Lessons from a great developmental biologist

The announcement that Sir John Gurdon had been awarded the 2012 Nobel Prize for Medicine or Physiology was received with great joy by developmental biologists. It was a very special occasion because of his total dedication to science and turning the Golden Rule of western civilization – love your neighbor as yourself – into a reality in our field. This essay attempts to explain how John became such a great scientific benefactor, and to review some of his discoveries that are less well known than the nuclear transplantation experiments. A few personal anecdotes are also included to illustrate the profound goodness of this unique man of science.     

Interactions with John Gurdon – muscle as a mesodermal read-out and the community effect

John Gurdon has made major contributions to developmental biology in addition to his Nobel prize winning work on nuclear reprogramming. With the frog, Xenopus, as a vertebrate model, his work on mesoderm induction led him to identify a community effect required for tissue differentiation after progenitor cells have entered a specific mesodermal programme. It is in the context of this biologically important concept, with myogenesis as an example, that we have had most scientific exchanges. Here I trace my contacts with him, from an interest in histone regulation of gene expression and reprogramming, to myogenic determination factors as markers of early mesodermal induction, to the role of the community effect in the spatiotemporal control of skeletal muscle formation. I also recount some personal anecdotes from encounters in Oxford, Paris and Cambridge, to illustrate my appreciation of him as a scientist and a colleague.     

Reflections provoked by Michael Banton's John Rex's main mistake

Banton's article provoked a number of reflections on working with John Rex in the 1960s. The idea of race has a long history both in human relations and sociological theory. But the possibility of there being a specific field of ‘race relations’ remains contested. Ideas of race and ethnicity are elided in public discourse, making the resolution of linguistic issues in the field especially difficult and as yet unresolved. These reflections touch upon the political environment in which John Rex's earlier writing on race was conducted and upon the breadth of influences upon a sociologist rooted in the classical tradition, especially the sociology of Max Weber.     

How serendipity shaped a life; an interview with John W. Saunders,Jr. by John F. Fallon

John W. Saunders Jr. is an outstanding contributor to the field of Developmental Biology. His analyses of the apical ectodermal ridge, discovery and study of the zone of polarizing activity, insights into cell death in development, and analytical studies of feather patterns are part of a legacy to developmental biology. The body of his published work remains central to the understanding of limb development and is a major reason for the premiere place that the developmental biology of limbs holds in our research and teaching today. Beyond these things known to nearly everyone, there is John's role as teacher that is equally impressive. His one-on-one style, in small groups or from the podium is engaging, encompassing, and above all else, enthusiastic about the study of the development of living things. His love of developmental biology comes through to students of all ages and is inspirational. And, of course, inimitable charm accompanies the substance of any interaction with John. He still teaches in the Embryology Course at MBL Woods Hole. Recent students say that hearing his lectures and his involvement in the laboratory are highlights of the course. His continued knowledge of science and delight in new advances is a model for students to follow and they recognize it. John Saunders is a scientist and educator par excellence. His contributions have stood the test of time. His personal interactions with colleagues and students have enriched their lives in innumerable ways, large and small. His is a lifetime of outstanding achievements. In this interview, he reflects on his six--going on seven--decades in science and his personal enjoyment of recent advances in Developmental Biology.     

Genome editing of human pluripotent stem cells to generate human cellular disease models

Disease modeling with human pluripotent stem cells has come into the public spotlight with the awarding of the Nobel Prize in Physiology or Medicine for 2012 to Drs John Gurdon and Shinya Yamanaka for the discovery that mature cells can be reprogrammed to become pluripotent. This discovery has opened the door for the generation of pluripotent stem cells from individuals with disease and the differentiation of these cells into somatic cell types for the study of disease pathophysiology. The emergence of genome-editing technology over the past few years has made it feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Here, recent technological advances in genome editing, and its utility in human biology and disease studies, are reviewed.     

