Optogenetics: opsins and optical interfaces in neuroscience.

Optogenetics is defined as the integration of optics and genetics to control well-defined events within specified cells of living tissue. In this introduction, we focus on the basic techniques necessary for employing microbial opsins as optogenetic tools in mammalian brains. We provide a guide for the fundamentals of optogenetic application-selecting an opsin, implementing expression of opsins based on the neuroscientific experimental requirements, and adapting the corresponding optical hardware for delivery of light into mammalian brains.

Establishing a fiber-optic-based optical neural interface.

Selective expression of opsins in genetically defined neurons makes it possible to control a subset of neurons without affecting nearby cells and processes in the intact brain, but light must still be delivered to the target brain structure. Light scattering limits the delivery of light from the surface of the brain. For this reason, we have developed a fiber-optic-based optical neural interface (ONI), which allows optical access to any brain structure in freely moving mammals. The ONI system is constructed by modifying the small animal cannula system from PlasticsOne. The system for bilateral stimulation consists of a bilateral cannula guide that has been stereotactically implanted over the target brain region, a screw cap for securing the optical fiber to the animal's head, a fiber guard modified from the internal cannula adapter, and a bare fiber whose length is customized based on the depth of the target region. For unilateral stimulation, a single-fiber system can be constructed using unilateral cannula parts from PlasticsOne. We describe here the preparation of the bilateral ONI system and its use in optical stimulation of the mouse or rat brain. Delivery of opsin-expressing virus and implantation of the ONI may be conducted in the same surgical session; alternatively, with a transgenic animal no opsin virus is delivered during the surgery. Similar procedures are useful for deep or superficial injections (even for neocortical targets, although in some cases surface light-emitting diodes or cortex-apposed fibers can be used for the most superficial cortical targets).

(Table 2) Mineralogy and carbon, oxygen, and hydrogen isotope ratios for secondary mineral samples from igneous rocks from ODP Hole 128-794D

The basaltic rocks of Hole 794D drilled during Leg 128 are strongly altered. Microprobe analyses and XRD spectra on small quantities of matter extracted from thin sections show that primary minerals and glassy zones of the groundmass are totally or partially replaced by clay minerals with chlorite/saponite mixed-layer composition whatever the rock sample considered. This mixed-layer was also identified in veins and vesicles where it crystallizes in spheroidal aggregates. The largest veins and vesicles are filled by a zoned deposit: the chlorite/saponite mixed-layer always occupies the central part and is rimmed by pure saponite. Calcite crystallizes in secondary fractures which crosscut the clayey veins and vesicles. Chemographic analysis based on the M+-4Si-3R2+ projection shows that the chemical composition of the saponite component in the mixed-layer is identical to that of the free saponite. This indicates that the clay mineral crystallization was controlled by the chemical composition of the alteration fluids. From petrographic evidence, it is suggested that both chlorite/saponite mixed-layer and free saponite belong to the same hydrothermal event and are produced by a temperature decrease. This is supported by the stable isotopic data. The isotopic data show very little variation: d18O saponite ranges from 13.1 per mil to 13.5 per mil, and dD saponite from -73.6 per mil to -70.0 per mil. d18O calcite varies from +19.7 per mil to +21.9 per mil vs SMOW and d13C from -3.2 per mil to +0.4 per mil vs. PDB. These values are consistent with seawater alteration of the basalt. The formation of saponite took place at 150°-180°C and the formation of calcite at about 65°C.

Paleoceanographic record since 13kyr BP of sediment core LaPAS-KF02

In this paper we present a paleoceanographic reconstruction of the southwestern South Atlantic for the past 13 kyr based on faunal and isotopic analysis of planktonic foraminifera from a high-resolution core retrieved at the South Brazil Bight continental slope. Our record indicates that oceanographic changes in the southwestern South Atlantic during the onset of the Holocene were comparable in strength to those that occurred during the Younger Dryas. Full interglacial conditions started abruptly after 8.2 kyr BP with a sharp change in faunal composition and surface hydrography (SST and SSS). Part of the observed events may be explained in terms of changes in thermohaline circulation while the other part suggests a dominant role of winds. Our data indicate that during the Early Holocene upwelling was significantly strengthened in the South Brazil Bight promoting high productivity and preventing the establishment of the typically interglacial menardiiform species. In general terms, oceanographic changes recorded by core KF02 occurred in synchrony with Antarctica's climate.

