Visualization of cell microtubules in their native state.

BACKGROUND INFORMATION Over the past decades, cryo-electron microscopy of vitrified specimens has yielded a detailed understanding of the tubulin and microtubule structures of samples reassembled in vitro from purified components. However, our knowledge of microtubule structure in vivo remains limited by the chemical treatments commonly used to observe cellular architecture using electron microscopy. RESULTS We used cryo-electron microscopy and cryo-electron tomography of vitreous sections to investigate the ultrastructure of microtubules in their cellular context. Vitreous sections were obtained from organotypic slices of rat hippocampus and from Chinese-hamster ovary cells in culture. Microtubules revealed their protofilament ultrastructure, polarity and, in the most favourable cases, molecular details comparable with those visualized in three-dimensional reconstructions of microtubules reassembled in vitro from purified tubulin. The resolution of the tomograms was estimated to be approx. 4 nm, which enabled the detection of luminal particles of approx. 6 nm in diameter inside microtubules. CONCLUSIONS The present study provides a first step towards a description of microtubules, in addition to other macromolecular assemblies, in an unperturbed cellular context at the molecular level. As the resolution appears to be similar to that obtainable with plunge-frozen samples, it should allow for the in vivo identification of larger macromolecular assemblies in vitreous sections of whole cells and tissues.

Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state.

The cell envelope of mycobacteria, which include the causative agents of tuberculosis and leprosy, is crucial for their success as pathogens. Despite a continued strong emphasis on identifying the multiple chemical components of this envelope, it has proven difficult to combine its components into a comprehensive structural model, primarily because the available ultrastructural data rely on conventional electron microscopy embedding and sectioning, which are known to induce artifacts. The existence of an outer membrane bilayer has long been postulated but has never been directly observed by electron microscopy of ultrathin sections. Here we have used cryo-electron microscopy of vitreous sections (CEMOVIS) to perform a detailed ultrastructural analysis of three species belonging to the Corynebacterineae suborder, namely, Mycobacterium bovis BCG, Mycobacterium smegmatis, and Corynebacterium glutamicum, in their native state. We provide new information that accurately describes the different layers of the mycobacterial cell envelope and challenges current models of the organization of its components. We show a direct visualization of an outer membrane, analogous to that found in gram-negative bacteria, in the three bacterial species examined. Furthermore, we demonstrate that mycolic acids, the hallmark of mycobacteria and related genera, are essential for the formation of this outer membrane. In addition, a granular layer and a low-density zone typifying the periplasmic space of gram-positive bacteria are apparent in CEMOVIS images of mycobacteria and corynebacteria. Based on our observations, a model of the organization of the lipids in the outer membrane is proposed. The architecture we describe should serve as a reference for future studies to relate the structure of the mycobacterial cell envelope to its function.

Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy

The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1(¹ππ*) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ~5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1ionization cross sections, we obtain energy dependent ISC quantum yields Q corr ISC =1% –5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4–1.5 ⋅ 10⁹ s⁻¹, the corresponding S1⇝S0internal conversion (IC) rates are 30–100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ⋅ 10⁹ s⁻¹ to the T1(³ππ*) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of ¹nOπ* character into the S1(¹ππ*) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm⁻¹ in the S1 state, S1⇝S0internal conversion dominates the nonradiative decay with kIC ≥ 2 ⋅ 10¹⁰ s⁻¹, (2) the calculated S1⇝T1 (¹ππ*⇝³ππ*) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ⋅ 10⁹ s⁻¹), and not ultrafast, as claimed by other calculations, and (4) at Eexc ~ 550 cm⁻¹ the IC rate increases by ~50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.

The elusive S2 state, the S1/S2 splitting, and the excimer states of the benzene dimer

