Ultraviolet polarization vision in fishes: possible mechanisms for coding e-vector

Polarization vision in vertebrates has been marked with significant controversy over recent decades. In the last decade, however, models from two laboratories have indicated that the spatial arrangement of photoreceptors provides the basis for polarization sensitivity Work in my laboratory, in collaboration with I. Novales Flamarique and F. I. Harosi, has shown that polarization sensitivity depends on a well-defined square cone mosaic pattern and that the biophysical properties of the square cone mosaic probably account for polarization vision in the ultraviolet spectrum. The biophysical mechanism appears to be based on the selective reflection of axial-polarized light by the partitioning membrane, formed along the contact zone between the members of the double cones, onto neighbouring ultraviolet-sensitive cones. In this short review, I discuss the historical development of this research problem.     

Statistical consistency and phylogenetic inference: a brief review

The claim that parsimony can be statistically inconsistent remains the chief criticism of the cladistic approach, and also the main justification for alternative model‐based approaches such as maximum likelihood and Bayesian inference. Despite its refutation in the 1980s, this persistent myth of parsimony's Achilles’ heel is entrenched in the primary literature, and has metastasized into textbooks, as well. Here, I review historical controversies, and offer three short arguments as to why statistical consistency is not only irrelevant to systematics, but to empirical science in general.     

Reviewing Literature in Bioethics Research: Increasing Rigour in Non‐Systematic Reviews

The recent interest in systematic review methods in bioethics has highlighted the need for greater transparency in all literature review processes undertaken in bioethics projects. In this article, I articulate features of a good bioethics literature review that does not aim to be systematic, but rather to capture and analyse the key ideas relevant to a research question. I call this a critical interpretive literature review. I begin by sketching and comparing three different types of literature review conducted in bioethics scholarship. Then, drawing on Dixon‐Wood's concept of critical interpretive synthesis, I put forward six features of a good critical interpretive literature review in bioethics: answering a research question, capturing the key ideas relevant to the research question, analysing the literature as a whole, generating theory, not excluding papers based on rigid quality assessment criteria, and reporting the search strategy.     

To be or not to be ... nicotinic acid adenine dinucleotide phosphate (NAADP): a new intracellular second messenger?

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a potent activator of intracellular Ca2+ release in several vertebrate and invertebrate systems. The role of the NAADP system in physiological processes is being extensively investigated at the present time. The NAADP receptor and its associated Ca2+ pool have been hypothesized to be important in several physiological processes including fertilization, T cell activation, and pancreatic secretion. However, whether NAADP is a new second messenger or a tool for the discovery of a new Ca2+ channel is still an unanswered question. Research developed over the last two years has provided some important clues to whether NAADP is or not a physiological cellular messenger. In this short review, I will discuss some of these new findings that are helping us to find an answer to the important question: Is NAADP a second messenger or not?     

Analyzing protein–protein interactions in the post-interactomic era. Are we ready for the endgame?

Mapping protein–protein interactions in genome-wide scales revealed thousands of novel binding partners in each of the explored model organisms. Organizing these hits in comprehensive ways is becoming increasingly important for systems biology approaches to understand complex cellular processes and diseases. However, proteome wide interaction techniques and their resulting global networks are not revealing the topologies of networks that are truly operating in the cell. In this short review I will discuss which prerequisites have to be fulfilled and which experimental methods might be practicable to translate primary protein interaction data into network presentations that help in understanding cellular processes.     

When pol I goes into high gear: processive DNA synthesis by pol I in the cell

Pol I is the most abundant polymerase in E. coli and plays an important role in short patch repair. In accord with this role in the cell, the purified polymerase exhibits low processivity and high fidelity in vitro. Pol I is also the polymerase responsible for leader strand synthesis during ColE1 plasmid replication. In a previous publication, we described the generation of a highly error-prone DNA polymerase I. Expression of this mutant Pol I results in errors during the replication of a ColE1 plasmid. The distribution and spectrum of mutations in the ColE1 plasmid sequence downstream the ori indicates that Pol I is capable of more processive replication in vivo than previously accepted. Here, we review evidence suggesting that Pol I may be recruited into a replisome-like holoenzyme and speculate that processive DNA replication by Pol I may play a role in recombination-dependent DNA replication in the cell.     

When Pol I Goes into High Gear: Processive DNA Synthesis by Pol I in the Cell

Pol I is the most abundant polymerase in E. coli and plays an important role in short patch repair. In accord with this role in the cell, the purified polymerase exhibits low processivity and high fidelity in vitro. Pol I is also the polymerase responsible for leader strand synthesis during ColE1 plasmid replication. In a previous publication, we described the generation of a highly error-prone DNA polymerase I. Expression of this mutant Pol I results in errors during the replication of a ColE1 plasmid. The distribution and spectrum of mutations in the ColE1 plasmid sequence downstream the ori indicates that Pol I is capable of more processive replication in vivo than previously accepted. Here, we review evidence suggesting that Pol I may be recruited into a replisome-like holoenzyme and speculate that processive DNA replication by Pol I in the cell may play a role in recombination-dependent DNA replication.     

