Adaptation genomics: the next generation

Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?     

WHO ARE THE BENEFICIARIES?

Is it defensible that society spends money on medical or research projects intended to help people solve their fertility problems? Suppose that we want to answer this question from the point of view of a utilitarian cost-benefit analysis. The answer to the question then depends, of course, on how expensive these projects turn out to be, relative to the costs of other possible projects. But it depends also on how we assess the benefits of these projects. To whom do they accrue? Who are the beneficiaries of these projects?     

Dynamics of Posttranslational Modification Systems: Recent Progress and Future Directions

Posttranslational modification of proteins is important for signal transduction, and hence significant effort has gone toward understanding how posttranslational modification networks process information. This involves, on the theory side, analyzing the dynamical systems arising from such networks. Which networks are, for instance, bistable? Which networks admit sustained oscillations? Which parameter values enable such behaviors? In this Biophysical Perspective, we highlight recent progress in this area and point out some important future directions. Along the way, we summarize several techniques for analyzing general networks, such as eliminating variables to obtain steady-state parameterizations, and harnessing results on how incorporating intermediates affects dynamics.     

The library in the digital age

Electronic publication is an increasingly popular forum within the scientific community, and many are talking about the possibility of dispensing with paper publications entirely in years to come. How likely is this to happen, and if so how quickly? What will be its impact on the way we use and contribute to the scientific knowledge base? This article discusses the elements of today's digital library and how they might evolve as we confront the online world.     

Nitrogen and phosphorus translocation of forest floor mosses as affected by a pulse of these nutrients

藓类是亚高山森林、北方针叶林和极地苔原等原始生态系统的重要组成部分。养分沉降是这些生态系统的主要养分来源。然而,对 藓类如何利用大气沉降这一时间上异质性较高的养分来源的认识缺乏,限制了我们对藓类在生态系统养分循环中作用的认识,也制约了模 拟和预测生态系统服务功能动态变化的有效性。本研究中,我们重点关注如下问题：(1)藓类新生部分的氮、磷含量随氮或磷沉降量的变化; (2)氮或磷养分沉降如何影响藓类的氮磷转运;(3)氮磷转运与藓类新生部分养分含量的关联性？为此,我们在位于青藏高原东部的亚高山 冷杉林中开展了设置有不同氮、磷施加量水平的突发养分沉降实验。以林下优势度最高的塔藓和锦丝藓为对象,我们在施加实验处理8天和1年后,分别测定了不同年龄藓类茎段中的氮、磷含量。研究结果发现,养分处理8天后,锦丝藓和塔藓的所有茎段的氮或磷含量均随处理中氮或磷施加量的增加而增加,表明它们能够高效率地吸收施加的氮或磷。养分处理1年后,形成于养分处理后的新生茎段中的氮、磷含量以及氮磷比与处理后8天的藓类茎段中氮、磷含量以及氮磷比呈正相关关系,表明藓类将吸收的养分转运至新生部分,转运过程受源—库关系的调控。磷转运效率解释了新生茎段21%–23%的氮磷比变化,而氮转运与新生茎段氮磷比没有显著关系,结果暗示磷转运对藓类生长的重要性。上述结果表明,养分转运是藓类植物利用间断的沉降养分的关键机制,也使藓类成为生态系统中重要的养分库。     

How we do business (or, Why does it take other journals so long to review your paper?)

Have you ever wondered why it takes so long to get comments back from reviewers at some journals? After all, how long should it take to review a paper? I suspect most of us have asked this question at one time or another. While recently contemplating this, I thought it was time to tell you a little about how we run Autophagy, and at the same time compare it to the practices at some other journals where I have, on occasion (notably before the start of Autophagy), sent my own papers.     

Breaking down the blood-brain barrier: signaling a path to cerebral malaria?

Cerebral malaria is a major killer in the developing world, but we still know very little about the causes of this disease. How does Plasmodium falciparum cause such a devastating neurological disease while it is in the brain vasculature? Why do some patients die, whereas others survive? What processes contribute to disease in the brain, and can we reverse them? Here, the latest evidence from post-mortem, in vitro and animal studies is reviewed to highlight the role of blood-brain barrier breakdown in cerebral malaria. Blood-brain barrier integrity is disturbed during severe malaria, causing leakage of cerebral vessels. Understanding how this happens and how it contributes to the pathogenesis of coma may provide new opportunities for the treatment of cerebral malaria.     

