Regulation of feeding mode by the sand dollar Dendraster excentricus in a shallow estuarine habitat

The sand dollar Dendraster excentricus is a facultative suspension feeder, which is relatively rare within the Order Clypeasteroida. Field studies of regulation of its feeding mode have been mostly conducted in exposed coastal habitats, where they are typically observed in an inclined position and oriented parallel to each other during suspension feeding. Physical (current speed and direction, reduction of drag and lift) and biological factors (increased efficiency of capture of particulates, and density) have been associated with regulation of its feeding mode in exposed coastal systems. We simultaneously measured the role of physical and biological factors in regulating the selection mode for feeding under varying tidal conditions in a shallow estuary in Baja California, Mexico. We used photographic records and direct sampling in fixed plots to determine the relationship between feeding behavior and environmental conditions. Current direction and speed, tidal level, density and content of organic matter in the water column and sediments were measured with respect to feeding mode (prone or inclined) and orientation relative to prevailing currents during spring and neap tides. Multiple regression analysis indicated that the percentage of inclined sand dollars was strongly and positively correlated only with tidal level at the densities found in the estuary (mean < 180 individuals m^− 2); there was no relationship with current velocity, density, and organic matter content of the water. The prone position, indicative of deposit feeding, was largely limited to low tidal levels. We used circular statistics to determine whether the orientation of inclined sand dollars was correlated with current direction and speed. Sand dollars were only oriented parallel to the prevailing currents during the strongest currents of spring tides (> 20 cm s^− 1). We did not observe the predominant oral:aboral configuration found in exposed coastal systems, which may be attributed to the relatively low densities of sand dollars in the exposed coastal environment (30-180 individuals m^− 2), compared to protected coastal habitats (up to 1000 individuals m^− 2). Our results suggest that regulation of the feeding mode of sand dollars in shallow and hydrodynamically complex estuarine systems differs from the feeding mode found in exposed coastal environments.     

Radiative forcing of natural forest disturbances

Forest disturbances are major sources of carbon dioxide to the atmosphere, and therefore impact global climate. Biogeophysical attributes, such as surface albedo (reflectivity), further control the climate‐regulating properties of forests. Using both tower‐based and remotely sensed data sets, we show that natural disturbances from wildfire, beetle outbreaks, and hurricane wind throw can significantly alter surface albedo, and the associated radiative forcing either offsets or enhances the CO₂ forcing caused by reducing ecosystem carbon sequestration over multiple years. In the examined cases, the radiative forcing from albedo change is on the same order of magnitude as the CO₂ forcing. The net radiative forcing resulting from these two factors leads to a local heating effect in a hurricane‐damaged mangrove forest in the subtropics, and a cooling effect following wildfire and mountain pine beetle attack in boreal forests with winter snow. Although natural forest disturbances currently represent less than half of gross forest cover loss, that area will probably increase in the future under climate change, making it imperative to represent these processes accurately in global climate models.     

Microtubule patterning in apical epidermal cells ofVinca minor preceding leaf emergence

Summary Serial thin sectioning for electron microscopy was carried out on the cortical cytoplasm of surface cells of the apical dome ofVinca minor. The cellulose reinforcement pattern in the outer epidermal walls forming this surface is known to correlate well with the decussate phyllotaxis pattern. The purpose of this study was to determine the location of microtubules immediately under these epidermal walls as a first step toward finding out how the cellulose pattern arises. First, correspondence between the patterns of microtubules and cellulose was checked. Second, the role of potential orienting cues for the alignment of microtubule arrays in specific cells was evaluated.Microtubule arrays which were well or moderately ordered (70% of the total interphase cells) generally had alignment parallel to the adjacent leaf base, as has been seen for cellulose. The aligned features or cues potentially correlating with a given array were: (1) orientation and length of the previous anticlinal cross-wall, (2) alignment of microtubules in adjacent cells, and (3) direction of inferred stretch, parallel to the nearby leaf bases. All three features were found to agree with the microtubule alignment in 17 of 34 cells with ordered arrays. At least two features agreed in 33 of the 34 cases. All 34 cells with ordered arrays had at least one feature parallel to the array. Random association between microtubule orientation and these features would lead to such correlations less than 0.01% of the time. Thirty percent of the interphase cells showed no obvious order. Most of these cells were located in the central linear corridor region of the apex. The unordered cells were more likely than the ordered cells to have more than one orientation specified by the potential cues; i.e., no single orientation parallel to all of the cues existed. This indicates that uniformity of the orientation cues may be as important as their direction.     

Biophysical insight into the heparin‐peptide interaction and its modulation by a small molecule

The heparin‐protein interaction plays a vital role in numerous physiological and pathological processes. Not only is the binding mechanism of these interactions poorly understood, studies concerning their therapeutic targeting are also limited. Here, we have studied the interaction of the heparin interacting peptide (HIP) from Tat (which plays important role in HIV infections) with heparin. Isothermal titration calorimetry binding exhibits distinct biphasic isotherm with two different affinities in the HIP‐heparin complex formation. Overall, the binding was mainly driven by the nonionic interactions with a small contribution from ionic interactions. The stoichiometric analysis suggested that the minimal site for a single HIP molecule is a chain of 4 to 5 saccharide molecules, also supported by docking studies. The investigation was also focused on exploiting the possibility of using a small molecule as an inhibitor of the HIP‐heparin complex. Quinacrine, because of its ability to mimic the HIP interactions with heparin, was shown to successfully modulate the HIP‐heparin interactions. This result demonstrates the feasibility of inhibiting the disease relevant heparin‐protein interactions by a small molecule, which could be an effective strategy for the development of future therapeutic agents.     