One "different kind of gentleman": Alfred Merle Norman (1831–1918), invertebrate zoologist

Alfred Merle Norman (1831–1918), an active clergyman in rural Co. Durham, England, came from an ancient Somerset family. He began to study marine biology during the early 1850s and during the 1860s was an important participant in John Gwyn Jeffreys' expeditions to the Shetland Islands. Norman's field collecting all over the British Isles was extensive and he made important trips to Norwegian fjords for dredging. His best known discoveries were Rhabdopleura and Synagoga , but he published major work on Protozoa, Porifera, Coelenterata, Mollusca, Crustacea, Echinodermata and other invertebrates. The publication Museum Normanianum summarized Norman's collection of 11,086 species, which was acquired by the British Museum (Natural History). His library, which incorporated John Gwyn Jeffreys' library on molluscs, is now in the Department of Zoology, Cambridge University. Norman was primarily a taxonomist secondarily interested in zoogeography who avoided Darwinian controversies.
A bibliography of Norman's 218 publications is included.     

Natural selection without survival of the fittest

Susan Mills and John Beatty proposed a propensity interpretation of fitness (1979) to show that Darwinian explanations are not circular, but they did not address the critics' chief complaint that the principle of the survival of the fittest is either tautological or untestable. I show that the propensity interpretation cannot rescue the principle from the critics' charges. The critics, however, incorrectly assume that there is nothing more to Darwin's theory than the survival of the fittest. While Darwinians all scoff at this assumption, they do not agree about what role, if any, this principle plays in Darwin's theory of natural selection. I argue that the principle has no place in Darwin's theory. His theory does include the idea that some organisms are fitter than others. But greater reproductive success is simply inferred from higher fitness. There is no reason to embody this inference in the form of a special principle of the survival of the fittest.I would like to thank John Beatty, Ron Giere, Philip Kitcher and John Winnie for detailed and helpful criticisms of an earlier draft of this paper.     

Curiosity, Recruitment, and Chaos: A Tribute to Bill Ricker’s Inquiring Mind

Synopsis Through three versions of a handbook on computations for biological statistics of fish populations, W.E. “Bill” Ricker played a pivotal role in founding the field of quantitative fishery science. His interests, however, extended far beyond the confines of quantifiable events to a deep appreciation for the natural world. In this article, I trace his development of fishery models from the 1940s to the 1970s, using examples that illustrate his approach to statistics and biological systems analysis. I describe changes in technology and statistics that have made it possible to extend his research in new directions, although his approach still lies at the core of all modern fishery models. His gentle, inquiring spirit persisted long after his retirement in 1973, as I illustrate from personal experiences with him during the 1990s.     

Selective cleavage of an azaGly peptide bond by copper(II). Long‐range effect of histidine residue

Several reports have highlighted the interest of replacing Gly, a frequent amino acid within bioactive peptides, by azaGly (Agly) to improve their stability, activity or for the design of prodrugs. Because metal catalysis is increasingly used for tailoring peptide molecules, we have studied the stability of Agly peptides in the presence of metal ions. In this study, we show that Cu(II), unlike other metal ions such as Fe(II), Fe(III), Pd(II), or Pt(II), induces the cleavage of Agly peptides at room temperature and pH 7.3. The cleavage occurred in the absence of an anchoring His residue within the peptide but it was accelerated when this amino acid was present in the sequence. The influence of His residue on the cleavage rate was minimal when His and Agly were adjacent, whereas large effects were observed for distant His residues. The reaction between Cu(II) and Agly peptides induced the formation of Cu(I) species, which could be detected using bicinchoninic acid as a probe. The nature of products formed in this reaction allowed suggesting a mechanism for the Cu(II)‐induced cleavage of Agly peptides. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Reversible major histocompatibility complex I-peptide multimers containing Ni(2+)-nitrilotriacetic acid peptides and histidine tags improve analysis and sorting of CD8(+) T cells