We observe the weak S 0 → S 2 transitions of the T-shaped benzene dimers (Bz)2 and (Bz-d 6)2 about 250 cm−1 and 220 cm−1 above their respective S 0 → S 1 electronic origins using two-color resonant two-photon ionization spectroscopy. Spin-component scaled (SCS) second-order approximate coupled-cluster (CC2) calculations predict that for the tipped T-shaped geometry, the S 0 → S 2 electronic oscillator strength f el (S 2) is ∼10 times smaller than f el (S 1) and the S 2 state lies ∼240 cm−1 above S 1, in excellent agreement with experiment. The S 0 → S 1 (ππ ∗) transition is mainly localized on the “stem” benzene, with a minor stem → cap charge-transfer contribution; the S 0 → S 2 transition is mainly localized on the “cap” benzene. The orbitals, electronic oscillator strengths f el (S 1) and f el (S 2), and transition frequencies depend strongly on the tipping angle ω between the two Bz moieties. The SCS-CC2 calculated S 1 and S 2 excitation energies at different T-shaped, stacked-parallel and parallel-displaced stationary points of the (Bz)2 ground-state surface allow to construct approximate S 1 and S 2 potential energy surfaces and reveal their relation to the “excimer” states at the stacked-parallel geometry. The f el (S 1) and f el (S 2) transition dipole moments at the C 2v -symmetric T-shape, parallel-displaced and stacked-parallel geometries are either zero or ∼10 times smaller than at the tipped T-shaped geometry. This unusual property of the S 0 → S 1 and S 0 → S 2 transition-dipole moment surfaces of (Bz)2 restricts its observation by electronic spectroscopy to the tipped and tilted T-shaped geometries; the other ground-state geometries are impossible or extremely difficult to observe. The S 0 → S 1/S 2 spectra of (Bz)2 are compared to those of imidazole ⋅ (Bz)2, which has a rigid triangular structure with a tilted (Bz)2 subunit. The S 0 → S 1/ S 2 transitions of imidazole-(benzene)2 lie at similar energies as those of (Bz)2, confirming our assignment of the (Bz)2 S 0 → S 2 transition.

Polar Nature of Biomimetic Fluorapatite/Gelatin Composites: A Comparison of Bipolar Objects and the Polar State of Natural Tissue

The correspondence of the state of alignment of macromolecules in biomimetic materials and natural tissues is demonstrated by investigating a mechanism of electrical polarity formation: An in vitro grown biomimetic FAp/gelatin composite is investigated for its polar properties by second harmonic (SHGM) and scanning pyroelectric microscopy (SPEM). Hexagonal prismatic seed crystals formed in gelatin gels represent a monodomain polar state, due to aligned mineralized gelatin molecules. Later growth stages, showing dumbbell morphologies, develop into a bipolar state because of surface recognition by gelatin functionality: A reversal of the polar alignment of macromolecules, thus, takes place close to that basal plane of the seed. In natural hard tissues (teeth and bone investigated by SPEM) and the biomimetic FAp/gelatin composite, we find a surprising analogy in view of growth-induced states of polarity: The development of polarity in vivo and in vitro can be explained by a Markov-type mechanism of molecular recognition during the attachment of macromolecules.

Assessing the Environmental Protection Agency's guidelines for cumulative risk assessment: Are they suitable for state agencies and EPA regional offices?

In the field of health risk analysis, cumulative risk assessment (CRA) is a necessary, although undeniably more complex approach to understanding the mixture of stressors, whether chemical or psychosocial, that exist in our environment, in all the pathways through which the chemicals may evolve—air, soil, or water, as well as the accumulation of these exposures over time. Related, or attached to the developing awareness of scientists understanding this mix of combined health effects is the burgeoning of the environmental justice movement, in which educated community advocates and even affected community members have called attention to evidence of a higher pollution burden in minority and/or lower SES communities. The intention of this paper is to 1) examine the development and understanding of CRA, primarily by the U.S. Environmental Protection Agency; 2) to assess several states agencies and some EPA regional offices' interpretation of CRA, again based primarily on EPA guidance, and 3) to analyze how CRA might be refined in its implementation—giving some cues as to how the EPA may more effectively interact with communities interested in CRA.^

Chemical Modification of Partially Hydrogenated Vegetable Oil to Improve its Functional Properties to Replace Petroleum Waxes

A novel, chemically-modified partially hydrogenated vegetable oil (PHVO) is described. The PHVO is produced by a three-step reaction process that includes epoxidation, a ringopening reaction, followed by esterification. The modified PHVO has improved kneadability and, if mixed with fully hydrogenated fat(s ), hardness comparable to umnodified PHVO.

