Virus, development and pluripotent stem cells - an interview with Rudolf Jaenisch

Rudolf Jaenisch explains how the quest for an answer to the simple question of viral tropism in the mouse lead him to a life-long career in regulation of gene expression in the early embryo and pluripotent stem cells. He shares his experience about what it takes to develop into a successful scientist; expresses his concern about the challenges facing young scientists entering the field - not all of them funding related - and candidly offers some solid tips on opportunities to take advantage of and mistakes to avoid. Being mindful of when to let go of a project, and staying focused on what is important, are probably obvious tips, but they need to be re-stated, since they also appear to be the most difficult to accomplish. Dr. Jaenisch continues to work tirelessly on the problem of epigenetic control in the early embryo and its connection with stem cells.     

The method of synthesis in ecology

Synthesis of results from different investigations is an important activity for ecologists but when compared with analysis the method of synthesis has received little attention. Ecologists usually proceed intuitively and this can lead to a problem in defining differences between the syntheses made by different scientists. It also leads to criticism from scientists favoring analytical approaches that the construction of general theory is an activity that does not follow the scientific method. We outline a methodology for scientific inference about integrative concepts and the syntheses made in constructing them and illustrate how this can be applied in the development of general theory from investigations into particular ecological systems. The objective is to construct a causal scientific explanation. This has four characteristics. (1) It defines causal and/or organizational processes that describe how systems function. (2) These processes are consistent – under the same conditions they will produce the same effect. (3) A causal scientific explanation provides general information about events of a similar kind. (4) When experiments are possible then a designed manipulation will produce a predictable response. The essential characteristic of making synthesis to construct a causal scientific explanation is that it is progressive and we judge progress made by assessing the coherence of the explanation using six criteria: acceptability of individual propositions including that they have been tested with data, consistency of concept definitions, consistency in the type of concepts used in making the explanation, that ad hoc propositions are not used, that there is economy in the number of propositions used, that the explanation applies to broad questions. We illustrate development of a causal scientific explanation for the concept of long-lived pioneer tree species, show how the coherence of this explanation can be assessed, and how it could be improved.     

Environmental indices and the politics of the Conservation Reserve Program

Environmental indicators can be used to target public programs to provide a variety of benefits. Social scientists, physical scientists, and politicians have roles in developing indicators that reflect the demands of diverse interest groups. We review the US Department of Agriculture’s Conservation Reserve Program (CRP), the largest agricultural conservation program the United States, to determine how a set of environmental indicators were developed and used, and assess results of their application. The use of such indicators has helped the CRP increase and broaden the program’s environmental benefits beyond erosion reduction, which was the primary focus of early program efforts, to meet other demands. This case study provides an example about how integration and assessment for the purpose of managing public resources requires more than natural science disciplines. Social science can help explain how public values influence what information is collected and how it is interpreted. Examples are given to show how the indices used for the CRP integrated science, politics and social values. In the end, the environmental benefits index (EBI) used to target US$ 20 billion of CRP funds reflects compromises made between science and policy considerations. It is our intention that studying this index will yield ideas and understanding from the natural science community that develops ecosystem indices about how to better plug in to programs in the future.     

Human teratogens update 2011: can we ensure safety during pregnancy?

Anniversaries of the identification of three human teratogens (i.e., rubella virus in 1941, thalidomide in 1961, and diethylstilbestrol in 1971) occurred in 2011. These experiences highlight the critical role that scientists with an interest in teratology play in the identification of teratogenic exposures as the basis for developing strategies for prevention of those exposures and the adverse outcomes associated with them. However, an equally important responsibility for teratologists is to evaluate whether medications and vaccines are safe for use during pregnancy so informed decisions about disease treatment and prevention during pregnancy can be made. Several recent studies have examined the safety of medications during pregnancy, including antiviral medications used to treat herpes simplex and zoster, proton pump inhibitors used to treat gastroesophageal reflux, and newer-generation antiepileptic medications used to treat seizures and other conditions. Despite the large numbers of pregnant women included in these studies and the relatively reassuring results, the question of whether these medications are teratogens remains. In addition, certain vaccines are recommended during pregnancy to prevent infections in mothers and infants, but clinical trials to test these vaccines typically exclude pregnant women; thus, evaluation of their safety depends on observational studies. For pregnant women to receive optimal care, we need to define the data needed to determine whether a medication or vaccine is "safe" for use during pregnancy. In the absence of adequate, well-controlled data, it will often be necessary to weigh the benefits of medications or vaccines with potential risks to the embryo or fetus.     

