Genome data: what do we learn?

Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of chromosome 1 from Leishmania major. The complete genomic sequences of five microbes were reported. Approaches to using data from completely sequenced microbial genomes in phylogenetic studies are being explored, as is the application of microarrays to whole genome expression analysis.     

Antioxidant activity: what do we measure?

Inhibition of oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) by free radicals generated by decomposition of 2,2'-azobis(2-amidopropane) (ABAP) by antioxidants and biological material was studied. A correlation was found between the ability of various substances to delay the onset of ABTS oxidation and their rapid reduction of the ABTS+* cation radical, and between the ability to reduce the maximal rate of ABTS oxidation and slow reduction of ABTS+*. The length of the lag period of ABTS oxidation was found to be independent of ABTS concentration. Similar decrease of peroxynitrite-induced ABTS+* formation by antioxidants was observed when the antioxidants were added before and after peroxynitrite. All these findings indicate that the main effect of antioxidants in this system is reduction of ABTS+* and not prevention of its formation. Reduction of oxidation products rather than inhibition of their formation may be the predominant mode of action of antioxidants in various assays of antioxidant activity.     

Lessons from Immune 1-3: what did we learn and what do we need to do in the future?

Sprague-Dawley rats were subjected to three 8-to-10 day space flights on the Space Shuttle. Housed in NASA's Animal Enclosure Modules, rats were flown to test the hypotheses that therapy with pegylated interleukin-2 or insulin-like growth factor-1 would ameliorate some of the effects of space flight on the immune system. As part of these experiments, we measured body and organ weights, blood cell differentials, plasma corticosterone, macrophage colony forming units, lymphocyte mitogenic, super-antigenic and interferon-gamma responses, bone marrow cell and peritoneal macrophage cytokine secretion and bone strength and mass. This paper compares some of the immunophysiological parameters of the control animals used in the Immune1-3 flight series and presents data from an animal infection model for use during space flight.     

UV radiation: what we know and do we protect ourselves adequately?

Chronic sun exposure causes degenerative changes in the skin that are recognized as photoaging, immunosuppression and photocarcinogenesis. Sun is necessary for life, so total sun avoidance is impossible. Sun exposure during the first 15 years of life and blistering sunburns before age 20 have been linked to an increased risk of melanoma. Individuals who have outdoor lifestyles, live in sunny climates, and are lightly pigmented will experience the greatest degree of photoaging. In our study, performed four years ago, we have shown the knowledge of more than 4000 people about the effects of UV rays on the skin. The results show us that sun exposure is still exaggerated and uncontrolled due to the lack of knowledge about this topic. Encouraging photoprotection and improving the awareness of the general public about the harmful effects of too much sun exposure must be the leading preventative health strategy.     

Imaging for lung physiology: what do we wish we could measure?

The role of imaging as a tool for investigating lung physiology is growing at an accelerating pace. Looking forward, we wished to identify unresolved issues in lung physiology that might realistically be addressed by imaging methods in development or imaging approaches that could be considered. The role of imaging is framed in terms of the importance of good spatial and temporal resolution and the types of questions that could be addressed as these technical capabilities improve. Recognizing that physiology is fundamentally a quantitative science, a recurring emphasis is on the need for imaging methods that provide reliable measurements of specific physiological parameters. The topics included necessarily reflect our perspective on what are interesting questions and are not meant to be a comprehensive review. Nevertheless, we hope that this essay will be a spur to physiologists to think about how imaging could usefully be applied in their research and to physical scientists developing new imaging methods to attack challenging questions imaging could potentially answer.     

Skin and diabetes mellitus: what do we know?

Diabetes mellitus (DM) is becoming increasingly prevalent worldwide. Although major complications of this condition involve kidney, retina and peripheral nerves, the skin of diabetic patients is also frequently injured. Hence, interest is mounting in the definition of the structural and molecular profile of non-complicated diabetic skin, i.e., before injuries occur. Most of the available knowledge in this area has been obtained relatively recently and, in part, derives from various diabetic animal models. These include both insulin-dependent and insulin-resistant models. Structural work in human diabetic skin has also been carried out by means of tissue samples or of non-invasive methods. Indications have indeed been found for molecular/structural changes in diabetic skin. However, the overall picture that emerges is heterogeneous, incomplete and often contradictory and many questions remain unanswered. This review aims to detail, as much as possible, the various pieces of current knowledge in a systematic and synoptic manner. This should aid the identification of areas in which key questions are still open and more research is needed. A comprehensive understanding of this field could help in determining molecular targets for the prevention and treatment of skin injuries in DM and markers for the monitoring of cutaneous and systemic aspects of the disease. Additionally, with the increasing development of non-invasive optics-based deep-tissue-imaging diagnostic technologies, precise knowledge of cutaneous texture and molecular structure becomes an important pre-requisite for the use of such methods in diabetic patients.     

Salt stress tolerance; what do we learn from halophytes?

Abiotic environmental stresses can give rise to morphological, biochemical and molecular changes that negatively affect plant growth and productivity. Among these stresses, soil salinity is the major threat. To deal and control effects of high salinity on plants, it is important to understand their responses to salt stress that disturbs the homeostatic equilibrium at cellular and molecular levels. In this regard halophytes (salt tolerant plants) can provide superior models for the study of salt stress defense parameters compared to salt sensitive species (glycophytes). Halophytes use highly developed, complex systems to tolerate salinity by maintaining a low cytosolic Na⁺/K⁺ ratio, sequestration of Na⁺ into vacuoles that then provides the osmotic potential sustaining water influx. Under low intensity stress conditions that moderately and/or transiently affect ion imbalance, the set of responses all plants initiate will be mostly to engage measures that assure ion balance. High salinity, especially over a prolonged time period, will challenge plant survival, which then requires different strategies that employ a variety of mechanisms. Plasticity and connectivity of these diverse mechanisms is engrained in species- and family-specific evolutionary history and their genetic complexity. Highlighting differences in the genetic and biochemical makeup between glycophytes and halophytes allows for comparisons between their approaches towards high salinity. This review provides a brief overview about different strategies and mechanism used by plants to avoid or confine adverse effects of high salinity.     