Planktonic foraminiferal oxygen isotopes of ODP Site 143-865 samples

Cool tropical sea surface temperatures (SSTs) are reported for warm Paleogene greenhouse climates based on the d18O of planktonic foraminiferal tests. These results are difficult to reconcile with models of greenhouse gas-forced climate. It has been suggested that this "cool tropics paradox" arises from postdepositional alteration of foraminiferal calcite, yielding erroneously high d18O values. Recrystallization of foraminiferal tests is cryptic and difficult to quantify, and the compilation of robust d18O records from moderately altered material remains challenging. Scanning electron microscopy of planktonic foraminiferal chamber-wall cross sections reveals that the basal area of muricae, pustular outgrowths on the chamber walls of species belonging to the genus Morozovella, contain no mural pores and may be less susceptible to postdepositional alteration. We analyzed the d18O in muricae bases of morozovellids from the central Pacific (Ocean Drilling Program Site 865) by ion microprobe using 10 ?m pits with an analytical reproducibility of ±0.34 per mil (2 standard deviations). In situ measurements of d18O in these domains yield consistently lower values than those published for conventional multispecimen analyses. Assuming that the original d18O is largely preserved in the basal areas of muricae, this new d18O record indicates Early Paleogene (~49-56 Ma) tropical SSTs in the central Pacific were 4°-8°C higher than inferred from the previously published d18O record and that SSTs reached at least ~33°C during the Paleocene-Eocene thermal maximum. This study demonstrates the utility of ion microprobe analysis for generating more reliable paleoclimate records from moderately altered foraminiferal tests preserved in deep-sea sediments.

Chemical and isotopic compositions of ocean authigenic carbonates

Oceanic authigenic carbonates are classified according to origin of the carbonate carbon source using a complex methodology that includes methods of sedimentary petrography, mineralogy, isotope geochemistry, and microbiology. Mg-calcite (protodolomite) and aragonite predominate among the authigenic carbonates. All authigenic carbonates are depleted in 13C and enriched in 18O (in PDB system) that indicates biological fractionation of isotopes during carbonate formation. Obtained results show that authigenic carbonate formation is a biogeochemical (microbial) process, which involves carbon from ancient sedimentary rocks, abiogenic methane, and bicarbonate-ion of hydrothermal fluids into the modern carbon cycle.

(Table 2) Mineralogy, stable isotopes, and mineral percentages of the carbonate fraction of samples from the South China Sea

Chemoherm carbonates, as well as numerous other types of methane seep carbonates, were discovered in 2004 along the passive margin of the northern South China Sea. Lithologically, the carbonates are micritic containing peloids, clasts and clam fragments. Some are highly brecciated with aragonite layers of varying thicknesses lining fractures and voids. Dissolution and replacement is common. Mineralogically, the carbonates are dominated by high magnesium calcites (HMC) and aragonite. Some HMCs with MgCO3 contents of between 30-38 mol%-extreme-HMC, occur in association with minor amounts of dolomite. All of the carbonates are strongly depleted in d13C, with a range from -35.7 to -57.5 per mil PDB and enriched in d18O (+ 4.0 to + 5.3 per mil PDB). Abundant microbial rods and filaments were recognized within the carbonate matrix as well as aragonite cements, likely fossils of chemosynthetic microbes involved in carbonate formation. The microbial structures are intimately associated with mineral grains. Some carbonate mineral grains resemble microbes. The isotope characteristics, the fabrics, the microbial structure, and the mineralogies are diagnostic of carbonates derived from anaerobic oxidation of methane mediated by microbes. From the succession of HMCs, extreme-HMC, and dolomite in layered tubular carbonates, combined with the presence of microbial structure and diagenetic fabric, we suggest that extreme-HMC may eventually transform into dolomites. Our results add to the worldwide record of seep carbonates and establish for the first time the exact locations and seafloor morphology where such carbonates formed in the South China Sea. Characteristics of the complex fabric demonstrate how seep carbonates may be used as archives recording multiple fluid regimes, dissolution, and early transformation events.