A history of farm animal embryo transfer and some associated techniques

Events over the last 125 years that have been particularly important to the development of embryo transfer in farm animals are reviewed, arguing that an appreciation of the history of a discipline helps shape its future. Special attention is paid to how the motivations of the scientists involved have changed over time, and how these changes have influenced the practical application of embryo transfer to animal breeding.     

Endometrial stromal cells and decidualized stromal cells: Origins,transformation and functions

Decidualization of endometrium, which is characterized by endometrial stromal cell (ESC) decidualization, vascular reconstruction, immune cell recruitment, and plentiful molecule production, is a crucial step for uterus to become receptive for embryo. When implantation takes place, ESCs surround and directly interact with embryo. Decidualized stromal cells (DSCs) are of great importance in endometrial decidualization, having a broad function in regulating immune activity and vascular remodeling of uterus. DSCs are shown to have a higher metabolic level and looser cytoskeleton than ESCs. What's the origin of ESCs and how ESCs successfully transform into DSCs had puzzled scientists in the last decades. Breakthrough had been achieved recently, and many studies had elucidated some of the characters and functions of DSCs. However, several questions still remain unclear. This paper reviews current understanding of where ESCs come from and how ESCs differentiate into DSCs, summarizes some characters and functions of DSCs, analyzes current studies and their limitations and points out research areas that need further investigation.     

Human teratogens update 2011: Can we ensure safety during pregnancy?

Anniversaries of the identification of three human teratogens (i.e., rubella virus in 1941, thalidomide in 1961, and diethylstilbestrol in 1971) occurred in 2011. These experiences highlight the critical role that scientists with an interest in teratology play in the identification of teratogenic exposures as the basis for developing strategies for prevention of those exposures and the adverse outcomes associated with them. However, an equally important responsibility for teratologists is to evaluate whether medications and vaccines are safe for use during pregnancy so informed decisions about disease treatment and prevention during pregnancy can be made. Several recent studies have examined the safety of medications during pregnancy, including antiviral medications used to treat herpes simplex and zoster, proton pump inhibitors used to treat gastroesophageal reflux, and newer‐generation antiepileptic medications used to treat seizures and other conditions. Despite the large numbers of pregnant women included in these studies and the relatively reassuring results, the question of whether these medications are teratogens remains. In addition, certain vaccines are recommended during pregnancy to prevent infections in mothers and infants, but clinical trials to test these vaccines typically exclude pregnant women; thus, evaluation of their safety depends on observational studies. For pregnant women to receive optimal care, we need to define the data needed to determine whether a medication or vaccine is “safe” for use during pregnancy. In the absence of adequate, well‐controlled data, it will often be necessary to weigh the benefits of medications or vaccines with potential risks to the embryo or fetus. Birth Defects Research (Part A), 2012. © Published 2012 Wiley Periodicals, Inc.     

A scientist's view of the ethics of human embryonic stem cell research

Scientists are rarely immoral and seldom even amoral. The ethical principles that underlie much of their own work are shared with scientists in other countries to a much greater degree than the cultural and religious differences among those countries would lead one to expect. Like me, few will have had any formal training in bioethics; so how might life scientists approach the varied ethical issues that arise in human embryo and stem cell research?     

