pierre-François Lenne (pierre-francois.lenne@univ-amu.fr)
The Ghavi-Helm lab for Developmental (Epi)Genomics at the Institut de Génomique Fonctionnelle de Lyon (IGFL) in France focuses on the 3D regulatory genomics of early Drosophila embryogenesis.
Our group aims to dissect the functional relevance of chromatin organization by combining state-of-the-art methods in genetics, genomics, and computational biology, including novel single-cell techniques, using Drosophila embryogenesis as a model system. We are looking for a creative and talented postdoctoral fellow to work at the intersection between genomics and developmental biology. The candidate will be expected to plan and carry out research tasks independently and write-up/present findings on a regular basis. The project is funded by an ERC Starting grant “Enhancer3D”.
The IGFL fosters an outstanding international environment at the interfaces of evolution, development, and integrative physiology using functional genomics, bioinformatics, genetics, and comparative approaches. The institute is housed in a new building at the Ecole Nationale Supérieure (ENS) of Lyon within the vibrant research community of the Lyon Gerland campus.
Lyon, the “gastronomic capital” of France, is a modern and dynamic city, with rich cultural and sport offerings. It’s an international transportation hub (< 2h from Paris or Marseille with high-speed train, 1h drive from the Alps).
Requirements for the role:
Ph.D. or MD-Ph.D. degree in biology
Prior research experience in genomics, molecular biology, developmental biology, genetics and/or biochemistry (including a track record of peer-reviewed publications)
Ability to work independently and as part of a team in a dynamic and multidisciplinary environment
Previous experience with single-cell genomics is a plus
Interest and/or experience in bioinformatics is a plus
The working language of the lab is English.
The contract will be initially for one year, renewable.
Start date: summer/fall 2018, negotiable.
Salary: commensurate with experience according to CNRS rules.
To get in touch, please send your CV, a brief description of your present and future research interests, and contact details for 3 references to yad.ghavi-helm@ens-lyon.fr. The deadline for applications is open; applications will be examined until the position is filled.
The focus of training will be on construction and automation of BioImage Analysis workflows, using as examples more than one toolbox and different exercises. The schools will be held in Edinburgh 16-19th of October 2018, hosted by the MRC Center for Regenerative Medicine/Imaging facility and co-organized by the University of Edinburgh and University of Dundee.
NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >30 specialists at the event) and “….a great mix of intensive learning and community networking” (former trainee testimonial!). The schools will include practical sessions and seminars on ImageJ for analysis and publication, scripting/macros in ImageJ and Matlab, Omero, CellProfiler, QuPath, Ilastik, Ethics in Image Analysis and work on own data.
Applications are now open (each school has 20 available seats and ~7 trainers)
Applicants are highly encouraged to bring their own laptops and data.
Within the COST framework (funders of NEUBIAS), 7 travel grants per school are offered to applicants who qualify.
Registration requires a “letter of motivation” (filled in the application form) and later a confirmation of status.
Application deadline: May 11th, 2018
Selection notification: 1st week of June 2018.
More information about schools (programme & trainers) and venue, travel & lodge available at our website (see the linked pages for each school in above)
We kindly ask that you help us reach all potentially interested applicants.
Stem cells are defined by the dual capacity to self-renew and to differentiate. These properties sustain homeostatic cell turnover in adult tissues and enable repair and regeneration throughout the lifetime of the organism. In contrast, pluripotent stem cells are generated in the laboratory from early embryos or by molecular reprogramming. They have the capacity to make any somatic cell type, including tissue stem cells.
Stem cell biology aims to identify and characterise which cells are true stem cells, and to elucidate the physiological, cellular and molecular mechanisms that govern self-renewal, fate specification and differentiation. This research should provide new foundations for biomedical discovery, biotechnological and biopharmaceutical exploitation, and clinical applications in regenerative medicine.
