Surface chemistry and reactivity of bacteriogenic iron oxides from Axial Volcano, Juan de Fuca Ridge, north-east Pacific Ocean

Iron oxides were collected from the caldera of Axial Volcano, a site of hydrothermal vent activity along the Juan de Fuca Ridge. Mineralogical inspection using X‐ray diffraction (XRD) revealed the majority of samples to be 2‐line ferrihydrite, with one of the samples corresponding to poorly ordered goethite. Examination using environmental scanning electron microscopy (ESEM) found the constituents of the iron oxides to consist predominantly of bacterial‐like structures that resembled the iron oxidizing bacteria Leptothrix ochracea, Gallionella ferruginea and a novel PV‐1 strain. X‐ray photoelectron spectroscopy (XPS) detected the presence of Fe, O, C, N, Ca, Si and P on all the samples with the exception of poorly ordered goethite, where Ca and P were absent, in addition to a weak N peak. Binding energy shifts of the Fe 2p and O 1s peaks were indicative of ferrihydrite and hydroxyl functional groups, while the presence and speciation of the C 1s peak was attributed to the presence of bacteria. Use of acid‐base titration data modelling in conjunction with a linear programming regression method (LPM) indicated that the iron oxides are composed of heterogeneous surface functional groups. Differences in iron oxide reactivity values correlated with differences in the bacterial and mineral fabric of the samples. The diverse surface chemistry and high reactivity of these iron oxides may be important in the global cycling of various elements throughout the oceans due to their presence along widespread mid‐ocean ridges.     

Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells

Analysis of one of the vital functions of retinal pigment epithelial (RPE) cells, the phagocytosis of spent aged distal fragments of photoreceptor outer segments (POS) can be performed in vitro. Photoreceptor outer segments with stacks of membranous discs containing the phototransduction machinery are continuously renewed in the retina. Spent POS are eliminated daily by RPE cells. Rodent, porcine/bovine and human RPE cells recognize POS from various species in a similar manner. To facilitate performing large series of experiments with little variability, a large stock of POS can be isolated from porcine eyes and stored frozen in aliquots. This protocol takes advantage of the characteristic of photopigments that display an orange color when kept in the dark. Under dim red light, retinae are collected in a buffer from opened eyecups cut in halves. The retinal cell suspension is homogenized, filtered and loaded onto a continuous sucrose gradient. After centrifugation, POS are located in a discrete band in the upper part of the gradient that has a characteristic orange color. POS are then collected, spun, resuspended sequentially in wash buffers, counted and aliquoted. POS obtained this way can be used for phagocytosis assays and analysis of protein activation, localization or interaction at various times after POS challenge. Alternatively, POS can be labeled with fluorophores, e.g., FITC, before aliquoting for subsequent fluorescence quantification of POS binding or engulfment. Other possible applications include the use of modified POS or POS challenge combined with stress conditions to study the effect of oxidative stress or aging on RPE cells.     

Organization and expression of mouse Hox3 cluster genes

Summary The three yolk protein genes (yp) of Drosophila melanogaster are transcribed in a sex- and tissue-limited fashion. We have searched for cis-regulatory sequences in regions flanking yp1 and yp2 to identify the elements that confer female-specific expression in the fat body. One such 127 by element has previously been identified in this region. We show here the existence of two additional regions which confer female fat body-specific expression on an Adh reporter gene and on the native yp2 gene, respectively. This suggests some redundancy in the regulation of expression of the yp genes. Computer searches for putative binding sites for the DSX protein, which regulates sex-specific expression of the yp genes, revealed several such sites in our constructs. However, the significance of these is unclear since many such sites also occur in genes which one would not expect to be regulated in a sex-specific manner (e.g. Adh, Actin 5C). We suggest that DSX acts in concert with other proteins to mediate sex- and tissue-specific expression of the yp genes.     

Cognitive Dysfunction Precedes the Onset of Motor Symptoms in the MitoPark Mouse Model of Parkinson’s Disease

Parkinson’s disease (PD) is a neurodegenerative disorder primarily characterized by progressive loss of dopamine neurons, leading to loss of motor coordination. However, PD is associated with a high rate of non-motor neuropsychiatric comorbities that often develop before the onset of movement symptoms. The MitoPark transgenic mouse model is the first to recapitulate the cardinal clinical features, namely progressive neurodegeneration and death of neurons, loss of motor function and therapeutic response to L-DOPA. To investigate whether MitoPark mice exhibit early onset of cognitive impairment, a non-motor neuropsychiatric comorbidity, we measured performance on a spatial learning and memory task before (∼8 weeks) or after (∼20 weeks) the onset of locomotor decline in MitoPark mice or in littermate controls. Consistent with previous studies, we established that a progressive loss of spontaneous locomotor activity began at 12 weeks of age, which was followed by progressive loss of body weight beginning at 16–20 weeks. Spatial learning and memory was measured using the Barnes Maze. By 20 weeks of age, MitoPark mice displayed a substantial reduction in overall locomotor activity that impaired their ability to perform the task. However, in the 8-week-old mice, locomotor activity was no different between genotypes, yet MitoPark mice took longer, traveled further and committed more errors than same age control mice, while learning to successfully navigate the maze. The modest between-day learning deficit of MitoPark mice was characterized by impaired within-day learning during the first two days of testing. No difference was observed between genotypes during probe trials conducted one or twelve days after the final acquisition test. Additionally, 8-week-old MitoPark mice exhibited impaired novel object recognition when compared to control mice. Together, these data establish that mild cognitive impairment precedes the loss of motor function in a novel rodent model of PD, which may provide unique opportunities for therapeutic development.     