MHC-peptide multimers containing biotinylated MHC-peptide complexes bound to phycoerythrin (PE) streptavidin (SA) are widely used for analyzing and sorting antigen-specific T cells. Here we describe alternative T cell-staining reagents that are superior to conventional reagents. They are built on reversible chelate complexes of Ni(2+)-nitrilotriacetic acid (NTA) with oligohistidines. We synthesized biotinylated linear mono-, di-, and tetra-NTA compounds using conventional solid phase peptide chemistry and studied their interaction with HLA-A*0201-peptide complexes containing a His(6), His(12), or 2×His(6) tag by surface plasmon resonance on SA-coated sensor chips and equilibrium dialysis. The binding avidity increased in the order His(6) < His(12) < 2×His(6) and NTA(1) < NTA(2) < NTA(4), respectively, depending on the configuration of the NTA moieties and increased to picomolar K(D) for the combination of a 2×His(6) tag and a 2×Ni(2+)-NTA(2). We demonstrate that HLA-A2-2×His(6)-peptide multimers containing either Ni(2+)-NTA(4)-biotin and PE-SA- or PE-NTA(4)-stained influenza and Melan A-specific CD8+ T cells equal or better than conventional multimers. Although these complexes were highly stable, they very rapidly dissociated in the presence of imidazole, which allowed sorting of bona fide antigen-specific CD8+ T cells without inducing T cell death as well as assessment of HLA-A2-peptide monomer dissociation kinetics on CD8+ T cells.     

Morphology and crystal structure of a recombinant silk-like molecule,SLP4

Morphology and crystal structure of a recombinant silk-like molecule, SLP4, were studied. Wide angle x-ray scattering (WAXS) and electron diffraction revealed that SLP4 lyophilized powder and thin films were isomorphic with the silk I crystal structure. Transmission electron microscopy of SLP4 thin films demonstrated a morphology of flat, variable width, crystallites that may aggregate in an epitaxial manner. Theoretical diffraction patterns from silk I crystal structure models were critically compared with SLP4 WAXS data. The analysis concluded that while the crankshaft model is capable of describing details of the SLP4 structural data well, the out-of-register model does not explain the experimental results. In particular, the predicted intensities of the crystallographic reflections for the out-of-register model are inconsistent with the SLP4 WAXS data. © 1998 John Wiley & Sons, Inc. Biopoly 45: 307–321, 1998     

Seven transmembrane receptors—A brief personal retrospective

Receptors have fascinated biologists for more than a century and they have fascinated me for the entirety of my own research career. The seven transmembrane receptors, also known as G protein coupled receptors, represent the largest of the several families of plasma membrane receptors, comprising more than a thousand genes and regulating virtually all known physiological processes in mammals. Moreover, they represent one of the commonest targets of currently used drugs. I have spent the entirety of my research career working on these receptors. Here I set down some personal reflections on the evolution of the field during the past 35 years, hanging the thread of the story on some of the work from my own laboratory.     

Seven transmembrane receptors: a brief personal retrospective

Receptors have fascinated biologists for more than a century and they have fascinated me for the entirety of my own research career. The seven transmembrane receptors, also known as G protein coupled receptors, represent the largest of the several families of plasma membrane receptors, comprising more than a thousand genes and regulating virtually all known physiological processes in mammals. Moreover, they represent one of the commonest targets of currently used drugs. I have spent the entirety of my research career working on these receptors. Here I set down some personal reflections on the evolution of the field during the past 35 years, hanging the thread of the story on some of the work from my own laboratory.     

Biological design — a neglected art

I ought now, perhaps, to offer a summary of what I have been trying to convey in this lecture — but I am haunted by the failure which attended an effort, by an eminent scholar of this city, to do something of the same kind many years ago. Sir John Sheppard, Provost of King's, once gave a public lecture during one of the University's ceremonial gatherings. His subject was the Trojan War. The large audience sat spellbound in admiration of his depth of insight, breadth of knowledge and grasp of detail. As he was leaving after the meeting, a young man came up to him and explained that he was a graduate studuent engaged in research on the economic consequences of the Trojan War. He had, however, been spellbound by the lecture and had been too engrossed to write anything down. Would Sir John be so kind as to lend him his notes so that he could make a summary of the lecture? “My dear chap”, said Sheppard, “I'd be delighted; here are my notes — use them as you wish and let me have them back whenever they have served your purpose”. So saying he handed the young man a postcard on which was written: Agamemnon — Achilles — Agamemnon.I hope that members of the audience won't mind if I leave them to make their own summary of my remarks to which they have listened so patiently this evening.     

