Plant and soil microbe responses to light, warming and nitrogen addition in a temperate forest

1. Temperate forests across Europe and eastern North America have become denser since the 1950s due to less intensive forest management and global environmental changes such as nitrogen deposition and climate warming. Denser tree canopies result in lower light availability at the forest floor. This shade may buffer the effects of nitrogen deposition and climate warming on understorey plant communities. 2. We conducted an innovative in situ field experiment to study the responses of co-occurring soil microbial and understorey plant communities to nitrogen addition, enhanced light availability and experimental warming in a full-factorial design. 3. We determined the effects of multiple environmental drivers and their interactions on the soil microbial and understorey plant communities, and assessed to what extent the soil microbial and understorey plant communities covary. 4. High light led to lower biomass of the soil microbes (analysed by phospholipid fatty acids), but the soil microbial structure, i.e. the ratio of fungal biomass to bacterial biomass, was not affected by light availability. The composition of the soil bacterial community (analysed by high-throughput sequencing) was affected by both light availability and warming (and their interaction), but not by nitrogen addition. Yet, the number of unique operational taxonomic units was higher in plots with nitrogen addition, and there were significant interactive effects of light and nitrogen addition. Light availability also determined the composition of the plant community; no effects of nitrogen addition and warming were observed. The soil bacterial and plant communities were co-structured, and light availability explained a large part of the variance of this co-structure. 5. We provide robust evidence for the key role of light in affecting both the soil microbial and plant communities in forest understoreys. Our results advocate for more multifactor global change experiments that investigate the mechanism underlying the (in) direct effects of light on the plant-soil continuum in forests

A Neural Model of Surface Perception: Lightness, Anchoring, and Filling-in

This article develops a neural model of how the visual system processes natural images under variable illumination conditions to generate surface lightness percepts. Previous models have clarified how the brain can compute the relative contrast of images from variably illuminate scenes. How the brain determines an absolute lightness scale that "anchors" percepts of surface lightness to us the full dynamic range of neurons remains an unsolved problem. Lightness anchoring properties include articulation, insulation, configuration, and are effects. The model quantatively simulates these and other lightness data such as discounting the illuminant, the double brilliant illusion, lightness constancy and contrast, Mondrian contrast constancy, and the Craik-O'Brien-Cornsweet illusion. The model also clarifies the functional significance for lightness perception of anatomical and neurophysiological data, including gain control at retinal photoreceptors, and spatioal contrast adaptation at the negative feedback circuit between the inner segment of photoreceptors and interacting horizontal cells. The model retina can hereby adjust its sensitivity to input intensities ranging from dim moonlight to dazzling sunlight. A later model cortical processing stages, boundary representations gate the filling-in of surface lightness via long-range horizontal connections. Variants of this filling-in mechanism run 100-1000 times faster than diffusion mechanisms of previous biological filling-in models, and shows how filling-in can occur at realistic speeds. A new anchoring mechanism called the Blurred-Highest-Luminance-As-White (BHLAW) rule helps simulate how surface lightness becomes sensitive to the spatial scale of objects in a scene. The model is also able to process natural images under variable lighting conditions.Air Force Office of Scientific Research (F49620-01-1-0397); Defense Advanced Research Projects Agency and the Office of Naval Research (N00014-95-1-0409); Office of Naval Research (N00014-01-1-0624

Awake chronic mouse model of targeted pial vessel occlusion via photothrombosis

Animal models of stroke are used extensively to study the mechanisms involved in the acute and chronic phases of recovery following stroke. A translatable animal model that closely mimics the mechanisms of a human stroke is essential in understanding recovery processes as well as developing therapies that improve functional outcomes. We describe a photothrombosis stroke model that is capable of targeting a single distal pial branch of the middle cerebral artery with minimal damage to the surrounding parenchyma in awake head-fixed mice. Mice are implanted with chronic cranial windows above one hemisphere of the brain that allow optical access to study recovery mechanisms for over a month following occlusion. Additionally, we study the effect of laser spot size used for occlusion and demonstrate that a spot size with small axial and lateral resolution has the advantage of minimizing unwanted photodamage while still monitoring macroscopic changes to cerebral blood flow during photothrombosis. We show that temporally guiding illumination using real-time feedback of blood flow dynamics also minimized unwanted photodamage to the vascular network. Finally, through quantifiable behavior deficits and chronic imaging we show that this model can be used to study recovery mechanisms or the effects of therapeutics longitudinally.R01 EB021018 - NIBIB NIH HHS; R01 MH111359 - NIMH NIH HHS; R01 NS108472 - NINDS NIH HHSPublished versio