Century‐long apparent decrease in intrinsic water‐use efficiency with no evidence of progressive nutrient limitation in African tropical forests

Forests exhibit leaf‐ and ecosystem‐level responses to environmental changes. Specifically, rising carbon dioxide (CO₂) levels over the past century are expected to have increased the intrinsic water‐use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long‐term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO₂ concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf‐level adaptation to increasing CO₂—that is, increasing photosynthesis‐related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ¹³C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on‐ground monitoring in the Congo Basin.     

Growth and resilience responses of Scots pine to extreme droughts across Europe depend on predrought growth conditions

Global climate change is expected to further raise the frequency and severity of extreme events, such as droughts. The effects of extreme droughts on trees are difficult to disentangle given the inherent complexity of drought events (frequency, severity, duration, and timing during the growing season). Besides, drought effects might be modulated by trees’ phenotypic variability, which is, in turn, affected by long‐term local selective pressures and management legacies. Here we investigated the magnitude and the temporal changes of tree‐level resilience (i.e., resistance, recovery, and resilience) to extreme droughts. Moreover, we assessed the tree‐, site‐, and drought‐related factors and their interactions driving the tree‐level resilience to extreme droughts. We used a tree‐ring network of the widely distributed Scots pine (Pinus sylvestris) along a 2,800 km latitudinal gradient from southern Spain to northern Germany. We found that the resilience to extreme drought decreased in mid‐elevation and low productivity sites from 1980–1999 to 2000–2011 likely due to more frequent and severe droughts in the later period. Our study showed that the impact of drought on tree‐level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances (i.e., magnitude and variability of growth) during the predrought period. We found significant interactive effects between drought duration and tree growth prior to drought, suggesting that Scots pine trees with higher magnitude and variability of growth in the long term are more vulnerable to long and severe droughts. Moreover, our results indicate that Scots pine trees that experienced more frequent droughts over the long‐term were less resistant to extreme droughts. We, therefore, conclude that the physiological resilience to extreme droughts might be constrained by their growth prior to drought, and that more frequent and longer drought periods may overstrain their potential for acclimation.     

Predicting soil carbon changes in switchgrass grown on marginal lands under climate change and adaptation strategies

The United States Great Lakes Region (USGLR) is a critical geographic area for future bioenergy production. Switchgrass (Panicum virgatum) is widely considered a carbon (C)‐neutral or C‐negative bioenergy production system, but projected increases in air temperature and precipitation due to climate change might substantially alter soil organic C (SOC) dynamics and storage in soils. This study examined long‐term SOC changes in switchgrass grown on marginal land in the USGLR under current and projected climate, predicted using a process‐based model (Systems Approach to Land‐Use Sustainability) extensively calibrated with a wealth of plant and soil measurements at nine experimental sites. Simulations indicate that these soils are likely a net C sink under switchgrass (average gain 0.87 Mg C ha^?1 year^?1), although substantial variation in the rate of SOC accumulation was predicted (range: 0.2–1.3 Mg C ha^?1 year^?1). Principal component analysis revealed that the predicted intersite variability in SOC sequestration was related in part to differences in climatic characteristics, and to a lesser extent, to heterogeneous soils. Although climate change impacts on switchgrass plant growth were predicted to be small (4%–6% decrease on average), the increased soil respiration was predicted to partially negate SOC accumulations down to 70% below historical rates in the most extreme scenarios. Increasing N fertilizer rate and decreasing harvest intensity both had modest SOC sequestration benefits under projected climate, whereas introducing genotypes better adapted to the longer growing seasons was a much more effective strategy. Best‐performing adaptation scenarios were able to offset >60% of the climate change impacts, leading to SOC sequestration 0.7 Mg C ha^?1 year^?1 under projected climate. On average, this was 0.3 Mg C ha^?1 year^?1 more C sequestered than the no adaptation baseline. These findings provide crucial knowledge needed to guide policy and operational management for maximizing SOC sequestration of future bioenergy production on marginal lands in the USGLR.     

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson‐Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two‐dimensional external molecular visualization software. This process has inherent limitations: visualization of three‐dimensional objects using a two‐dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol‐APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.