Retinal coding of visual scenes -- repetitive and redundant too?

Visual information reaches the brain by way of a fine cable, the optic nerve. The million or so axons in the optic nerve represent an information bottleneck in the visual pathway-where the fewest number of neurons convey the visual scene. It has long been thought that to make the most of the optic nerve's limited capacity the retina may encode visual information in an optimally efficient manner. In this issue of Neuron, Puchalla et al. report a test of this hypothesis using multielectrode recordings from retinal ganglion cells stimulated with movies of natural scenes. The authors find substantial redundancy in the retinal code and estimate that there is an approximately 10-fold overrepresentation of visual information.     

Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture

Endothelial cells can function differently in vitro and in vivo; however, the degree of microenvironmental modulation in vivo remains unknown at the molecular level largely because of analytical limitations. We use multidimensional protein identification technology (MudPIT) to identify 450 proteins (with three or more spectra) in luminal endothelial cell plasma membranes isolated from rat lungs and from cultured rat lung microvascular endothelial cells. Forty-one percent of proteins expressed in vivo are not detected in vitro. Statistical analysis measuring reproducibility reveals that seven to ten MudPIT measurements are necessary to achieve > or =95% confidence of analytical completeness with current ion trap equipment. Large-scale mapping of the proteome of vascular endothelial cell surface in vivo, as demonstrated here, is advisable because distinct protein expression is apparently regulated by the tissue microenvironment that cannot yet be duplicated in standard cell culture.     

Increasing liana abundance and biomass in tropical forests: emerging patterns and putative mechanisms

Tropical forests are experiencing large-scale structural changes, the most apparent of which may be the increase in liana (woody vine) abundance and biomass. Lianas permeate most lowland tropical forests, where they can have a huge effect on tree diversity, recruitment, growth and survival, which, in turn, can alter tree community composition, carbon storage and carbon, nutrient and water fluxes. Consequently, increasing liana abundance and biomass have potentially profound ramifications for tropical forest composition and functioning. Currently, eight studies support the pattern of increasing liana abundance and biomass in American tropical and subtropical forests, whereas two studies, both from Africa, do not. The putative mechanisms to explain increasing lianas include increasing evapotranspirative demand, increasing forest disturbance and turnover, changes in land use and fragmentation and elevated atmospheric CO?. Each of these mechanisms probably contributes to the observed patterns of increasing liana abundance and biomass, and the mechanisms are likely to be interrelated and synergistic. To determine whether liana increases are occurring throughout the tropics and to determine the mechanisms responsible for the observed patterns, a widespread network of large-scale, long-term monitoring plots combined with observational and manipulative studies that more directly investigate the putative mechanisms are essential.     

Systems analysis of endothelial cell plasma membrane proteome of rat lung microvasculature

Background  

Endothelial cells line all blood vessels to form the blood-tissue interface which is critical for maintaining organ homeostasis and facilitates molecular exchange. We recently used tissue subcellular fractionation combined with several multi-dimensional mass spectrometry-based techniques to enhance identification of lipid-embedded proteins for large-scale proteomic mapping of luminal endothelial cell plasma membranes isolated directly from rat lungs in vivo. The biological processes and functions of the proteins expressed at this important blood-tissue interface remain unexplored at a large scale.     

Overcoming Key Technological Challenges in Using Mass Spectrometry for Mapping Cell Surfaces in Tissues