The Influence of Receptor-Mediated Interactions on Reaction-Diffusion Mechanisms of Cellular Self-organisation

Understanding the mechanisms governing and regulating self-organisation in the developing embryo is a key challenge that has puzzled and fascinated scientists for decades. Since its conception in 1952 the Turing model has been a paradigm for pattern formation, motivating numerous theoretical and experimental studies, though its verification at the molecular level in biological systems has remained elusive. In this work, we consider the influence of receptor-mediated dynamics within the framework of Turing models, showing how non-diffusing species impact the conditions for the emergence of self-organisation. We illustrate our results within the framework of hair follicle pre-patterning, showing how receptor interaction structures can be constrained by the requirement for patterning, without the need for detailed knowledge of the network dynamics. Finally, in the light of our results, we discuss the ability of such systems to pattern outside the classical limits of the Turing model, and the inherent dangers involved in model reduction.     

Xenotransplantation of Human Stem Cells into the Chicken Embryo

The chicken embryo is a classical animal model for studying normal embryonic and fetal development and for xenotransplantation experiments to study the behavior of cells in a standardized in vivo environment. The main advantages of the chicken embryo include low cost, high accessibility, ease of surgical manipulation and lack of a fully developed immune system. Xenotransplantation into chicken embryos can provide valuable information about cell proliferation, differentiation and behavior, the responses of cells to signals in defined embryonic tissue niches, and tumorigenic potential. Transplanting cells into chicken embryos can also be a step towards transplantation experiments in other animal models. Recently the chicken embryo has been used to evaluate the neurogenic potential of human stem and progenitor cells following implantation into neural anlage^1-6. In this video we document the entire procedure for transplanting human stem cells into the developing central nervous system of the chicken embryo. The procedure starts with incubation of fertilized eggs until embryos of the desired age have developed. The eggshell is then opened, and the embryo contrasted by injecting dye between the embryo and the yolk. Small lesions are made in the neural tube using microsurgery, creating a regenerative site for cell deposition that promotes subsequent integration into the host tissue. We demonstrate injections of human stem cells into such lesions made in the part of the neural tube that forms the hindbrain and the spinal cord, and into the lumen of the part of the neural tube that forms the brain. Systemic injections into extraembryonic veins and arteries are also demonstrated as an alternative way to deliver cells to vascularized tissues including the central nervous system. Finally we show how to remove the embryo from the egg after several days of further development and how to dissect the spinal cord free for subsequent physiological, histological or biochemical analyses.     

Experiments,measurements, and mathematical modeling to decipher time signals in development

Good progress has been made in identifying key signaling molecules and explaining how they are used to generate spatial patterns during embryonic development. In contrast, little is known about the control of timing or how cells use time signals in the developing embryo. In this review, I describe how direct measurements from the embryo combined with mathematical modeling could bring new insights. To illustrate this point, I discuss three examples: the Dpp gradient during growth of the Drosophila wing imaginal disc; the Polycomb‐based epigenetic silencing during vernalization in plants; and the Notch‐dependent somite segmentation clock. Birth Defects Research (Part C) 96:121–131, 2012. © 2012 Wiley Periodicals, Inc.     

THE CONTRIBUTIONS OF EMPIRICAL EVIDENCE TO SOCIO‐ETHICAL DEBATES ON FRESH EMBRYO DONATION FOR HUMAN EMBRYONIC STEM CELL RESEARCH

This article is a response to McLeod and Baylis (2007) who speculate on the dangers of requesting fresh ‘spare’ embryos from IVF patients for human embryonic stem cell (hESC) research, particularly when those embryos are good enough to be transferred back to the woman. They argue that these embryos should be frozen instead. We explore what is meant by ‘spare’ embryos. We then provide empirical evidence, from a study of embryo donation and of embryo donors' views, to substantiate some of their speculations about the problems associated with requesting fresh embryos. However, we also question whether such problems are resolved by embryo freezing, since further empirical evidence suggests that this raises other social and ethical problems for patients. There is little evidence that the request for embryos for research, in itself, causes patients distress. We suggest, however, that no requests for fresh embryos should be made in the first cycle of IVF treatment. Deferring the request to a later cycle ensures that potential donors are better informed (by experience and reflection) about the possible destinations of their embryos and about the definition of ‘spare embryos’. Both this article, and that by McLeod and Baylis, emphasize the need to consider the views and experiences of embryo donors when evaluating the ethics of embryo donation for hESC research.     