Chemical, and Sr and Li isotopic composition of pore fluids and sediments from ODP Leg 170 and Leg 205 sites

Pore fluid and sediment chemical and isotopic data were obtained for samples from Ocean Drilling Program (ODP) Leg 205 Sites 1253, 1254, and 1255 in the Costa Rica subduction zone. The chemical and isotopic data reported here were generated in our shore-based laboratories to complement shipboard inorganic geochemical data. Li isotopic analyses were carried out by L.-H. Chan at Louisiana State University (USA). The data reported herein include fluoride, bromide, rubidium, cesium, and barium concentrations; Li and Sr isotopic compositions in pore fluids; and Rb, Cs, and Ba concentrations in representative bulk sediments. The data also include new pore fluid fluoride and bromide concentrations from corresponding ODP Leg 170 Sites 1039, 1040, and 1043. O.M. Saether's Site 1039 and 1040 fluoride concentration data are shown for comparison. Basal sediment fluoride concentrations and Li and Sr isotope ratios at both Sites 1253 and 1039 show reversals that approach modern seawater values. Br/Cl ratios are, however, conservative throughout the sediment section at Sites 1039 and 1253. The observed sharp F and Br concentration maxima, Rb and K concentration minima, the most radiogenic 87Sr/86Sr ratios, and highest 7Li values along the décollement and fracture zone (Sites 1040, 1043, 1254, and 1255) strengthen the evidence obtained during Leg 170 that a deeply sourced fluid, originating from fluid-rock reactions at ~150°C and corresponding to between 10 and 15 km depth, is transporting solutes to the ocean.

Chemical and Sr isotopic compositions of 3 step leachates and residues of bulk samples, zeolites, and smectites from Lower Miocene sediments at ODP Site 166-1007

Massive clinoptilolite authigenesis was observed at about 1105 meters below sea floor (mbsf) in lower Miocene wellcompacted carbonate periplatform sediments from the Great Bahama Bank [Ocean Drilling Program, ODP Leg 166, Site 1007]. The diagenetic assemblage comprises abundant zeolite crystallized within foraminifer tests and sedimentary matrix, as well as Mg smectites. In carbonate-rich deposits, the formation of the zeolite requires a supply of silica. Thus, the objective of the study is to determine the origin of the silica supply, its diagenetic evolution, and consequently the related implications on interpretation of the sedimentary record, in terms of local or global paleoceanographic change. For lack of evidence for any volcaniclastic input or traces of Si-enriched deep fluids circulation, an in situ biogenic source of silica is validated by isotopic data and chemical modeling for the formation of such secondary minerals in shallow-water carbonate sequences. Geochemical and strontium isotopic data clearly establish the marine signature of the diagenetic zeolite, as well as its contemporaneous formation with the carbonate deposition (Sr model ages of 19.6-23.2 Ma). The test of saturation for the pore fluids specifies the equilibrium state of the present mineralogical assemblage. Seawater-rock modeling specifies that clinoptilolite precipitates from the dissolution of biogenic silica, which reacts with clay minerals. The amount of silica (opal-A) involved in the reaction has to be significant enough, at least 10 wt.%, to account for the observed content of clinoptilolite occurring at the most zeolite-rich level. Modeling also shows that the observed amount of clinoptilolite (~19%) reflects an in situ and short-term reaction due to the high reactivity of primary biogenic silica (opal-A) until its complete depletion. The episodic occurrence of these well-lithified zeolite-rich levels is consistent with the occurrence of seismic reflectors, particularly the P2 seismic sequence boundary located at 1115 mbsf depth and dated as 23.2 Ma. The age range of most zeolitic sedimentary levels (biostratigraphic ages of 21.5-22 Ma) correlates well with that of the early Miocene glaciation Mi-1 and Mi-1a global events. Thus, the clinoptilolite occurrence in the shallow carbonate platform environment far from volcanogenic supply, or in other sensitive marine areas, is potentially a significant new proxy for paleoproductivity and oceanic global events, such as the Miocene events, which are usually recognized in deep-sea pelagic sediments and high latitude deposits.

Chemical and isotopic composition of rocks and minerals at ODP Site 209-1275

This paper reports results of an investigation of a representative collection of samples recovered by deep-sea drilling from the oceanic basement 10 miles west of the rift valley axis in the crest zone of the Mid- Atlantic Ridge at 15°44'N (Sites 1275B and 1275D). Drilling operations were carried out during Leg 209 of the Drilling Vessel JOIDES Resolution within the framework of the Ocean Drilling Program (ODP). The oceanic crust was penetrated to depth of 108.7 m at Site 1275B and 209 m at Site 1275D. We reconstructed the following sequence of magmatic and metamorphic events resulting in the formation of a typical oceanic core complex of slow-spreading ridges: (1) formation of strongly fractionated (enriched in iron and titanium) tholeiitic magmatic melt parental to gabbroids under investigation in a large magma chamber located in a shallow mantle and operating for a long time under steady-state conditions; (2) transfer of the parental magmatic melt of the gabbroids to the base of the oceanic crust, its interaction with host mantle peridotites, and formation of troctolites and plagioclase peridotites; (3) intrusion of enriched trondhjemite melts as veins and dikes in the early formed plutonic complex, contact recrystallization of the gabbro, and development in the peridotite-gabbro complex of enriched geochemical signatures owing to influence of trondhjemite injections; (4) emplacement of dolerite dikes (transformed to diabases); (5) metamorphism of upper epidoteamphibolite facies with participation of marine fluids; and (6) rapid exhumation of the plutonic complex to the seafloor accompanied by greenschist-facies metamorphism. Distribution patterns of Sr and Nd isotopes and strongly incompatible elements in the rocks suggest contributions from two melt sources to the magmatic evolution of the MAR crest at 15°44'N: a depleted reservoir responsible for formation of the gabbros and diabases and an enriched reservoir, from which trondhjemites (granophyres) were derived.