Microcomputer control of behavior and the acquisition of digital and analog data

Advances in technology and decreasing costs are enabling microcomputers to displace more traditional devices in the scientific laboratory. The availability of various approaches to software-system development for the use of microcomputers in the on-line control of experiments has contributed to the trend. This report describes a software system developed to control conditioned behavior during schedules of reinforcement while simultaneously accumulating behavioral data and physiological (analog) data using a hardware system based on the Radio Shack TRS-80 Model I microcomputer. The software utilizes a high-level interpretive language (Microsoft BASIC), assembly language and compiled BASIC to attain an acceptable execution speed and ease of programming.     

Unraveling the Photosystem I Reaction Center: A History,or the Sum of Many Efforts

This article describes some aspects of the history of the discovery of the structure and function of Photosystem I (PS I). PS I is the largest and most complex membrane protein for which detailed structural and functional information is now available. This short historical review cannot cover all the work that has been carried out over more than 50 years, nor provide a deep insight into the structure and function of this protein complex. Instead, this review focuses on more personal views of some of the key discoveries, starting in the 1950s with the discovery of the existence of two photoreactions in oxygenic photosynthesis, and ending with the race towards an atomic structure of PS I.     

Personal recollections

I hope that this article will provide a short review of my involvement with physical and biological aspects of 'excluded volume' or 'molecular crowding'. The list of references is not exhaustive, but is meant primarily to acknowledge my debt to my many colleagues.     

Plant Communities of Western Amazonia

In this review I focus on the socially and ecologically important western Amazon basin and its associated plant communities. I delineate this vast area as between the Andes to the west and the confluence of the Amazon and its first major black-water river, the Rio Negro, to the east. Although scientists have explored here, and local people have lived here for years, we still have—unfortunately—only a most basic understanding of its plant communities. This review is motivated by that lack of knowledge, and attempts both to add a level of organization to what we do know and to suggest future avenues of research. I do this by first realizing that plant communities here must be fundamentally differentiated by the degree of flooding they experience, the kind of water involved, and how regularly that flooding occurs. Within that context, plant communities can then be further defined by such characteristics as soil type, micro-topological relief, and human-induced disturbance regime. After completing the review, I suggest that the diversity of plant communities, not just the plants themselves, is large and likely to grow substantially as we sample more and more, that is to say the peak of the plant community-sampling area curve has not yet been reached. I close with basic questions to help guide future efforts, ideas on how plant communities could be defined quantitatively, and a call for more research funding of the Western Amazon.     

Variation in female mate choice within guppy populations: population divergence,multiple ornaments and the maintenance of polymorphism

The evolutionary significance of variation in mate choice behaviour is currently a subject of some debate and considerable empirical study. Here, I review recent work on variation within and among guppy (Poecilia reticulata) populations in female mate choice and mating preferences. Empirical results demonstrate that there is substantial variation within and among populations in female responsiveness and choosiness, and much of this variation is genetic. Evidence for variation in preference functions also exists, but this appears to be more equivocal and the relative importance of genetic variation is less clear cut. In the second half of this review I discuss the potential significance of this variation to three important evolutionary issues: the presence of multiple male ornaments, the maintenance of polymorphism and divergence in mate recognition among populations. Studies of genetic variation in mate choice within populations indicate that females have complex, multivariate preferences that are able to evolve independently to some extent. These findings suggest that the presence of multiple male ornaments may be due to multiple female mating preferences. The extreme polymorphism in male guppy colour patterns demands explanation, yet no single satisfactory explanation has yet emerged. I review several old ideas and a few new ones in order to identify the most promising potential explanations for future empirical testing. Among these are negative frequency dependent selection, environmental heterogeneity coupled with gene flow, and genetic constraints. Last, I review the relative extent of within and among-population variation in mate choice and mating preferences in order to assess why guppies have not speciated despite a history of isolation and divergence. I argue that variation within guppy populations in mate choice and enhanced mating success of new immigrants to a pool are major impediments to population divergence of the magnitude that would be required for speciation to occur.     