Scientists’ Prioritization of Communication Objectives for Public Engagement

Amid calls from scientific leaders for their colleagues to become more effective public communicators, this study examines the objectives that scientists’ report drive their public engagement behaviors. We explore how scientists evaluate five specific communication objectives, which include informing the public about science, exciting the public about science, strengthening the public’s trust in science, tailoring messages about science, and defending science from misinformation. We use insights from extant research, the theory of planned behavior, and procedural justice theory to identify likely predictors of scientists'' views about these communication objectives. Results show that scientists most prioritize communication designed to defend science from misinformation and educate the public about science, and least prioritize communication that seeks to build trust and establish resonance with the public. Regression analyses reveal factors associated with scientists who prioritize each of the five specific communication objectives. Our findings highlight the need for communication trainers to help scientists select specific communication objectives for particular contexts and audiences.     

Cell-level finite element studies of viscous cells in planar aggregates

A new cell-level finite element formulation is presented and used to investigate how epithelia and other planar collections of viscous cells might deform during events such as embryo morphogenesis and wound healing. Forces arising from cytoskeletal components, cytoplasm viscosity, and cell-cell adhesions are included. Individual cells are modeled using multiple finite elements, and cell rearrangements can occur. Simulations of cell-sheet stretching indicate that the initial stages of sheet stretching are characterized by changes in cell shape, while subsequent stages are governed by cell rearrangement. Inferences can be made from the simulations about the forces that act in real cell sheets when suitable experimental data are available.     

Can biological control benefit from genetically‐modified crops? Tritrophic interactions on insect‐resistant transgenic plants

Abstract. The use of recombinant DNA technology to develop genetically‐modified crops is considered as a major breakthrough for agriculture by many scientists. However, some scientists, and an even larger proportion of the general public, are sceptical about the advantages and are even more concerned about the potential risk of this new technology. To evaluate this novel technology, cost‐benefit analyses are needed in which the real risks are measured and judged against the benefits. A tiered risk assessment scheme is described herein. This allows comparisons to be made with other insect‐control technologies (e.g. insecticides) and risks to be determined, rather than only hazards being identified. Recombinant DNA technology could allow plants to be designed that are well suited for use alongside biological control programmes. Unfortunately, plant breeders have continued to attempt to breed for total resistance, and biocontrol specialists have ignored the role of the plant in ensuring successful foraging behaviour by insect natural enemies. Although some scientists have highlighted the need to consider both the bottom‐up (plant defence) and top‐down (biocontrol) control of insect pests, there have been few serious attempts to combine these approaches. As more is understood about the proximate and ultimate causes of direct and indirect defences, the potential exists for engineering plants that combine both strategies. This new possibility for controlling insect pests, which will combine both ‘nature’s' own defences with man's ingenuity, may stack the odds in our favour in the continual struggle against insect pests.     

The second warning to humanity—Why ethology matters?

In 2017, more than 15,000 scientists signed a second warning to humanity to halt human-made destruction of our planet. The authors of that study encouraged further contributions highlighting specific subjects. With this perspectives article, we follow their call and explore why and how behavioural studies can matter for a better stewardship of the planet. The second warning article suggested 13 effective steps humanity needs to take to transition to a sustainable life. Here, we first provide some examples of how concepts and tools of behavioural biology can aid understanding and solving real-world conservation problems relating to some of the effective sustainability steps suggested by Ripple et al., (Bioscience, 67, 2017, 1026). Then, we outline how ethological research can contribute to sustainability beyond its contributions to conserving species. Finally, we turn to the second warning and the behaviour of scientists themselves. Science has provided unequivocal evidence that we are destroying the very basis of the existence of millions of species including ourselves. To convince humanity about the urgent necessity to halt and change our behaviour, science organizations, funding bodies and scientists themselves need to become role models for sustainability.     

