How do plants make mitochondria?

Plant mitochondria can differ in size, shape, number and protein content across different tissue types and over development. These differences are a result of signaling and regulatory processes that ensure mitochondrial function is tuned in a cell-specific manner to support proper plant growth and development. In the last decade, the processes involved in mitochondrial biogenesis are becoming clearer, including; how dormant seeds transition from empty promitochondria to fully functional mitochondria with extensive cristae structures and various biochemical activities, the regulation of nuclear genes encoding mitochondrial proteins via regulators of the diurnal cycle in plants, the mitochondrial stress response, the targeting of proteins to mitochondria and other organelles and connections between the respiratory chain and protein import complexes. All these findings indicate that mitochondrial function is a part of an integrated cellular network, and communication between mitochondria and other cellular processes extends beyond the known exchange or transport of metabolites. Our current knowledge now needs to be used to gain more insight into the molecular components at various levels of this hierarchical and complex regulatory and communication network, so that mitochondrial function can be predicted and modified in a rational manner.     

How do invasive species travel to and through urban environments?

Globalisation has resulted in the movement of organisms outside their natural range, often with negative ecological and economic consequences. As cities are hubs of anthropogenic activities, with both highly transformed and disturbed environments, these areas are often the first point of entry for alien species. We compiled a global database of cities with more than one million inhabitants that data had on alien species occurrence. We then identified the most prominent pathways of introduction and vectors of spread of alien species in these cities. Most species were intentionally introduced to cities and were released or escaped from confinement. The majority of alien species then spread within cities through natural means (primarily unaided dispersal). Pathway prominence varied across the taxonomic groups of alien species: the most prominent pathway for plants and vertebrates was the escape pathway; for invertebrates the stowaway and contaminant pathways were most likely to facilitate introductions. For some organisms, pathway prominence varied with the geographical and climatic characteristics of the city. The characteristics of the cities also influenced the prominence of vectors of spread for alien species. Preventing the natural spread of alien species within cities, and into adjacent natural environments will be, at best, difficult. To prevent invasions, both the intentional and unintentional introduction of potentially harmful alien species to cities must be prevented. The pathways of introduction and vectors of spread identified here should be prioritised for management.     

Physician prescribing practices: What do we know? Where do we go? How do we get there?

Although drug prescribing is one of the most important components of medical care, little is known about how prescribing practices are determined and how they can be influenced. Enhancing the quality and effectiveness of drug prescribing requires research and better dissemination of information to physicians and other decision-makers. This requires a collaborative effort and a coordinated action plan. Participants at the Physician Prescribing Practices Workshop, held in Ottawa in October 1995, addressed issues and made recommendations in three areas: current knowledge and issues for research in the field of prescribing practices, and the capacity of Canadian databases to study these issues, strategies for disseminating and implementing knowledge and research findings to enhance the quality of prescribing; and the formation of a network to foster collaboration among stakeholders.     

How do genes make teeth to order through development?

This introduction to new patterning theories for the vertebrate dentition outlines the historical concepts to explain graded sequences in tooth shape in mammals (incisors, canines, premolars, molars) which change in evolution in a linked manner, constant for each region. The classic developmental models for shape regulation, known as the 'regional field' and 'dental clone' models, were inspired by the human dentition, where it is known that the last tooth in each series is the one commonly absent. The mouse, as a valuable experimental model, has provided data to test these models and more recently, based on spatial-temporal gene expression data, the 'dental homeobox code' was proposed to specify regions and regulate tooth shape. We have attempted to combine these hypotheses in a new model of the combinatorial homeobox gene expression pattern with the clone and field theories in one of 'co-operative genetic interaction'. This also explains the genetic absence of teeth in humans ascribed to point mutations in mesenchymally expressed genes, which affect tooth number in each series.     

How do we compare hundreds of bacterial genomes?

The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.     

How do neutrophils and pathogens interact?

Many pathogens can manipulate macrophages after phagocytosis yet are efficiently killed by neutrophils. This poses the question of whether neutrophils have mechanisms that enable them to specifically recognise pathogens and have pathogens evolved mechanisms to modulate neutrophil function? Here, we review recent work on neutrophils and their interaction with four different bacteria: Staphylococcus aureus, Helicobacter pylori, Anaplasma phagocytophilum and members of the Enterobacteriae family.     

How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water‐limiting conditions in C₃ species. Nevertheless, only a few studies have described the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places. However, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (g_s), mesophyll conductance (g_m) and carbon fixation, mostly driven by RuBisCO carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin–Benson cycle enzymes, and RuBisCO evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole‐plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.     

How do we get a perfect complement of digits?

A crucial issue in limb development is how a correct set of precisely shaped digits forms in the digital plate. This process relies on patterning across the anterior-posterior axis of the limb bud, which is under the control of Sonic hedgehog emanating from the zone of polarizing activity. Recently, Sonic hedgehog function in the limb bud has been shown to have a dual character controlling both growth and patterning of the digital field. This finding has prompted the proposal of new models of how these two functions are achieved, and this will be discussed in this review.     