CAMBRIDGE STEM CELL COMMUNITY
The University of Cambridge is exceptional in the depth and diversity of its research in Stem Cell Biology, and has a dynamic and interactive research community that is ranked amongst the foremost in the world. By bringing together members of both the Schools of Biology and Medicine, this studentship will enable you to take advantage of the strength and breadth of stem cell research available in Cambridge. Choose from over 50 participating host laboratories using a range of experimental approaches and organisms.
PROGRAMME OUTLINE
Students are expected to have chosen a laboratory for their thesis research prior to application, and to have obtained the support of the PI. A list of eligible supervisors can be found here.
Students will have access to our Discussion course during the first year, where they will:
Study fundamental aspects of Stem Cell Biology through a series of teaching modules led by leaders in the field.
Learn a variety of techniques, such as advanced imaging, flow cytometry, and management of complex data sets.
ELIGIBILITY
We welcome applications from those who hold a relevant first degree at the highest level (minimum of a UK II.i Honours Degreeor equivalent) as well as a Master’s Degree in a relevant discipline. You must have a passion for scientific research.
Wellcome provide full funding at the ‘Home/EU’ rate. Funding does not include overseas fees, so non-EU applicants will need to find alternative funding sources to cover these.
Another bumper month for developmental biology and related preprints, this time featuring spiders, lampreys, amphiouxus and plenty of zebrafish, worm and fly research. Also a big month for fans of Sox genes, which turned up in the title of five preprints! My visual highlight is the preprint from David Parichy’s group on zebrafish scale development – well worth downloading the PDF to gawp at the imaging.
The preprints were hosted on bioRxiv, PeerJ, andarXiv. Use these links to get to the section you want:
Discovery of a new path for red blood cell generation in the mouse embryo
Irina Pinheiro, Ozge Vargel Bolukbasi, Kerstin Ganter, Laura A. Sabou, Vick Key Tew, Giulia Bolasco, Maya Shvartsman, Polina V. Pavlovich, Andreas Buness, Christina Nikolakopoulou, Isabelle Bergiers, Valerie Kouskoff, Georges Lacaud, Christophe Lancrin
Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth
Andrew Cox, Allison Tsomides, Dean Yimlamai, Katie Hwang, Joel Miesfeld, Giorgio Galli, Brendan Fowl, Michael Fort, Kimberly Ma, Mark Sullivan, Aaron Hosios, Erin Snay, Min Yuan, Kristin Brown, Evan Lien, Sagar Chhangawala, Matthew Steinhauser, John Asara, Yariv Houvras, Brian Link, Matthew Vander Heiden, Fernando Camargo, Wolfram Goessling
Tracking mandibular arch cell rearrangements in Tao, et al.’s preprint
Oscillatory cortical forces promote three dimensional cell intercalations that shape the mandibular arch
Hirotaka Tao, Min Zhu, Kimberly Lau, Owen Whitley, Mohammad Samani, Xiao Xiao, Xiao Xiao Chen, Noah A. Hahn, Weifan Liu, Megan Valencia, Min Wu, Xian Wang, Kelli D. Fenelon, Clarissa C. Pasiliao, Di Hu, Jinchun Wu, Shoshana Spring, James Ferguson, Edith P. Karuana, R. Mark Henkelman, Alexander Dunn, Huaxiong Huang, Hsin-Yi Henry Ho, Radhika Atit, Sidhartha Goyal, Yu Sun, Sevan Hopyan
Tracking development of the zebrafish retina, from Matejcic, et al.’s preprint
Single-cell analysis identifies EpCAM+/CDH6+/TROP-2- cells as human liver progenitors.