(Table 1) Stable isotope data of chemoherm carbonates at Hydrate Ridge on the Cascadia continental margin

Two active chemoherm build-ups growing freely up into the oceanic water column, the Pinnacle and the South East-Knoll Chemoherms, have been discovered at Hydrate Ridge on the Cascadia continental margin. These microbially-mediated carbonate formations rise above the seafloor by several tens of meters and display a pinnacle-shaped morphology with steep flanks. The recovered rocks are pure carbonates dominated by aragonite. Based on fabric and mineralogic composition different varieties of authigenic aragonite can be distinguished. Detailed visual and petrographic investigations unambiguously reveal the involvement of microbes during the formation of the carbonates. The fabric of the cryptocrystalline and fibrous aragonite can be described as thrombolitic. Fossilized microbial filaments in the microcrystalline aragonite indicate the intimate relationship between microbes and carbonates. The strongly 13C-depleted carbon isotope values of the samples (as low as -48.1 per mill PDB) are characteristic of methane as the major carbon source for the carbonate formation. The methane-rich fluids from which the carbonates are precipitated originate most probably from a gas reservoir below the bottom-simulating reflector (BSR) and rise through fault systems. The d18O values of the aragonitic chemoherm carbonates are substantially higher (as high as 5.0 per mill PDB) than the expected equilibrium value for an aragonite forming from ambient seawater (3.5 per mill PDB). As a first approximation this indicates formation from glacial ocean water but other factors are considered as well. A conceptual model is presented for the precipitation of these chemoherm carbonates based on in situ observations and the detailed petrographic investigation of the carbonates. This model explains the function of the consortium of archaea and sulfate-reducing bacteria that grows on the carbonates performing anaerobic oxidation of methane (AOM) and enabling the precipitation of the chemoherms above the seafloor surrounded by oxic seawater. Beggiatoa mats growing on the surface of the chemoherms oxidize the sulfide provided by sulfate-dependent anaerobic oxidation of methane within an oxic environment. The contact between Beggiatoa and the underlying microbial consortium represents the interface between the overlying oxic water column and an anoxic micro-environment where carbonate formation takes place.

Geochemistry of sediments and kerogenes of ODP Hole

The organic matter contained within a series of Albian to Cenomanian, dark gray to black marls was characterized using pyrolysis techniques and analysis (elemental and carbon isotopes) of isolated kerogens. It was concluded that this material had a marine affinity. Variations in geochemical characteristics reflect differences in the extent of preservation, rather than changes in organic provenance. These changes appear to reflect differences in water depth and the position of the depositional site relative to the oxygen-minimum zone. Sediments displaying the most elevated levels of organiccarbon and hydrogen enrichment probably reflect sedimentation within the oxygen-minimum zone. Waters within the oxygen-minimum zone were probably dysaerobic, rather than anoxic. The presence of at least trace quantities of oxygen at the depositional site explains the poor degree of organic preservation and the material's largely gas-prone characteristics.

Carbonate mineralogical and isotopic analyses of TV-guided grab samples and TV-guided box corer samples from the Shumagin area

Methane seepage leads to Mg-calcite and aragonite precipitation at a depth of 4,850 m on the Aleutian accretionary margin. Stromatolitic and oncoid growth structures imply encrustation of microorganisms (microbial mats) in the host sediment with a unique growth direction downward into the sediment, forming crust-shaped lithologies. Biomarker investigations of the residue after carbonate dissolution show strong enrichments in crocetane and archaeol, which contain extremely low d13C values. This indicates the presence of methane-consuming archaea, and d13C values of -42 to -51 per mill PDB indicate that methane is the carbon source for the carbonate crusts. Thus, it appears that stromatolitic encrustations of methanotrophic anaerobic archaea probably occurs in a consortium with sulphate-reducing bacteria and that carbonate precipitation proceeds downward into the sediment, where ascending cold fluids provide a methane source. Strontium and oxygen isotope analyses as well as 14C ages of the carbonates suggest that the fluids come from deep within the sediment and that carbonate precipitation began about 3,000 years ago.