Autolytic proteolysis within the function to find domain (FIIND) is required for NLRP1 inflammasome activity

Nucleotide-binding domain leucine-rich repeat proteins (NLRs) play a key role in immunity and disease through their ability to modulate inflammation in response to pathogen-derived and endogenous danger signals. Here, we identify the requirements for activation of NLRP1, an NLR protein associated with a number of human pathologies, including vitiligo, rheumatoid arthritis, and Crohn disease. We demonstrate that NLRP1 activity is dependent upon ASC, which associates with the C-terminal CARD domain of NLRP1. In addition, we show that NLRP1 activity is dependent upon autolytic cleavage at Ser(1213) within the FIIND. Importantly, this post translational event is dependent upon the highly conserved distal residue His(1186). A disease-associated single nucleotide polymorphism near His(1186) and a naturally occurring mRNA splice variant lacking exon 14 differentially affect this autolytic processing and subsequent NLRP1 activity. These results describe key molecular pathways that regulate NLRP1 activity and offer insight on how small sequence variations in NLR genes may influence human disease pathogenesis.     

Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution

The structure of Mn(III) superoxide dismutase (Mn(III)SOD) from Thermus thermophilus, a tetramer of chains 203 residues in length, has been refined by restrained least-squares methods. The R-factor [formula: see text] for the 54,056 unique reflections measured between 10.0 and 1.8 A (96% of all possible reflections) is 0.176 for a model comprising the protein dimer and 180 bound solvents, the asymmetric unit of the P4(1)2(1)2 cell. The monomer chain forms two domains as determined by distance plots: the N-terminal domain is dominated by two long antiparallel helices (residues 21 to 45 and 69 to 89) and the C-terminal domain (residues 100 to 203) is an alpha + beta structure including a three-stranded sheet. Features that may be important for the folding and function of this MnSOD include: (1) a cis-proline in a turn preceding the first long helix; (2) a residue inserted at position 30 that distorts the helix near the first Mn ligand; and (3) the locations of glycine and proline residues in the domain connector (residues 92 to 99) and in the vicinity of the short cross connection (residues 150 to 159) that links two strands of the beta-sheet. Domain-domain contacts include salt bridges between arginine residues and acidic side chains, an extensive hydrophobic interface, and at least ten hydrogen-bonded interactions. The tetramer possesses 222 symmetry but is held together by only two types of interfaces. The dimer interface at the non-crystallographic dyad is extensive (1000 A2 buried surface/monomer) and incorporates 17 trapped or structural solvents. The dimer interface at the crystallographic dyad buries fewer residues (750 A2/monomer) and resembles a snap fastener in which a type I turn thrusts into a hydrophobic basket formed by a ring of helices in the opposing chain. Each of the metal sites is fully occupied, with the Mn(III) five-co-ordinate in trigonal bipyramidal geometry. One of the axial ligands is solvent; the four protein ligands are His28, His83, Asp166 and His170. Surrounding the metal-ligand cluster is a shell of predominantly hydrophobic residues from both chains of the asymmetric unit (Phe86A, Trp87A, Trp132A, Trp168A, Tyr183A, Tyr172B, Tyr173B), and both chains collaborate in the formation of a solvent-lined channel that terminates at Tyr36 and His32 near the metal ion and is presumed to be the path by which substrate or other inner-sphere ligands reach the metal.(ABSTRACT TRUNCATED AT 400 WORDS)     

McArthur revisited: fluorescence microscopes for field diagnostics

Few scientific instruments become eponymous with their inventors. Among those that have is the 'McArthur'. As a student in the 1930s, John Norris McArthur wanted a portable microscope to take on field trips. His rugged pocket field microscope [Mcarthur, J. (1958) A new concept in microscope design for tropical medicine. Am. J. Trop. Med. Hyg. 7, 382-385] remains a classic of compact design and performance, and has been used for malaria diagnosis over several decades. The 'McArthur' has dimensions of 102x63x51mm (McArthur folded the 160mm path length with a prism) and uses phase-contrast and specialised oil immersion objective lenses. Later, a plastic version was developed and further adapted for the Open University by Kirk & Sons, UK [McArthur J. (1971) The McArthur microscope--open university model. Trans. R. Soc. Trop. Med. Hyg. 65, 438].