Towards an understanding of how policy making groups use indicators

Groupthink is a known weakness leading to a number of problems relating primarily to false senses of consensus. But, positive group ‘wisdom’ is an ideal which many aspire to make happen but few manage to achieve in practice. The mystery of the group comes at a number of levels and raises various issues. What is the relative importance of how groups assemble? How they are motivated? The value of inducement? How can group work be assessed and how is a ‘good’ group identified? How is positive and not negative group working achieved? How is group working linked to what the group achieves? In the area of policy use of indicators the function of the group becomes more critical. In an age of transparency in decision making and calls for more evidence-based policy, the importance of good group work is becoming vital if the project is to succeed. Based on research undertaken around the European Union between 2009 and 2010 this paper explores some of these questions by providing a series of ‘rich pictures’ of indicator use, the meanings ascribed to the pictures by the group members and some insights regarding the dynamics of the groups that rest behind them and how this may have influenced the stories told by the pictures. We argue that in many ways the pictures represent a window to the understanding of the groups use of indicators.     

Tangles of neurogenetics, neuroethics, and culture

Neurogenetics promises rich insights into how the mind works. Researchers investigating the range of topics from normal brain functioning to pathological states are increasingly looking to genetics for clues on human variability and disease etiology. Is it fair to assume this interest in neurogenetics is universal? How should researchers and clinicians approach ideas of consent to research or prediction of disease when a subject or patient understands the mind with concepts or language incompatible with neurogenetics? In this paper we consider how non-Western philosophies bring complexity to ideas of individual and community consent and confidentiality in the context of neurogenetics.     

Pods and Nods: a new look at symbiotic nitrogen fixing bacteria

How can growing a crop plant make a field more fertile? With legumes, this is precisely what happens. Working in partnership with symbiotic bacteria that can create root nodules on their chosen host, legumes can fix atmospheric nitrogen and enhance the nitrogen status of soils. How does this symbiosis develop? And how did it evolve? Bacterial and plant genomics are beginning to provide the answers.     

The Evaluation of Protein Structure Prediction Results

Methods for protein structure prediction are flourishing and becoming widely available to both experimentalists and computational biologists. However, how good are they? What is their range of applicability and how can we know which method is better suited for the task at hand? These are the questions that this review tries to address, by describing the worldwide Critical Assessment of techniques for protein Structure Prediction (CASP) initiative and focusing on the specific problems of assessing the quality of a protein 3D model.     

Toward a dynamic model of deposition and utilization of yolk steroids

The discovery by Schwabl that maternal steroid hormones aretransferred to the egg yolk and have effects on the phenotypeof offspring revealed a new pathway for non-genetic maternaleffects. The initial model relied on passive transfer. The thinkingwas that steroids passively entered the lipophillic yolk duringyolk deposition and then were deposited in the yolk until theywere passively delivered to the embryo as the yolk was used.Subsequent studies revealed that the system is much more dynamicthan that. Here, we explore questions about how dynamic thesystem really is and look at questions like: Is transfer ofmaternal steroids to the yolk passive or is it actively regulated?At what stages of the maternal reproductive cycle are steroidstransferred? During reproduction, how dynamic are the levelsof yolk steroids? Especially in the case of potentially deleterioussteroids (e.g., androgens in female offspring; glucocorticoids),once deposited can they come out of the yolk over time? Canthey be metabolized by the yolk or by the embryo? During incubation,how much do steroid levels in the yolk change? Can steroidsdiffuse from the yolk to the embryo prior to yolk utilization?Does the embryo contribute to yolk steroid levels as it develops?We believe that comprehensive answers to questions like thesewill eventually allow us to generate a much more accurate andcomplete model of the transfer and utilization of yolk steroidsand that this model will be much more dynamic and active thanthe one initially proposed.     