Where the Tadpole Meets the World--Observations and Speculations on Biomechanical and Biochemical Factors that Influence Metamorphosis in Anurans

SYNOPSIS. A diversity of issues related to metamorphosis arediscussed in this paper, ranging from biomechanical constraintson behavior in premetamorphic anurans, to environmental factorsthat regulate metamorphosis. I begin by reviewing key behavioralfeatures of tadpoles that have implications to their form andlocomotion. Tadpoles lack all visceral behaviors, such as emesis, coughing,and egg-laying, that require major elevations of pressure inthe pleuroperitoneal cavity. I suggest that the inability toforcefully elevate pleuroperitoneal pressure is a consequenceof the tadpoles' short and inflexible spine. Although postmetamorphicfrogs have a similarly short vertebral column, they can compressviscera by movement at sacroiliac joints, which are absent intadpoles. I argue that the short torso of tadpoles is a necessaryconsequence of the need to innervate the frog's limbs earlyin development so that they can be fully functional by the endof metamorphosis. The short torso is a good mechanical design for the saltatoryfrog, but afflicts the tadpoles with a distinctly globous shapethat intuitively appears inefficient for aquatic locomotion.Computational fluid dynamics (CFD) models, however, reveal thattadpoles are, in fact, efficient undulatory swimmers comparedto subcarangiform fishes and that their swimming kinematicswork in concert with their shape to help generate thrust. Furthermorethe CFD models show that the crease in the dorsal profile oftadpoles, where the body abruptly meets the tail, produces a"dead water" zone immediately behind the body of the tadpole.As a result, tadpoles can grow hindlimbs in this region withoutthose limbs seriously impeding flow. Thus the shape of tadpolesnicely matches their need to transform into limbed tetrapods. In the latter half of this paper I review ideas on how environmentalfactors could influence metamorphosis in anurans. One speculationis that tadpoles may secrete a metamorphic inhibitor in theiroral mucus, which they then ingest with their food, with theresult that metamorphosis is delayed when food is abundant.An epidermal growth factor-like peptide has been suggested asa possible metamorphic inhibitor along the pathway just proposed.Strengths and weaknesses of this hypothesized agent and pathwayare reviewed. An experiment to test the hypothesis that orallyingested EGF inhibits metamorphosis yielded inconclusive results.Orally secreted EGF-like peptide may not inhibit metamorphosisof the tadpole gut, but other yet-to-be-identified factors intadpole oral mucus could still play a role in regulating metamorphosisof the alimentary tract in anurans. The essay ends with some broad speculations on the role thatpeptides in frogs' skin may play in the metamorphic processas well as several unanswered questions about how other organismsand the physical environment influence tadpole metamorphosis.     

Tree invasion and establishment in old fields at Hutcheson Memorial Forest

In this review I present results from pattern analysis and field experiments in New Jersey, United States concerning tree invasion and establishment in old fields. Hutcheson Memorial Forest Center (HMF) is the New Jersey study site and a logical choice to anchor a review of this topic. HMF contains the longest and largest old field permanent plot study in the USA including extensive data concerning tree invasion and establishment. HMF has also been the site of considerable old field tree experimental research. In addition, I review other investigations of old field tree invasion and establishment of the eastern deciduous biome and contrast them with HMF. I identify critical questions concerning tree invasion and establishment, indicate what progress has been made towards answering these questions and propose future experimentation. I also synthesize results into a conceptual model and investigate the relative importance of seed and seedling processes in determining tree dynamics in old fields. The idea of a possibility or “window” for tree invasion and establishment and its variation form the basis for this review. For example, the temporal variation of windows is reflected in tree establishment patterns at HMF because wind- and bird-dispersed species invaded one year after cessation of cultivation while mammal-dispersed species were not present until year 12. Although analysis of size classes of individual HMF trees imply that windows close quickly, studies are of too short duration to tell definitely. Spatial variation in invasion and establishment pattern includes exponential decline in seed and stem density with distance from forest edge which deteriorates with time as the old field becomes more structurally complex. Additional spatial heterogeneity occurs when seeds and seedlings of bird-dispersed species clump which conversely becomes more pronounced with time. Many of these HMF patterns are seen in other eastern United States old field sites. When reviewing field experiments from my site and others, I focus on the spatial and temporal variation and the difference between species in the effect of processes on tree seeds and seedlings. I do this because this variation relates directly to the dynamic nature of windows whose quantification is necessary for modeling. Combining my pattern analysis with a survey of variation in seed and seedling mortality caused by different successional processes in old fields, I conclude that seed dispersal, conditions necessary for seed germination and seed and seedling predation are the critical processes controlling and constraining tree invasion and establishment in old fields. Competition and indirect effects of litter and the environment, which modify how these processes affect tree dynamics, are also important. Therefore, processes involving the interaction of species with the environment and with other species form the principal filters on and limitations to tree invasion and establishment and not the non-interactive life-history traits of individual tree species such as growth rate or longevity. The interaction of pattern and process and the affect of many of these processes on old field community structure are also discussed.     

Absence of evidence is not evidence of absence

Imperfect detection of a species is often a problem when attempting to establish its presence or absence at a set of locations. Failing to find the required evidence that a species is present at a location does not imply that the species is absent, merely that it has not been found. Some of the consequences of imperfect detection is that assessments of factors influencing species presence/absence can be misleading, and how certain can one be that the species is really absent given it has not detected at a location. In this talk I shall briefly review some of the consequences of imperfect detection, methodological advances that enable the detection process to be explicitly accounted for, and practical ways in which the required additional information can be collected.     