Examining the developing bone: What do we measure and how do we do it?

The clinical tools available to evaluate bone development in children are often ambiguous, and difficult to interpret. Unfortunately bone densitometry methods (i.e., dual energy X-ray absorptiometry, DXA) which have a relatively straightforward application in adult osteoporosis, are far more difficult to evaluate in the growing skeleton. Even with adequate "adjustment" for bone size or maturity, bone "density" (areal or volumetric) alone often gives an inaccurate assessment of bone strength--especially in children. Ideally, we would like to measure both material and geometric properties of bone to accurately estimate "strength". Mechanically meaningful measures of bone geometry (bone cross-sectional area, cortical thickness) and estimates of bending strength (section modulus, or SSI) are available with non-invasive techniques such as (p)QCT and some DXA software. With new technology it might be possible to also measure bone material properties, which will be especially important in some pediatric disorders. In children, we also need to know something about the loads imposed on a child's bone and consider not only absolute bone strength, but also the strength of bone relative to the physiologic loads. Interpreting bone strength in light of the loads imposed (particularly muscle force) is critical for an accurate diagnosis of the developing bone.     

How do we Measure the Environment? Linking Intertidal Thermal Physiology and Ecology Through Biophysics

Recent advances in quantifying biochemical and cellular-levelresponses to thermal stress have facilitated a new explorationof the role of climate and climate change in driving intertidalcommunity and population ecology. To fruitfully connect thesedisciplines, we first need to understand what the body temperaturesof intertidal organisms are under field conditions, and howthey change in space and time. Newly available data logger technologymakes such an exploration possible, but several potential pitfallsmust be avoided. Body temperature during aerial exposure isdriven by multiple, interacting climatic factors, and extremesduring low tide far exceed those during submersion. Moreover,because of effects of body size and morphology, two organismsexposed to identical climatic conditions can display very differentbody temperatures, which can also be substantially differentfrom the temperature of the surrounding air. These same factorsdrive the temperature recorded by data loggers, and one loggertype is unlikely to serve as an effective proxy for all organismsat a site. Here I describe the difficulties involved in quantifyingpatterns of body temperature in intertidal organisms, and explorethe implications of this complexity for intertidal physiologicalecology. I do so using data from temperature loggers designedto mimic the thermal characteristics of the mussel Mytilus californianus,and deployed at multiple sites along the West Coast of the UnitedStates. Results indicate a highly intricate pattern of thermalstress, where the interaction of climate with the dynamics ofthe tidal cycle determines the timing and magnitude of temperatureextremes, creating a unique "thermal signal" at each site.     

Linking science and practice in ecological research and management: How can we do it better?

Summary In conservation management, ensuring that the most appropriate research is conducted and results are actually put into practice is a complex and challenging process. While there are success stories, many hurdles can reduce the likelihood of appropriate research being initiated and its findings communicated and implemented. This article describes the ideal research–management cycle, summarizes the major factors that impede it and draws on the experiences of the authors to provide a series of examples of successful approaches to help keep the cycle going. We consider that the major impediments to a functioning research–management cycle relate to a lack of collaboration, poor communication, inappropriate funding and political timelines, change inertia and a lack of capacity. Although addressing structural difficulties such as matching funding timelines to those required for ecological research is a fundamental challenge, we can make incremental improvements to the way in which we operate that will improve the chances that research is both useful and used. The principles underpinning our success stories are (i) strategic development of capacity, (ii) increased breadth and depth of collaborations between researchers and managers and (iii) improved communications. Participants in the research–management cycle must seek to involve stakeholders through all project stages from project conception, to implementation, evaluation and knowledge updating. Finally, we should only see the first iteration of the research process as complete when new knowledge is applied operationally with monitoring and ongoing evaluation in place.     

How many fungi make sclerotia?

Most fungi produce some type of durable microscopic structure such as a spore that is important for dispersal and/or survival under adverse conditions, but many species also produce dense aggregations of tissue called sclerotia. These structures help fungi to survive challenging conditions such as freezing, desiccation, microbial attack, or the absence of a host. During studies of hypogeous fungi we encountered morphologically distinct sclerotia in nature that were not linked with a known fungus. These observations suggested that many unrelated fungi with diverse trophic modes may form sclerotia, but that these structures have been overlooked. To identify the phylogenetic affiliations and trophic modes of sclerotium-forming fungi, we conducted a literature review and sequenced DNA from fresh sclerotium collections. We found that sclerotium-forming fungi are ecologically diverse and phylogenetically dispersed among 85 genera in 20 orders of Dikarya, suggesting that the ability to form sclerotia probably evolved ≥14 different times in fungi.