Elemental and isotope compositions of lipids, kerogens and asphaltenes from samples of DSDP Hole 41-368

The thermal effects of three (one major and two minor) Miocene diabase intrusions on Cretaceous black shales from DSDP site 41-368 have been analyzed. A concentration gradient was observed, especially for the hydrocarbons, decreasing towards the major intrusion and between the three sills. The thermally-altered samples in the proximity of and between the sills contained elemental sulfur and an excess of thermally-derived pristane over phytane. whereas, the unaltered sediments contained no elemental sulfur, and more phytane than pristane. A maximum yield of the extractable hydrocarbons was observed at a depth of 7 m below the major sill. Two classes of molecular markers were present in this bitumen suite. The first was sesqui-, di- and triterpenoids and steranes. which could be correlated with both terrigenous and autochthonous sources. They were geologically mature and showed no significant changes due to the thermal stress. The second class was found in the altered samples, which contained only polynuclear aromatic hydrocarbons with low alkyl substitution and sulfur and oxygen heterocyclic aromatic compounds. These compounds were derived from pyrolytic reactions during the thermal event. Kerogen was isolated from all of these samples, but only traces of humic substances were present. The H/C, N/C, d13C, d34S and dD all exhibit the expected effects of thermal stress. The kerogen becomes more aromatized and richer in 13C, 34S and D in the proximity of and between the sills. Maturation trends were also measured by the vitrinite reflectance and electron spin resonance, where the thermal stress could be correlated with an elevated country rock temperature and an increased degree of aromaticity. The effects of in situ thermal stress on the organic-rich shales resulted in the generation and expulsion of petroliferous material from the vicinity of the sills.

Contents of organic compounds in sediments from DSDP Legs 1 and 4

Fifteen sediment samples were studied from five drill sites recovered by the Glomar Challenger on Legs I and IV in the Gulf of Mexico and western Atlantic. This study concentrated on compounds derived from biogenic precursors, namely: (1) hydrocarbons, (2) fatty acids, (3) pigments and (4) amino acids. Carbon isotope (dC13) data [values <(-26)?, relative to PDB], long-chain n-alkyl hydrocarbons (>>C27) with odd carbon numbered molecules dominating even carbon numbered species, and presence of perylene proved useful as possible indicators for terrigenous contributions to the organic matter in some samples. Apparently land-derived organic matter can be transported for distances over 1000 km into the ocean and their source still recognized. The study was primarily designed to investigate: (i) the sources of the organic matter present in the sediment, (ii) their stability with time of accumulation and (iii) the conditions necessary for in situ formation of new compounds.

Geochemical and isotopic composition of sediments and pore waters from ODP Leg 164 sites

Authigenic carbonates were recovered from several horizons between 0 and 52 mbsf in sediments that overlay the Blake Ridge Diapir on the Carolina Rise (Ocean Drilling Program [ODP] Site 996). Active chemosynthetic communities at this site are apparently fed by fluid conduits extending beneath a bottom-simulating reflector (BSR). Gas hydrates occur at several depth intervals in these near-surface sediments. The carbonate nodules are composed of rounded to subangular intraclasts and carbonate cemented mussel shell fragments. Electron microprobe and X-ray diffraction (XRD) investigations show that aragonite is the dominant authigenic carbonate. Authigenic aragonite occurs both as microcrystalline, interstitial cement, and as cavity-filling radial fibrous crystals. The d13C values of the authigenic aragonite vary between -48.4 per mil and -30.5 per mil (Peedee belemnite [PDB]), indicating that carbon derived from 13C-depleted methane is incorporated into these carbonates. The d13C of pore water sum CO2 values are most negative in the upper 10 mbsf, near the sediment/water interface (-38 per mil ± 5 per mil), but noticeably more positive below 25 mbsf (+5 per mil ± 6 per mil). Because carbonates derive their carbon from HCO3-, dissimilarities between the d13C values of carbonate precipitates recovered from greater than 10 mbsf and d13C values of the associated pore fluids suggests that these carbonates formed near the seafloor. Differences of about 1 per mil in the oxygen isotopic composition of carbonate precipitates from different depths are possibly related to changes in bottom-water conditions during glacial and interglacial time periods. Measurements of the strontium isotopic composition on 13 carbonate samples show 87Sr/86Sr values between 0.709125 and 0.709206 with a mean of 0.709165, consistent with the approximate age of their host sediment. Furthermore, the 87Sr/86Sr values of six pore-water samples from Site 996 vary between 0.709130 and 0.709204. The similarity of these values to seawater (87Sr/86Sr = 0.709175), and to 87Sr/86Sr values of pore water from similar sample depths elsewhere on the Blake Ridge (Sites 994, 995, and 997), indicates a shallow Sr source. The 87Sr/86Sr values of the authigenic carbonates at Site 996 are not consistent with the Sr isotopic values predicted for carbonates precipitated from fluids transported upward along fault conduits extending through the base of the gas hydrate-stability zone. Based on our data, we see no evidence of continuing carbonate diagenesis with depth. Therefore, with the exception of their seafloor expression as carbonate crusts, fossil vent sites will not be preserved. Because these authigenic features apparently form only at the seafloor, their vertical distribution and sediment age imply that seepage has been going on in this area for at least 600,000 yr.