Host cell invasion by apicomplexans: what do we know?

Apicomplexan zoites enter host cells by forming and actively moving through a tight junction (TJ) formed between the parasite and host cell surfaces. Although the TJ was first described decades ago, its molecular characterization has proved difficult mainly because of its transient existence during an internalization process that lasts only seconds. In the past 7 years, work has led to a model of the TJ in which the association between AMA1 and RON proteins structures the TJ and bridges the cytoskeletons of the two cells. However, more recent work questions this view. Here, we critically discuss the current model and speculate on alternative models of the AMA1-RON association and of the apicomplexan TJ.     

Dying with dementia: what do we know about it?

Death with dementia is increasingly common, yet research on end of life with dementia and end-of-life care for such patients has been sparse. This article reviews recent studies in this area, most of which were done in US nursing homes. Research focused on five domains: prognosis, decision making, treatment, patient's health and suffering, and family's circumstances and satisfaction with care. Prognostication focused on developing risk scores for mortality within 6 months or a year, and while decision making was usually studied qualitatively, the other three domains were largely covered by a series of small, retrospective studies. Future direction in research is discussed, including the ongoing CASCADE project in Boston and the Dutch End of Life with Dementia Study (DEOLD). Both of these prospective studies in nursing home residents assess decision making, as well as factors associated with family's satisfaction and patient suffering. These studies will provide insight into interventions that are most likely to improve end of life care of patients with dementia in the respective countries and elsewhere.     

Fish cognition: what can we learn, and what do they need to learn?

Fish provide a wonderful opportunity to explore processes that shape and select cognitive ability. In this presentation, I will illustrate three aspects of work that my colleagues and I have used to investigate fish learning and memory over the last decade. First, I will discuss how comparing different populations sampled from contrasting habitats allows differences in cognitive ability to be related to the evolutionary ecology of the fish. I will use examples that have investigated how differences in learning ability between populations of the same species can arise. Here, the examples will be taken from the ubiquitous three‐spined stickleback, and a Panamanian poecilid, Brachyraphis .
The second approach has used fish cognition as a tool to quantify behaviour to enable assessment of different aspects of fish welfare. For example, the recent work investigating pain perception in trout required the use of a learning task to quantify how fish behaviour was modified after noxious stimulation. Ways in which these, and similar, processes can be used in future studies of fish welfare will be discussed.
The final part of the presentation will consider recent work that addresses the problems of releasing hatchery‐reared fish for restocking purposes. Although a common practice, most of the hatchery‐reared fish die shortly after they are released. Much of the observed mortality apparently stems from the fishes' inexperience with a variable environment. Experiments with juvenile cod and brown trout suggest that both age, and the early rearing environment, have profound effects on fish learning and behaviour. I will discuss how simple modifications to current rearing practices may have large beneficial effects on the post‐release survival of hatchery‐reared fish.     

Mechanisms of tolerance to herbivore damage:what do we know?

Identifying mechanisms of tolerance to herbivore damage will facilitate attempts to understand the role of tolerance in the evolutionary and ecological dynamics of plants and herbivores. Investigations of the physiological and morphological changes that occur in plants in response to herbivore damage have identified several potential mechanisms of tolerance. However, it is unlikely that all physiological changes that occur following damage are tolerance mechanisms. Few studies have made direct comparisons between the expression of tolerance and the relative expression of putative mechanisms. I briefly review empirical evidence for some of the better-studied potential mechanisms, including increased photosynthetic activity, compensatory growth, utilization of stored reserves, and phenological delays. For each of these mechanisms I discuss reasons why the relationship between tolerance and these characters may be more complicated than it first appears. I conclude by discussing several empirical approaches, including herbivore manipulations, quantitative trait loci (QTL) analysis, and selection experiments, that will further our understanding of tolerance mechanisms. This revised version was published online in July 2006 with corrections to the Cover Date.     

Modeling memory: what do we learn from attractor neural networks?

In this paper we summarize some of the main contributions of models of recurrent neural networks with associative memory properties. We compare the behavior of these attractor neural networks with empirical data from both physiology and psychology. This type of network could be used in models with more complex functions.     

Microplastics and freshwater microalgae: what do we know so far?

The constant entry of microplastics in several environmental matrices has been of great concern to the scientific community and to society in general, mainly due to the mysteries that surround the implications of this pollutant in the environment. Freshwater ecosystems are resources especially susceptible to variations in environmental quality, and the lack of data on the impacts caused by plastic fragments exacerbates the vulnerability of this environment. Considering the results of other studies, which demonstrate the increasing entry of polymeric fragments in the aquatic environment can lead to algae growth inhibition, an investigation was carried out to determine the current state of research on the interaction between microplastics and freshwater microalgae. In total, 20 scientific articles were analyzed. Different species were subjected to toxicological tests under controlled conditions in the laboratory with small microplastics (size range between 0.1 and 1000 µm), primary and secondary microplastics of different types of polymer. Four toxicity class of indicators were chosen to assess the microalgae response to exposure to microplastic in the selected studies: growth inhibition; photosynthetic activity; pigment analysis; and enzymatic activity and oxidative stress. In this review, a critical analysis is made on the effects of the shape, size, concentration, and duration of exposure to microplastics and research gaps are identified to guide future research priorities in this area of study.