Joe M Segal, Daniel J Wesche, Maria Paola Serra, Bénédicte Oulés, Deniz Kent, Soon Seng Ng, Gozde Kar, Guy Emerton, Samuel Blackford, Spyros Darmanis, Rosa Miquel, Tu Vinh, Ryo Yamamoto, Andrew Bonham, Alessandra Vigilante, Sarah Teichmann, Stephen R Quake, Hiromitsu Nakauchi, S Tamir Rashid
Randal Burns, Eric Perlman, Alex Baden, William Gray Roncal, Ben Falk, Vikram Chandrashekhar, Forrest Collman, Sharmishtaa Seshamani, Jesse Patsolic, Kunal Lillaney, Michael Kazhdan, Robert Hider Jr., Derek Pryor, Jordan Matelsky, Timothy Gion, Priya Manavalan, Brock Wester, Mark Chevillet, Eric T. Trautman, Khaled Khairy, Eric Bridgeford, Dean M. Kleissas, Daniel J. Tward, Ailey K. Crow, Matthew A. Wright, Michael I. Miller, Stephen J Smith, R. Jacob Vogelstein, Karl Deisseroth, Joshua T. Vogelstein
| Genome tools
An optimized toolkit for precision base editing
Maria Paz Zafra, Emma M Schatoff, Alyna Katti, Miguel Foronda, Marco Breinig, Anabel Y Schweitzer, Amber Simon, Teng Han, Sukanya Goswami, Emma Montgomery, Jordana Thibado, Francisco J Sanchez-Rivera, Junwei Shi, Christopher R Vakoc, Scott W Lowe, Darjus F Tschaharganeh, Lukas E Dow
Robust single-cell DNA methylome profiling with snmC-seq2
Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, Joseph R Nery, Antonio Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O’Connor, Seth Ruga, Marc E Van Eden, David A Davis, Deborah C Mash, M. Margarita Behrens, Joseph R Ecker
Community-driven data analysis training for biology
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Lariviere, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Rolf Backofen, James Taylor, Anton Nekrutenko, Björn Grüning
Seán I O’Donoghue, Benedetta F Baldi2, Susan J Clark, Aaron E Darling, James M Hogan, Sandeep Kaur, Lena Maier-Hein, Davis J McCarthy, William J Moore, Esther Stenau, Jason R Swedlow, Jenny Vuong, James B Procter
David Trafimow, Valentin Amrhein, Corson N. Areshenkoff, Carlos Barrera-Causil, Eric J. Beh, Yusuf Bilgiç, Roser Bono, Michael T. Bradley, William M. Briggs, Héctor A. Cepeda-Freyre, Sergio E. Chaigneau, Daniel R. Ciocca, Juan Carlos Correa, Denis Cousineau, Michiel R. de Boer, Subhra Sankar Dhar, Igor Dolgov, Juana Gómez-Benito, Marian Grendar, James Grice, Martin E. Guerrero-Gimenez, Andrés Gutiérrez, Tania B. Huedo-Medina, Klaus Jaffe, Armina Janyan, Ali Karimnezhad, Fränzi Korner-Nievergelt, Koji Kosugi, Martin Lachmair, Rubén Ledesma, Roberto Limongi, Marco Tullio Liuzza, Rosaria Lombardo, Michael Marks, Gunther Meinlschmidt, Ladislas Nalborczyk, Hung T. Nguyen, Raydonal Ospina, Jose D. Perezgonzalez, Roland Pfister, Juan José Rahona, David A. Rodríguez-Medina, Xavier Romão, Susana Ruiz-Fernández, Isabel Suarez, Marion Tegethoff, Mauricio Tejo, Rens van de Schoot, Ivan Vankov, Santiago Velasco-Forero, Tonghui Wang, Yuki Yamada, Felipe C. Zoppino, Fernando Marmolejo-Ramos