Plasma membranes form a critical biological interface between the inside of every cell and its external environment. Their roles in multiple key cellular functions make them important drug targets. However the protein composition of plasma membranes in general is poorly defined as the inherent properties of lipid embedded proteins, such as their hydrophobicity, low abundance, poor solubility and resistance to digestion and extraction makes them difficult to isolate, solubilize, and identify on a large scale by traditional mass spectrometry methods. Here we describe some of the significant advances that have occurred over the past ten years to address these challenges including: i) the development of new and improved membrane isolation techniques via either subfractionation or direct labeling and isolation of plasma membranes from cells and tissues; ii) modification of mass spectrometry methods to adapt to the hydrophobic nature of membrane proteins and peptides; iii) improvements to digestion protocols to compensate for the shortage of trypsin cleavage sites in lipid-embedded proteins, particularly multi-spanning proteins, and iv) the development of numerous bioinformatics tools which allow not only the identification and quantification of proteins, but also the prediction of membrane protein topology, membrane post-translational modifications and subcellular localization. This review emphasis the importance and difficulty of defining cells in proper patho- and physiological context to maintain the in vivo reality. We focus on how key technological challenges associated with the isolation and identification of cell surface proteins in tissues using mass spectrometry are being addressed in order to identify and quantify a comprehensive plasma membrane for drug and target discovery efforts.Plasma membranes (PM)¹ and their associated proteins are part of a key biological interface between the outside and the inside of the cell. They are implicated in important cellular functions, such as small molecule transport, cell communication, and signaling. Such proteins are critical in sensing changes in the external environment and in transmitting signals into and out of the cell. Impaired cellular signaling, often involving PM proteins, is apparent in many cancers (1, 2). Membrane proteins represent one-third of the proteins encoded by the human genome (3) but represent more than two-thirds of the known protein targets for existing drugs (4). Thus, defining the proteome of PMs is critical for understanding cellular functions and fundamental biological processes and for finding new targets for drug discovery efforts.In an ideal world, the PM proteome of all cell types would be analyzed comprehensively to (i) better understand why and where different membrane proteins are expressed, (ii) reveal new functions for the PM in various cell types, (iii) identify cell-specific surface-accessible markers as targetable proteins for local drug delivery, and (iv) identify diagnostic or prognostic indicators in healthy and diseased cell or tissue states. This can be attempted relatively easily in cell culture using a homogenous cell population as compared with the heterogeneity of cells within any tissue or organ from which they are derived. Unfortunately, once cells are isolated from different organs and even more so when cultured and grown in vitro, the cells can change dramatically in appearance, structure, and responsiveness, and protein expression and distribution within the cell can change (5, 6). Biomarkers readily disappear, and the cultured cells do not reflect the in vivo reality. Most importantly, they lose expression of tissue-specific proteins and dedifferentiate into a more common phenotype. Mass spectrometry (MS) analysis revealed that as much as 40% of the proteins expressed by endothelial cells in vivo are not found in vitro (6). Thus, several groups have tried to address this problem by capturing the PMs in as close to an in vivo situation as possible as discussed below.PM proteins in general may not serve as suitable targets for drug treatment regimens mainly because of their inaccessibility to intravenously injected agents. Although most small molecule drugs can readily penetrate and accumulate in almost any tissue, often a high dose must be administered for the therapeutic dosage to accumulate in the diseased tissue of interest. However, major problems can arise when such drugs are toxic to both normal and healthy tissue, e.g. chemotherapeutic agents, which can accumulate in healthy tissue, resulting in the unwanted and often severe side effects associated with these drugs. Thus, even if a protein expressed on the surface of a cell is indicative of a disease state, it would be relatively impossible to target this cell specifically while avoiding the accumulation in healthy tissue using current drug delivery approaches, especially if the cell of interest is embedded within a tissue or organ. This is simply because multiple barriers, e.g. endothelium, epithelium, etc., must be crossed to access the cell regardless of the route of administration. As a result, great effort is now being focused on developing more targeted approaches where the toxic agents are specifically delivered to the organ or tissue of interest (7–9). With such targeting approaches, dosages can be significantly reduced, thus increasing the therapeutic efficacy while minimizing the side effects (10, 11). Consequently, proteins that are expressed on the surface of endothelial cells (ECs) that line the luminal surface of all vasculature are attractive targets for drugs and imaging agents as these proteins are in direct contact with the circulating blood and are thus inherently more accessible to intravenously administered agents than PM proteins of cells residing deep inside tissues and organs. Proteins expressed on the outer luminal EC surface can readily bind antibodies and other agents that are circulating in the blood. Thus, identifying and characterizing the proteins that line the vasculature of each organ and tissue is highly desirable for drug delivery and diagnostic imaging.PM proteins, regardless of the cell or tissue of origin, have generally been under-represented in proteomics analysis mainly because of their low abundance. In addition, the inherent insolubility of membrane proteins due to their hydrophobic nature has rendered them difficult to isolate and identify compared with their counterparts in the soluble cytosol and nuclear fractions. In many high throughput protein identification approaches, soluble proteomes are readily characterized, and it is fairly common for thousands of proteins to be identified in such samples. However, when more challenging proteomes, such as those of the PM, are of interest, the numbers of proteins identified are significantly lower. There are many technical reasons for such a dramatic decrease in protein identification when membrane proteomes are of interest. This review focuses on how we and other laboratories are overcoming key technological challenges associated with using traditional MS-based approaches, which were initially developed for the identification of more soluble proteins, for the mapping of membrane proteomes and in particular the in vivo cell surface proteome of endothelial cells.     

Complex facilitation and competition in a temperate grassland: loss of plant diversity and elevated CO2 have divergent and opposite effects on oak establishment

Encroachment of woody vegetation into grasslands is a widespread phenomenon that alters plant community composition and ecosystem function. Woody encroachment is often the result of fire suppression, but it may also be related to changes in resource availability associated with global environmental change. We tested the relative strength of three important global change factors (CO₂ enrichment, nitrogen deposition, and loss of herbaceous plant diversity) on the first 3 years of bur oak (Quercus macrocarpa) seedling performance in a field experiment in central Minnesota, USA. We found that loss of plant diversity decreased initial oak survival but increased overall oak growth. Conversely, elevated CO₂ increased initial oak seedling survival and reduced overall growth, especially at low levels of diversity. Nitrogen deposition surprisingly had no net effect on survival or growth. The magnitude of these effects indicates that long-term woody encroachment trends may be most strongly associated with those few individuals that survive, but grow much larger in lower diversity patches. Further, while the CO₂ results and the species richness results appear to describe opposing trends, this is due only to the fact that the natural drivers are moving in opposite directions (decreasing species richness and increasing CO₂). Interestingly, the mechanisms that underlie both patterns are very similar, increased CO₂ and increased species richness both increase herbaceous biomass which (1) increases belowground competition for resources and (2) increases facilitation of early plant survival under a more diverse plant canopy; in other words, both competition and facilitation help determine community composition in these grasslands.     

The negative effect of lianas on tree growth varies with tree species and season

Lianas reduce tree growth, reproduction, and survival in tropical forests. Liana competition can be particularly intense in isolated forest fragments, where liana densities are high, and thus, host tree infestation is common. Furthermore, lianas appear to grow particularly well during seasonal drought, when they may compete particularly intensely with trees. Few studies, however, have experimentally quantified the seasonal effects of liana competition on multiple tree species in tropical forests. We used a liana removal experiment in a forest fragment in southeastern Brazil to test whether the effects of lianas on tree growth vary with season and tree species identity. We conducted monthly diameter measurements using dendrometer bands on 88 individuals of five tree species for 24 months. We found that lianas had a stronger negative effect on some tree species during the wet season compared to the dry season. Furthermore, lianas significantly reduced the diameter growth of two tree species but had no effect on the other three tree species. The strong negative effect of lianas on some trees, particularly during the wet season, indicates that the effect of lianas on trees varies both seasonally and with tree species identity. Abstract in Portuguese is available with online material.