A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium

The fungi Fusarium oxysporum and Fusarium fujikuroi produce carotenoids, lipophilic terpenoid pigments of biotechnological interest, with xanthophyll neurosporaxanthin as the main end product. Their carotenoid biosynthesis is activated by light and negatively regulated by the RING-finger protein CarS. Global transcriptomic analysis identified in both species a putative 1-kb lncRNA that we call carP, referred to as Fo-carP and Ff-carP in each species, upstream to the gene carS and transcribed from the same DNA strand. Fo-carP and Ff-carP are poorly transcribed, but their RNA levels increase in carS mutants. The deletion of Fo-carP or Ff-carP in the respective species results in albino phenotypes, with strong reductions in mRNA levels of structural genes for carotenoid biosynthesis and higher mRNA content of the carS gene, which could explain the low accumulation of carotenoids. Upon alignment, Fo-carP and Ff-carP show 75-80% identity, with short insertions or deletions resulting in a lack of coincident ORFs. Moreover, none of the ORFs found in their sequences have indications of possible coding functions. We conclude that Fo-carP and Ff-carP are regulatory lncRNAs necessary for the active expression of the carotenoid genes in Fusarium through an unknown molecular mechanism, probably related to the control of carS function or expressio

Retrieval of Leaf Area Index (LAI) and Soil Water Content (WC) Using Hyperspectral Remote Sensing under Controlled Glass House Conditions for Spring Barley and Sugar Beet

Leaf area index (LAI) and water content (WC) in the root zone are two major hydro-meteorological parameters that exhibit a dominant control on water, energy and carbon fluxes, and are therefore important for any regional eco-hydrological or climatological study. To investigate the potential for retrieving these parameter from hyperspectral remote sensing, we have investigated plant spectral reflectance (400-2,500 nm, ASD FieldSpec3) for two major agricultural crops (sugar beet and spring barley) in the mid-latitudes, treated under different water and nitrogen (N) conditions in a greenhouse experiment over the growing period of 2008. Along with the spectral response, we have measured soil water content and LAI for 15 intensive measurement campaigns spread over the growing season and could demonstrate a significant response of plant reflectance characteristics to variations in water content and nutrient conditions. Linear and non-linear dimensionality analysis suggests that the full band reflectance information is well represented by the set of 28 vegetation spectral indices (SI) and most of the variance is explained by three to a maximum of eight variables. Investigation of linear dependencies between LAI and soil WC and pre-selected SI's indicate that: (1) linear regression using single SI is not sufficient to describe plant/soil variables over the range of experimental conditions, however, some improvement can be seen knowing crop species beforehand; (2) the improvement is superior when applying multiple linear regression using three explanatory SI's approach. In addition to linear investigations, we applied the non-linear CART (Classification and Regression Trees) technique, which finally did not show the potential for any improvement in the retrieval process

Fast fluorescence microscopy for imaging the dynamics of embryonic development

Live imaging has gained a pivotal role in developmental biology since it increasingly allows real-time observation of cell behavior in intact organisms. Microscopes that can capture the dynamics of ever-faster biological events, fluorescent markers optimal for in vivo imaging, and, finally, adapted reconstruction and analysis programs to complete data flow all contribute to this success. Focusing on temporal resolution, we discuss how fast imaging can be achieved with minimal prejudice to spatial resolution, photon count, or to reliably and automatically analyze images. In particular, we show how integrated approaches to imaging that combine bright fluorescent probes, fast microscopes, and custom post-processing techniques can address the kinetics of biological systems at multiple scales. Finally, we discuss remaining challenges and opportunities for further advances in this field