Christos D Arvanitidis, Richard M Warwick, Paul J Somerfield, Christina Pavloudi, Evangelos Pafilis, Anastassis Oulas, Giorgos Chatzigeorgiou, Vasilis Gerovasileiou, Theodoros Patkos, Nicolas Bailly, Francisco Hernandez, Bart Vanhoorne, Leen Vandepitte, Ward Appeltans, Robert Adlard, Peter Adriaens, Ahn Kee-Jeong, Ahyong Shane, Akkari Nesrine, Gary Anderson, Angel Martin, Claudia Arango, Tom Artois, Stephen Atkinson, Ruud Bank, Anthony D Barber, Joao P Barbosa, Ilse Bartsch, Denise Bellan-Santini, Jimmy Bernot, Annalisa Berta, Rüdiger Bieler, Magda Błażewicz, Phil Bock, Ruth Böttger-Schnack, Philippe Bouchet, Nicole Boury-Esnault, Geoff Boxshall, Christopher B Boyko, Simone Nunes Brandão, Rod Bray, Niel L Bruce, Stephen Cairns, Tania N Campinas Bezerra, Paco Cárdenas, Benny KK Chan, Tin-Yam Chan, Lanna Cheng, Morgan Churchill, Laure Corbari, Ralf Cordeiro, Astrid Cornils, Keith A Crandall, Thomas Cribb, Jean-Loup D’hondt, Meg Daly, Mikhail Daneliya, Jean-Claude Dauvin, Peter Davie, Claude De Broyer, Valentin De Mazancourt, Nicole De Voogd, Peter Decker, Danielle Defaye, Henk Dijkstra, Martin Dohrmann, Daryl Domning, Rachel Downey, Inna Drapun, Ursula Eisendle-Flöckner, Christine Ewers-Saucedo, Marien Faber, Diego Figueroa, Julian Finn, Gustavo Fonseca, Ewan Fordyce, William Foster, Hidetaka Furuya, Horia Galea, Oscar Garcia-Alvarez, Rade Garic, Rebeca Gasca, Santiago Gaviria-Melo, Sarah Gerken, David Gibson, João Gil, Arjan Gittenberger, Chris Glasby, Serge Gofas, Samuel E Gómez-Noguera, David González-Solís, Dennis Gordon, Michal Grabowski, Cinzia Gravili, José M Guerra-García, Roberto Guidetti, Katja Guilini, Kerry A Hadfield, Ed Hendrycks, Bachiller Herrera, Ju-Shey Ho, Jens Høeg, Oleksandr Holovachov, Matthew D Hooge, John Hooper, Tammy Horton, Lauren Hughes, Matús Hyžný, Luiz IF Moretti, Tohru Iseto, Viatcheslav N Ivanenko, Gerhard Jarms, Damià Jaume, Krzysztof Jazdzewski, Ivana Karanovic, Young-Hyo Kim, Rachael King, Michelle Klautau, Jürgen Kolb, Alexey Kotov, Traudl Krapp-Schickel, Antonina Kremenetskaia, Reinhardt Kristensen, Andreas Kroh, Sven Kullander, Rafael La Perna, Sara LeCroy, Daniel Leduc, Rafael Lemaitre, Anne-Nina Lörz, Jim Lowry, Enrique Macpherson, Larry Madin, Tomasz Mamos, Renata Manconi, Bruce Marshall, David J Marshall, Patrick Martin, Sandra McInnes, Jan Mees, Tõnu Meidla, Kelly Merrin, Dmitry Miljutin, Claudia Mills, Vadim Mokievsky, Tina Molodtsova, Rich Mooi, André C Morandini, Rosana Moreira Da Rocha, Fabio Moretzsohn, Jonas Mortelmans, Jeanne Mortimer, Luigi Musco, Thomas A Neubauer, Eike Neubert, Peter NG Neuhaus, Anh D Nguyen, Claus Nielsen, Jon Norenburg, Tim O’Hara, Hisayo Okahashi, Dennis Opresko, Masayuki Osawa, Yuzo Ota, Gustav Paulay, Vincent Perrier, William Perrin, Iorgu Petrescu, Bernard Picton, John F Pilger, Andrzej Pisera, Dan Polhemus, Gary Poore, James D Reimer, Hans Reip, Michael Reuscher, Pilar Rios Lopez, Marc Rius, Klaus Rützler, Alexander Rzhavsky, José Saiz-Salinas, André F Sartori, Heinrich Schatz, Bernd Schierwater, Andreas Schmidt-Rhaesa, Simon Schneider, Christine Schönberg, André R Senna, Cristiana Serejo, Shabuddin Shaik, Shokoofeh Shamsi, Jyotsna Sharma, Noa Shenkar, Andrew Shinn, Jacek Sicinski, Volker Siegel, Petra Sierwald, Elizabeth Simmons, Frederic Sinniger, Duncan Sivell, Boris Sket, Harry Smit, Nicole Smol, Jesser F Souza-Filho, Jörg Spelda, Sérgio N Stampar, Eric Stienen, Pavel Stoev, Sabine Stöhr, Malin Strand, Eduardo Suárez-Morales, Mindi Summers, Billie J Swalla, Stefano Taiti, Masaatsu Tanaka, Anne H Tandberg, Danny Tang, Mark Tasker, Harry ten Hove, Jan J ter Poorten, Jim Thomas, Erik V Thuesen, Ben Thuy, Juan T Timi, Antonio Todaro, Xavier Turon, Peter Uetz, Sergiy Utevsky, Jean Vacelet, Risto Väinölä, Sancia ET van der Meij, Ton van Haaren, Virág Venekey, Chris Vos, Genefor Walker-Smith, Chad T Walter, Les Watling, Matthew Wayland, Christopher Whipps, Gary Williams, Robin Wilson, Moriaki Yasuhara, Joana Zanol, Wolfgang Zeidler