Illusion susceptibility in domestic dogs

Domestic dogs play many vital roles in human lives; however, relatively little is known about how they perceive the world visually. Given dogs’ recent popularity as a subject in cognitive and behavioural studies, it is important to understand how they visually interpret the world around them. One way to evaluate perception is to assess illusion susceptibility; specifically, how visual information is processed, interpreted and modified post-retinally. While illusion susceptibility has been used across a variety of species to comparatively assess the similarities and differences in visual processing and perception, this relatively novel methodological approach has only recently been adapted to evaluate perception in domestic dogs. Here, we present a comprehensive overview of the findings from studies that have evaluated domestic dogs’ illusion susceptibility, highlighting the relevance of these results for those studying illusion susceptibility in animals as well as canine behaviour and cognition. More specifically, the ultimate goal of this review is to answer the questions: (a) Are dogs susceptible to visual illusions? (b) If so, are they susceptible to illusions in a way that parallels humans and/or other animals? (c) Are findings, within dogs, consistent and if not, how might these be interpreted and explained?     

Abu Sayyaf: Displays of Violence and the Proliferation of Contested Identities among Philippine Muslims

Violence between and among Christians and Muslims of the southwestern Philippines provides the ethnographic setting for an investigation of Herzfeld's paradox of social indifference. But there is yet another paradox in this case: Why has this 400-year conflict been characterized by a proliferation of contested identities among the insurgents, those who most need to be united?
Is this another case of the force of "hegemony," with the oppressed somehow duped into practices detrimental to their own interests? But how? And by what agency? The Philippine case reveals the challenging complexities of identity construction to be faced in any attempt to reach an understanding of these issues.     

Motor neurons and the sense of place

Seventy years ago George Romanes began to document the anatomical organization of the spinal motor system, uncovering a multilayered topographic plan that links the clustering and settling position of motor neurons to the spatial arrangement and biomechanical features of limb muscles. To this day, these findings have provided a structural foundation for analysis of the neural control of movement and serve as?a guide for studies to explore mechanisms that direct the wiring of spinal motor circuits. In this brief essay we outline the?core of Romanes's findings and place them in the context of recent studies that begin to provide insight?into molecular programs that assign motor pool position and to resolve how motor neuron position shapes circuit assembly. Romanes's findings reveal how and why neuronal positioning contributes to sensory-motor connectivity and may have relevance to circuit organization in other regions of the central nervous system.     

The pessimist's and optimist's views of adult neurogenesis

The reports by Bonaguidi et?al. (in this issue of Cell) and Encinas et?al. (in Cell Stem Cell) come to differing conclusions about whether and how the proliferation of radial glia-like stem cells of the adult hippocampus impacts their long-term potential for neurogenesis.     

How we do business (or,why does it take other journals so long to review your paper?)

Have you ever wondered why it takes so long to get comments back from reviewers at some journals? After all, how long should it take to review a paper? I suspect most of us have asked this question at one time or another. While recently contemplating this question I thought it was time to tell you a little about how we run Autophagy, and at the same time compare it to the practices at some other journals where I have, on occasion (notably before the start of Autophagy), sent my own papers.     

Lymphocyte choriomeningitis virus plays hide-and-seek with type 1 interferon

In this issue, Macal et?al. (2012); Walsh et?al. (2012), and Wang et?al. (2012) examine how adaptive immune responses to acute and chronic lymphocyte choriomeningitis virus infection are regulated by type 1 interferon produced early during infection by different cell types upon activation by intracellular nucleic acid sensors.     

A genetic push to understand motion detection

Two articles in this issue of Neuron (Eichner et?al. and Clark et?al.) attack the problem of explaining how neuronal hardware in Drosophila implements the Reichardt motion detector, one of the most famous computational models in neuroscience, which has proven intractable up to now.     

Sex, strains and virulence

When are populations of infectious agents likely to evolve into distinct strains? Are they likely to differ in their virulence? Will genetically distinct strains or clones remain stable long enough to be useful as epidemiological markers? Sexual recombination can break down the genetic associations that define a strain structure, but if sex is rare or inbreeding is common, can strains persist? In this paper Ian Hastings and Bruce Wedgwood-Oppenheim show how some simple population genetic theory may provide a basis for addressing these questions.