Reproductive biotechnology and "big" biological questions

In recent decades, scientists have learned to manipulate that cardinal characteristic of life, reproduction, with powerful techniques like artificial insemination, contraception, embryo transfer, cryopreservation, and cloning by nuclear transfer. While these technologies often are used for practical applications and basic research, they have another profound intrinsic quality, which is to engender deep-seated thinking about important biological questions. Examples that stimulate such thinking include a goat's giving birth to her identical twin sister via splitting embryos, cryopreservation, and embryo transfer; that a parthenogenetic embryo can never become an animal but can become a genetic mother via an aggregation chimera; or that a somatic cell can become the sole genetic parent of a calf via cloning. In this paper, I illustrate this thought-stimulating quality by considering contributions of reproductive technologies to understanding, if not completely answering, several important biological questions.     

In ovo electroporations of HH stage 10 chicken embryos

Large size and external development of the chicken embryo have long made it a valuable tool in the study of developmental biology. With the advent of molecular biological techniques, the chick has become a useful system in which to study gene regulation and function. By electroporating DNA or RNA constructs into the developing chicken embryo, genes can be expressed or knocked down in order to analyze in vivo gene function. Similarly, reporter constructs can be used for fate mapping or to examine putative gene regulatory elements. Compared to similar experiments in mouse, chick electroporation has the advantages of being quick, easy and inexpensive. This video demonstrates first how to make a window in the eggshell to manipulate the embryo. Next, the embryo is visualized with a dilute solution of India ink injected below the embryo. A glass needle and pipette are used to inject DNA and Fast Green dye into the developing neural tube, then platinum electrodes are placed parallel to the embryo and short electrical pulses are administered with a pulse generator. Finally, the egg is sealed with tape and placed back into an incubator for further development. Additionally, the video shows proper egg storage and handling and discusses possible causes of embryo loss following electroporation.     

To make the most of what we have: extracting phenological data from nestling measurements

To study the ecological and evolutionary effects of climate change on timing of annual events, scientists need access to data that have been collected over long time periods. High-quality long-term phenology data are rare and costly to obtain and there is therefore a need to extract this information from other available data sets. Many long-term studies on breeding birds include detailed information on individually marked parents and offspring, but do not include information on timing of breeding. Here, we demonstrate how a study of repeated standard measurements of white-throated dipper Cinclus cinclus nestlings in our study system in southernmost Norway can be used for modeling nestling growth, and how this statistical model can be used to estimate timing of breeding for birds with sparser data. We also evaluate how the accuracies of nestling growth models based on different morphological traits (mass and feather length) differ depending on the nestling age, present user guidelines and demonstrate how they can be applied to an independent data set. In conclusion, the approach presented is likely to be useful for a wide variety of species, even if the preferred measurement may differ between species.     

How do genes regulate simple behaviours? Understanding how different neurons in the vertebrate spinal cord are genetically specified

Understanding how the vertebrate central nervous system develops and functions is a major goal of a large body of biological research. This research is driven both by intellectual curiosity about this amazing organ that coordinates our conscious and unconscious bodily processes, perceptions and actions and by the practical desire to develop effective treatments for people with spinal cord injuries or neurological diseases. In recent years, we have learnt an impressive amount about how the nerve cells that communicate with muscles, motoneurons, are made in a developing embryo and this knowledge has enabled researchers to grow motoneurons from stem cells. Building on the success of these studies, researchers have now started to unravel how most of the other nerve cells in the spinal cord are made and function. This review will describe what we currently know about spinal cord nerve cell development, concentrating on the largest category of nerve cells, which are called interneurons. I will then discuss how we can build and expand upon this knowledge base to elucidate the complete genetic programme that determines how different spinal cord nerve cells are made and connected up into neural circuits with particular functions.