In January 2018, twenty-one graduate students and early career researchers from across South and North America participated in the International Course on Developmental Biology, an EMBO Practical Course held at the Marine Biology Station of Quintay-Chile (CIMARQ). This two-week course was led by eight world-renowned researchers, Drs. Roberto Mayor, Nipam Patel, John Ewer, Raymond Keller, Alejandro Sánchez-Alvarado, Kathleen Whitlock, Claudio Stern and Andrea Streit, many of whom started or currently base their careers in Latin American countries. First offered in 1999, the creation of this course reflected the enthusiasm of Latin American researchers to promote and enhance the field of Developmental Biology in this region by providing an opportunity for young scientific investigators to learn current research techniques and become familiar with model organisms used in this field. A successful outcome from the course was the creation of the Latin American Society of Developmental Biology (LASDB) in 2003, which holds biannual meetings for researchers to disseminate their findings and network with colleagues throughout Latin America. Although the changing political, social and economic climate still presents challenges for young researchers, remarkable progress has been made over the past 20 years. Notably, with several of the recent participants of this course having supervisors who also completed the course earlier in their career, the International Course on Developmental Biology is clearly an important part of the emerging research landscape.
For many centuries, Developmental Biology was thought of as a descriptive science. Naturalists dedicated themselves to describing the extensive modifications that occur during the development of various species, characterizing and defining embryo size and shape, as well as the duration of different developmental stages. They addressed fundamental questions that remain to this day: How does a single cell give rise to a complete organism? What are the molecular signals involved? To answer these questions, scientists began using organisms at different levels of complexity, establishing the classical experimental models of Developmental Biology: the roundworm, fruitfly, frog, zebrafish, chicken and mouse, or C. elegans, Drosophila, Xenopus, Danio rerio, Gallus gallus and Mus musculus, as they are affectionately known by scientists. Developmental Biology began to revolutionize in the ‘70s when new technologies such as recombinant DNA became available to study how genes specify different tissue identities. In the ‘80s, we began to talk about homeobox genes, promoters, transcription factors and enhancers, and started using gene expression techniques such as in situ hybridization. As questions at the genetic and morphogenetic level began to be clarified, other questions started to arise: How does evolution shape developmental processes? How can development be modified by the surrounding environment? How can we take advantage of the plasticity of development?
