500,000 Years of Environmental History in Eastern Anatolia: The PALEOVAN Drilling Project

International Continental Scientific Drilling Program (ICDP) drilled a complete succession of the lacustrine sediment sequence deposited during the last ~500,000 years in Lake Van, Eastern Anatolia (Turkey). Based on a detailed seismic site survey, two sites at a water depth of up to 360 m were drilled in summer 2010, and cores were retrieved from sub-lake-floor depths of 140 m (Northern Basin) and 220 m (Ahlat Ridge). To obtain a complete sedimentary section, the two sites were multiple-cored in order to investigate the paleoclimate history of a sensitive semi-arid region between the Black, Caspian, and Mediterranean seas. Further scientific goals of the PALEOVAN project are the reconstruction of earthquake activity, as well as the temporal, spatial, and compositional evolution of volcanism as reflected in the deposition of tephra layers. The sediments host organic matter from different sources and hence composition, which will be unravelled using biomarkers. Pathways for migration of continental and mantle-derived noble gases will be analyzed in pore waters. Preliminary 40Ar/39Ar single crystal dating of tephra layers and pollen analyses suggest that the Ahlat Ridge record encompasses more than half a million years of paleoclimate and volcanic/geodynamic history, providing the longest continental record in the entire Near East to date

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions

The vertebrate retina: a model for neuronal polarization in vivo.

The vertebrate retina develops rapidly from a proliferative neuroepithelium into a highly ordered laminated structure, with five distinct neuronal cell types. Like all neurons, these cells need to polarize in appropriate orientations order integrate their neuritic connections efficiently into functional networks. Its relative simplicity, amenability to in vivo imaging and experimental manipulation, as well as the opportunity to study varied cell types within a single tissue, make the retina a powerful model to uncover how neurons polarize in vivo. Here we review the progress that has been made thus far in understanding how the different retinal neurons transform from neuroepithelial cells into mature neurons, and how the orientation of polarization may be specified by a combination of pre-established intrinsic cellular polarity set up within neuroepithelial cells, and extrinsic cues acting upon these differentiating neurons

Inhibitory neuron migration and IPL formation in the developing zebrafish retina.

The mature vertebrate retina is a highly ordered neuronal network of cell bodies and synaptic neuropils arranged in distinct layers. Little, however, is known about the emergence of this spatial arrangement. Here, we investigate how the three main types of retinal inhibitory neuron (RIN) - horizontal cells (HCs), inner nuclear layer amacrine cells (iACs) and displaced amacrine cells (dACs) - reach their specific laminar positions during development. Using in vivo time-lapse imaging of zebrafish retinas, we show that RINs undergo distinct phases of migration. The first phase, common to all RINs, is bipolar migration directed towards the apicobasal centre of the retina. All RINs then transition to a less directionally persistent multipolar phase of migration. Finally, HCs, iACs and dACs each undergo cell type-specific migration. In contrast to current hypotheses, we find that most dACs send processes into the forming inner plexiform layer (IPL) before migrating through it and inverting their polarity. By imaging and quantifying the dynamics of HCs, iACs and dACs from birth to final position, this study thus provides evidence for distinct and new migration patterns during retinal lamination and insights into the initiation of IPL formation

Whole-brain activity mapping onto a zebrafish brain atlas

In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal-regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors

Cellular Requirements for Building a Retinal Neuropil

How synaptic neuropil is formed within the CNS is poorly understood. The retinal inner plexiform layer (IPL) is positioned between the cell bodies of amacrine cells (ACs) and retinal ganglion cells (RGCs). It consists of bipolar cell (BC) axon terminals that synapse on the dendrites of ACs and RGCs intermingled with projections from Müller glia (MG). We examined whether any of these cellular processes are specifically required for the formation of the IPL. Using genetic and pharmacological strategies, we eliminated RGCs, ACs, and MG individually or in combination. Even in the absence of all of these partner cells, an IPL-like neuropil consisting of only BC axon terminals still forms, complete with presynaptic specializations and sublaminar organization. Previous studies have shown that an IPL can form in the complete absence of BCs; therefore, we conclude that neither presynaptic nor postsynaptic processes are individually essential for the formation of this synaptic neuropil

A neuronal blueprint for directional mechanosensation in larval zebrafish.

Animals have a remarkable ability to use local cues to orient in space in the absence of a panoramic fixed reference frame. Here we use the mechanosensory lateral line in larval zebrafish to understand rheotaxis, an innate oriented swimming evoked by water currents. We generated a comprehensive light-microscopy cell-resolution projectome of lateralis afferent neurons (LANs) and used clustering techniques for morphological classification. We find surprising structural constancy among LANs. Laser-mediated microlesions indicate that precise topographic mapping of lateral-line receptors is not essential for rheotaxis. Recording neuronal-activity during controlled mechanical stimulation of neuromasts reveals unequal representation of water-flow direction in the hindbrain. We explored potential circuit architectures constrained by anatomical and functional data to suggest a parsimonious model under which the integration of lateralized signals transmitted by direction-selective LANs underlies the encoding of water-flow direction in the brain. These data provide a new framework to understand how animals use local mechanical cues to orient in space

Biomarkers in Lake Van sediments reveal dry conditions in eastern Anatolia during 110.000-10.000 years B.P.

Lipid biomarkers were analyzed in Lake Van sediments covering the last 600 ka, with a focus on the period between 110 and 10 ka, when a broad maximum in pore water salinity as a relict from the past suggests dry conditions. The occurrence and distribution of biomarkers indicative for terrestrial plants (long-chain n-alkane C29), haptophyte algae (methyl alkenones C37) and halophilic archaea (archaeol) all point toward a dry climate in Lake Van region during this time interval. The hydrogen isotopic composition of C29 n-alkanes (δDC29) and C37 alkenones (δDC37) is enriched between MIS 4 and MIS 2, which is interpreted as a decrease in the regional ratio of precipitation to evaporation. Similarly, the low abundance of the acyclic glycerol dialkyl glycerol tetraether GDGT-0 relative to archaeol, quantified by the Archaeol and Caldarchaeol Ecometric (ACE) is assumed to reflect the presence of halophilic euryarchaeota adapted to high salinity water. The climate around Lake Van appears in phase with the Yammouneh basin 800 km southwest and Lake Urmia 250 km southeast of Lake Van over the last two glacial periods. The results highlight the potential of combining ACE, δDC29, and δDC37 for reconstructing salinity changes and regional precipitation to evaporation ratio from lake sediments

Expansion microscopy of zebrafish for neuroscience and developmental biology studies

Expansion microscopy (ExM) allows scalable imaging of preserved 3D biological specimens with nanoscale resolution on fast diffraction-limited microscopes. Here, we explore the utility of ExM in the larval and embryonic zebrafish, an important model organism for the study of neuroscience and development. Regarding neuroscience, we found that ExM enabled the tracing of fine processes of radial glia, which are not resolvable with diffraction-limited microscopy. ExM further resolved putative synaptic connections, as well as molecular differences between densely packed synapses. Finally, ExM could resolve subsynaptic protein organization, such as ring-like structures composed of glycine receptors. Regarding development, we used ExM to characterize the shapes of nuclear invaginations and channels, and to visualize cytoskeletal proteins nearby. We detected nuclear invagination channels at late prophase and telophase, potentially suggesting roles for such channels in cell division. Thus, ExM of the larval and embryonic zebrafish may enable systematic studies of how molecular components are configured in multiple contexts of interest to neuroscience and developmental biology