Characterizing the microenvironment surrounding protein sites.

Sites are microenvironments within a biomolecular structure, distinguished by their structural or functional role. A site can be defined by a three-dimensional location and a local neighborhood around this location in which the structure or function exists. We have developed a computer system to facilitate structural analysis (both qualitative and quantitative) of biomolecular sites. Our system automatically examines the spatial distributions of biophysical and biochemical properties, and reports those regions within a site where the distribution of these properties differs significantly from control nonsites. The properties range from simple atom-based characteristics such as charge to polypeptide-based characteristics such as type of secondary structure. Our analysis of sites uses non-sites as controls, providing a baseline for the quantitative assessment of the significance of the features that are uncovered. In this paper, we use radial distributions of properties to study three well-known sites (the binding sites for calcium, the milieu of disulfide bridges, and the serine protease active site). We demonstrate that the system automatically finds many of the previously described features of these sites and augments these features with some new details. In some cases, we cannot confirm the statistical significance of previously reported features. Our results demonstrate that analysis of protein structure is sensitive to assumptions about background distributions, and that these distributions should be considered explicitly during structural analyses.     

Increased leaf reflectance in tropical trees under elevated CO2

Globally increasing atmospheric CO₂ concentrations are known to affect many aspects of plant physiology and development; however, little attention has been given to leaf and canopy optical properties. Three tropical trees in the Leguminosae, an important canopy tree family in many tropical forests, responded similarly to an experimental doubling of CO₂ partial pressure with a 9–23% increase in spectral leaf reflectance to light in the visible (400–700 nm) waveband. Decreased leaf chlorophyll content under elevated CO₂ may explain part of the observed increase in reflectance. However, analyses that statistically corrected for chlorophyll content effects on reflectance still indicated a significant CO₂ effect. This results, in conjunction with the spectral pattern of the response, suggests that the primary mechanism is increased optical masking of chlorophyll under elevated CO₂. The magnitude of the increase in leaf reflectance is sufficient to suggest that increased canopy reflectance of tropical forests (and possibly other terrestrial ecosystems) may be an important negative feedback in the response of global net radiative climate forcing to increasing atmospheric CO₂.     

Demographic Stochasticity, Environmental Variability, and Windows of Invasion Risk for Bythotrephes Longimanus in North America

Biological invasions are a leading threat to freshwater biodiversity worldwide. A central unanswered question of invasion ecology is why some introduced populations establish while most fail. Answering this question will allow resource managers to increase the specificity and effectiveness of control efforts and policy. We studied the establishment of spiny water flea (Bythotrephes longimanus) in the United States and Canada by modeling introduction failure caused by demographic stochasticity, environmental variation, and seasonal environmental forcing. We compared predicted establishment rates with observed invasions of inland lakes in Ontario, Canada. Our findings suggest that environmental forcing can cause “windows” of invasion opportunity so that timing of introductions might be a greater determinant of population establishment than demographic stochasticity and random environmental variation. We expect this phenomenon to be exhibited by species representing a wide range of life histories. For spiny water flea in North America, a large window of invasion opportunity opens around the fourth week of May, persists through the summer, and closes with decreasing water temperatures in autumn. These results show how timing of introductions with respect to seasonally forced environmental drivers can be a key determinant of establishment success. By focusing on introductions during windows of invasion opportunity, resource managers can more effectively control invasion rates.     

How to Study Basement Membrane Stiffness as a Biophysical Trigger in Prostate Cancer and Other Age-related Pathologies or Metabolic Diseases

Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via the Maillard reaction. Examples of laboratory techniques that can be used to confirm AGE generation, non-enzymatic crosslinking and increased stiffness in GLA treated rBM are outlined. These include preparation of native rBM (treated with phosphate-buffered saline, PBS) and stiff rBM (treated with GLA) for determination of: its AGE content by photometric analysis and immunofluorescent microscopy, its non-enzymatic crosslinking by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) as well as confocal microscopy, and its increased stiffness using rheometry. The procedure described here can be used to increase the rigidity (elastic moduli, E) of rBM up to 3.2-fold, consistent with measurements made in healthy versus diseased human prostate tissue. To recreate the biophysical microenvironment associated with the aging and diseased prostate gland three prostate cell types were introduced on to native rBM and stiff rBM: RWPE-1, prostate epithelial cells (PECs) derived from a normal prostate gland; BPH-1, PECs derived from a prostate gland affected by benign prostatic hyperplasia (BPH); and PC3, metastatic cells derived from a secondary bone tumor originating from prostate cancer. Multiple parameters can be measured, including the size, shape and invasive characteristics of the 3D glandular acini formed by RWPE-1 and BPH-1 on native versus stiff rBM, and average cell length, migratory velocity and persistence of cell movement of 3D spheroids formed by PC3 cells under the same conditions. Cell signaling pathways and the subcellular localization of proteins can also be assessed.