Today, Developmental Biology is a highly-regarded field of study, being a course requirement of most undergraduate programs in the biological sciences. But why did we, as young scientific investigators choose it as our research discipline? We all agree: when you first observe a developing organism under the lens of a microscope, the entire world becomes fascinating. We see life’s great questions in our work. For instance, when does a cell leave it’s past behind and enter into it’s destiny? What makes a cell unique? What are the costs of differentiation? Could it be immobility, like for osteocytes; or programmed cell death, without which the fingers would not exist; or perhaps pruning, like what more than half of the brain’s synaptic connections undergo to achieve functionality. Then there are the milestones. In one of our seminars by Prof. Roberto Mayor, we were given to ponder the famous quote by Lewis Wolpert, that it is “not birth, marriage or death, but gastrulation which is truly the most important time in your life”. With such intriguing insights into the facts of life, how could any other subject area compare?
Simply exploring your surroundings in Latin America leaves one searching for answers. With unique habitats holding nearly one-fifth of the world’s plant and vertebrate species (Myers et al., 2000), it has been called “a living laboratory” and is a place of continuous discovery. This was made evident to us, by exploring just a few meters on the coastal shore of the Quintay waters, where we observed a great diversity of organisms, protected between the rocks before being revealed under our microscope lenses. Unfortunately, human activities that trigger climate change, diseases, and species introductions are affecting natural ecosystems. So we are given the challenge to find new research models to discover unique molecular and cellular mechanisms before they are lost entirely. Several research groups such as Dr. Alejandro Sánchez-Alvarado’s lab are investigating emerging model systems which may help us to overcome types of illness and injury not possible today.
Despite the benefits of conducting Developmental Biology research in Latin America, the reality is that resources and funding are limited. Countries that have an established tradition of scientific investment such as Brazil, Argentina, Mexico and Chile (Marcellini et al., 2017) are more equipped than others; however, careful experimental design, collaboration and creative problem solving are essential. All of us came with different backgrounds: free or paid access to undergraduate studies, different levels of research experience, different levels of English fluency, among others, which showed us the challenges that everyone was going through in the road to pursuing our dream of becoming scientists. However, all of these differences were set aside during the two-week course. The appreciation of the personal value of each participant and faculty member, the willingness to help each other, the equality with which the faculty and participants exchanged ideas was indicative of the underlying message of this course: advance together as one.
As scientists who study the transient process of life as it acquires it’s form and function, we are part of a minority that has the knowledge and the opportunity to make the world a better place. With climate change, wildlife extinction, food and resource crisis at our doors, difficult times are ahead of us. It is our responsibility to observe what is going on around us, make predictions, test hypotheses, and not simply resign ourselves to the way things are. We must share our knowledge, explain science and impact our society. It is in our hands to spread scientific knowledge to the general public and especially, to future scientists at a young age. This can be achieved by creating outreach programs, such as the television series that Dr. Kate Whitlock created, La Alegría de la Ciencia, which can stimulate children and adults to be interested in Developmental Biology. Science must be inclusive and not limited to scientists. Funding reviewers and government decision makers also need to be informed about our work. Here it is our duty as Developmental Biologists to explain that our research is more than simply “basic science” with no significant contribution to solve current problems. Rather, it is through studying processes such as cell migration, epithelial-mesenchymal transition, control of gene expression, and cell death that we can solve problems in reproduction, development, disease, aging and regeneration.
The personal and professional experiences of this two-week happy confinement in Quintay are some of the most illuminating and transforming that many of us have. Although separated now in different countries and continents, we have shared unforgettable moments of life and learning in this course and the doors were left open to continue working together in the future. We go forward knowing that we CAN make a difference if only we keep pushing towards a better future.