Chemical and isotopic compositions of authigenic carbonates from the area of the Sakhalin-Deryugin gas anomaly, Sea of Okhotsk

Features of sedimentation of carbonate mineral associations in the northeastern shelf of Sakhalin and other regions of the Sea of Okhotsk are considered. Special attention is paid to correlation between carbonate neoformations and abnormal fluxes of methane. In bottom sediments with high contents of methane carbonate-sulfide associations occur, their generation has been influenced by gas (mostly methane) fields. Joint consideration of distribution of gas and geochemical fields and mineral associations in the Sea of Okhotsk allows to understand better a mechanism of mineral generation in bottom sediments, possible formation of ore accumulations, and to use them as indicators for prognosis of mineral resources.

Relative abundance and isotopic composition of calcite, dolomite and siderite from ODP Leg 164 sites

Authigenic carbonate mineral distributions are compared to pore-water geochemical profiles and used to evaluate diagenesis within sedimentary sections containing gas hydrates on the Blake Ridge (Ocean Drilling Program Sites 994, 995, and 997). Carbonate mineral distributions reveal three distinct diagenetic zones. (1) Carbonate minerals in the upper 20 m are primarily biogenic and show no evidence of diagenesis. The d13C and d18O values of calcite within this zone reflects marine carbonate (~0 per mil Peedee belemnite [PDB]) formed in equilibrium with seawater. (2) Between 20 and 100 mbsf, calcite d13C values are distinctly negative (as low as -7.0 per mil), and authigenic dolomite is common (~2-40 wt%) with d13C values between -3.6 per mil and 13.7 per mil. (3) Below 100 mbsf, dolomite abundance decreases to trace amounts, and disseminated siderite becomes the pervasive (~2-30 wt%) authigenic carbonate. Both siderite textures and stable isotope values indicate direct precipitation from pore fluids rather than dolomite replacement. The d13C and d18O values of siderite vary from 5.0 per mil to 10.9 per mil and 2.9 per mil to 7.6 per mil, respectively. Comparisons between the d13C profiles of dissolved inorganic carbon (DIC) and pore-water concentration gradients, with the d13C and d18O values of authigenic carbonates, delineate a distinct depth zonation for authigenic carbonate mineral formation. Coincidence of the most negative d13CDIC values (<=-38 per mil) and negative d13C values of both calcite and dolomite, with pore-water alkalinity increases, sulfate depletion, and decreases in interstitial Ca2+ and Mg2+ concentrations at and below 20 mbsf, suggests that authigenic calcite and dolomite formation is initiated at the base of the sulfate reduction zone (~21 mbsf) and occurs down to ~100 mbsf. Siderite formation apparently occurs between 120 and 450 mbsf; within, and above, the gas hydrate-bearing section of the sediment column (~200-450 mbsf). Siderite d13C and d18O values are nearly uniform from their shallowest occurrence to the bottom of the sedimentary section. However, present-day pore-water d13CDIC values are only similar to siderite d13C values between ~100 and 450 mbsf. Furthermore, calculated equilibrium d18O values of siderite match the measured 18O values of siderite between 120 and 450 mbsf. This interval is characterized by high alkalinity (40-120 mM) and low Ca2+ and Mg2+ concentrations, conditions that are consistent with siderite formation.