Discovery of myosin I and Pollard-san

In this short review, I describe a brief history of the discovery of myosin I isolated from Acanthamoeba in 1973 by Tom Pollard and Ed Korn. Today, myosins form a large “family tree” that includes more than 30 types of myosins. I discuss the importance of the relationship among actin, myosin, and other actin-binding proteins, many of which were pioneered by Pollard-san (“-san” is a Japanese honorific suffix showing respect, politeness and friendship). At the first conference devoted to actin, Pollard-san, Korn-san, and I discussed the importance of the nucleotide bound at the two ends of the actin filament. I conclude that life is a dynamic accumulation of molecule-molecule bindings, and although we do not yet know how they coordinate with each other to operate a living cell, many enthusiastic and excellent researchers like Pollard-san will unveil mechanisms that will show us what life really looks like.     

Will technology trample peer review in ecology? Ongoing issues and potential solutions

The classical view of peer review is that it is our primary process for assessing and judging whether research results should be published in a scholarly journal. However, the increased pressure to publish and technological developments are transforming peer review such that it is becoming a system that judges where work is published rather than whether the research is publishable (a ‘where rather than if’ process). Ecology is a field in which publication numbers puts a particular pressure on the review system. In this forum piece, I summarize the issues with the current publication system and discuss how technology is changing it, while suggesting solutions for important prior and ongoing issues with the peer review system. The view explored here is that technological developments (e.g. ease of creating journals, internet sites, storage, data generation, sharing of data and analytical code) will not eliminate peer review per se but will allow for a new set of parameters in which ethics and the optimal use of public funding will play a vital role in the evolution of the review process. Synthesis The number of papers and journals in Ecology has increased dramatically in the past decade. I present a critical overview of our review system and proposes that pressure to publish and technological developments have transformed peer review into a system that decides “where rather than if” papers are publishable. While reviewing the current pressures and factors playing a vital role in the evolution of the review and publication systems, I propose potential solutions to deal with current and future challenges to the peer review and publication systems.     

Recombinant human insulin-like growth factor I (IGF-I): risks and benefits of normalizing blood IGF-I concentrations

Recombinant human (rh) insulin-like growth factor I (IGF-I) is being developed as a therapy for short stature caused by IGF deficiency (IGFD) and also for diabetes mellitus. To complement the human efficacy and safety data, a large amount of information is available regarding the pharmacology and toxicology of rhIGF-I in animals. This review summarizes the risks and benefits of normalizing blood IGF-I concentrations in IGFD, especially with regard to carcinogenicity, and compares and contrasts safety data for rhIGF-I, recombinant human growth hormone (rhGH), and insulin. A major difference between rhIGF-I and rhGH is that rhIGF-I (like insulin) has hypoglycaemic activity, whereas rhGH opposes insulin action and is diabetogenic. In most of their actions, GH and IGF-I are similar. IGF-I mediates most of the actions of GH, so the safety of rhGH and that of rhIGF-I also share many common features. In animals, the transgenic expression of hGH has been shown to act directly, by activating the prolactin receptor, to increase the incidence of mammary and prostate tumours. In comparison, the over-expression of IGF-I in animals or the administration of rhIGF-I does not have a carcinogenic effect. In formal toxicology and carcinogenicity studies, rhIGF-I has similar effects to insulin in that it can increase food intake, body size, and the growth rate of existing tumours. In animals and humans, IGFD has many long-term detrimental effects besides short stature: it increases the risk of diabetes, cardiovascular disease, and low bone mineral density. Therefore, a case can be made for replacement therapy with rhIGF-I to normalize blood IGF-I levels and reverse the detrimental effects of IGFD.     

Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!     

CRISPR/Cas9基因组编辑技术在农业动物中的应用

CRISPR(Clustered regularly interspaced short palindromic repeats)/Cas(CRISPR associated proteins)是在细菌和古细菌中发现的一种用来抵御病毒或质粒入侵的获得性免疫系统.目前已发现的CRISPR/Cas系统包括Ⅰ,Ⅱ和Ⅲ型,其中Ⅱ型系统的组成较简单,由其改造成的CRISPR/Cas9技术已成为一种高效的基因组编辑工具.自2013年CRISPR/Cas9技术成功用于哺乳动物基因组定点编辑以来,应用该技术进行基因组编辑的报道呈现出爆发式的增长.农业动物不仅是重要的经济动物,也是人类疾病和生物医药研究的重要模式动物.本文综述了CRISPR/Cas9技术在农业动物中的研究和应用进展,简述了该技术的脱靶效应及减少脱靶的主要方法,并展望了该技术的应用前景.