Group photo, taken moments before getting soaked by an incoming wave. Bottom row, left to right: Emma Rangel Huerta, Angelly Vasquez, Mateus Antonio Berni, Lorena Agostini Maia, Jessica Cristina Marin Llera, Nancy María Farfán, Nipam Patel. Middle row, left to right: Lautaro Gándara, Jennifer Giffin, Maria Belen Palacios, Luiza Saad, Estefanía Sánchez-Vásquez, Jorge Antolio Domínguez-Bautista, Adrián Romero, Roberto Mayor, Raymond Keller. Top row, left to right: Fernando Faunes, John Rojas, Sandra Edwards, Elias Barriga, Lucía Bartolomeu, Eugene Tine, Soraya Villaseca, Paula M. González, Matías Preza, Maria Fernanda Palominos.
“A continent whose thriving biodiversity represents endless forms most beautiful and most wonderful that are a source of inspiration and opportunities for the Evo-Devo community” (Marcellini et al., 2017).
Written by the participants of the 2018 International Course on Developmental Biology.
References
Marcellini S, González FA, Sarrazin AF, Pabón-Mora N, Benítez M, Piñeyro-Nelson A, Rezende GL, Maldonado E, Schneider PN, Grizante MB, Da Fonseca RN, Vergara-Silva F, Suaza-Gaviria V, Zumajo-Cardona C, Zattara EE, Casasa S, Suárez-Baron H, Brown FD. (2017). Evolutionary developmental biology (Evo-Devo) research in Latin America. J. Exp. Zool. (Mol. Dev. Evol.) 328B:5-40.
Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J. (2000). Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
As well as publishing Development and four other journals, and supporting scientists through travelling fellowships and meeting grants, The Company of Biologists also runs a successful series of Workshops.
The Workshops bring leading experts and early career scientists from a diverse range of scientific backgrounds to focus on one topic together. Topics are often interdisciplinary and cover some of the most exciting current biology, as you can see in the archive.
The Workshop Committee are currently seeking proposals for four Workshops to be held during 2020. They are particularly keen to receive proposals from postdocs for one of the Workshops.We at the Node would also encourage applicants from developmental biology to think about applying!
The Marine Biological Laboratory is seeking applicants for full-time Research Assistant and Research Associate positions with the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (http://www.mbl.edu/jbpc/).
To develop CRISPR in rotifers:
We seek a motivated, creative and innovative Research Assistant or Research Associate to join the laboratories of Kristin Gribble and David Mark Welch. Our research combines comparative genomics, biochemistry, and life history to study aging, maternal effects, and DNA damage prevention and repair using rotifers, a novel aquatic invertebrate model system for studies of aging, neurobiology, genome evolution, and ecology. The successful candidate will develop genome editing techniques in rotifers, including CRISPR/Cas9, as part of a broad initiative at the MBL to advance new aquatic and marine models for biological discovery. We invite individuals with experience in genome editing in other animals to join this expanding program.
To study the biochemistry of DNA repair in bdelloids:
We seek a Research Assistant to join the laboratory of David Mark Welch. Our research combines comparative genomics, biochemistry, and life history to study the evolution of bdelloid rotifers, extraordinarily resilient animals adapted to highly stressful environmental conditions. The successful candidate will contribute to an ongoing project to clone, express, purify, and assay a variety of rotifer proteins involved in DNA damage prevention and repair. There is considerable opportunity for motivated, self-directed individuals to participate in technique development, manuscript development and publication. Position level and salary will depend on education and experience.
We seek applicants for a full-time Research Assistant position with the Keck Sequencing Facility of the Josephine Bay Paul Center. The successful applicant will contribute to projects that will explore diversity of microbes in various communities and the influence of changing environments on microbial population structures. Responsibilities include, but are not limited to, laboratory management, preparation and massively high-throughput next-generation sequencing of marker gene and metagenomic libraries from environmental genomic DNA, and computational analysis of such datasets.
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The focus of training will be on construction and automation of BioImage Analysis workflows, using as examples more than one toolbox and different exercises. The schools will be held in Edinburgh 16-19th of October 2018, hosted by the MRC Center for Regenerative Medicine/Imaging facility and co-organized by the University of Edinburgh and University of Dundee.