Chemical and Sr isotopic compositions of pore fluids and marine carbonates from ODP Hole 130-807A

The 87Sr/86Sr ratios and Sr concentrations in sediment and pore fluids are used to evaluate the rates of calcite recrystallization at ODP Site 807A on the Ontong Java Plateau, an 800-meter thick section of carbonate ooze and chalk. A numerical model is used to evaluate the pore fluid chemistry and Sr isotopes in an accumulating section. The deduced calcite recrystallization rate is 2% per million years (%/Myr) near the top of the section and decreases systematically in older parts of the section such that the rate is close to 0.1/age (in years). The deduced recrystallization rates have important implications for the interpretation of Ca and Mg concentration profiles in the pore fluids. The effect of calcite recrystallization on pore fluid chemistry is described by the reaction length, L, which varies by element, and depends on the concentration in pore fluid and solid. When L is small compared to the thickness of the sedimentary section, the pore fluid concentration is controlled by equilibrium or steady-state exchange with the solid phase, except within a distance L of the sediment-water interface. When L is large relative to the thickness of sediment, the pore fluid concentration is mostly controlled by the boundary conditions and diffusion. The values of L for Ca, Sr, and Mg are of order 15, 150, and 1500 meters, respectively. L_Sr is derived from isotopic data and modeling, and allows us to infer the values of L_Ca and L_Mg. The small value for L_Ca indicates that pore fluid Ca concentrations, which gradually increase down section, must be equilibrium values that are maintained by solution-precipitation exchange with calcite and do not reflect Ca sources within or below the sediment column. The pore fluid Ca measurements and measured alkalinity allow us to calculate the in situ pH in the pore fluids, which decreases from 7.6 near the sediment-water interface to 7.1+/-0.1 at 400-800 mbsf. While the calculated pH values are in agreement with some of the values measured during ODP Leg 130, most of the measurements are artifacts. The large value for L_Mg indicates that the pore fluid Mg concentrations at 807A are not controlled by calcite-fluid equilibrium but instead are determined by the changing Mg concentration of seawater during deposition, modified by aqueous diffusion in the pore fluids. We use the pore fluid Mg concentration profile at Site 807A to retrieve a global record for seawater Mg over the past 35 Myr, which shows that seawater Mg has increased rapidly over the past 10 Myr, rather than gradually over the past 60 Myr. This observation suggests that the Cenozoic rise in seawater Mg is controlled by continental weathering inputs rather than by exchange with oceanic crust. The relationship determined between reaction rate and age in silicates and carbonates is strikingly similar, which suggests that reaction affinity is not the primary determinant of silicate dissolution rates in nature.

(Table A1) Chemical composition of abyssal peridotites from ODP Hole 153-920

The compatibility of vanadium (V) during mantle melting is a function of oxygen fugacity (fO2): at high fO2's, V becomes more incompatible. The prospects and limitations of using the V content of peridotites as a proxy for paleo-fO2 at the time of melt extraction were investigated here by assessing the uncertainties in V measurements and the sensitivity of V as a function of degree of melt extracted and fO2. V-MgO and V-Al2O3 systematics were found to be sensitive to fO2 variations, but consideration of the uncertainties in measurements and model parameters indicates that V is sensitive only to relative fO2 differences greater than ~2 log units. Post-Archean oceanic mantle peridotites, as represented by abyssal peridotites and obducted massif peridotites, have V-MgO and -Al2O3 systematics that can be modeled by 1.5 GPa melting between FMQ - 3 and FMQ - 1. This is consistent with fO2's of the mantle source for mid-ocean ridge basalts (MORBs) as determined by the Fe3+ activity of peridotitic minerals and basaltic glasses. Some arc-related peridotites have slightly lower V for a given degree of melting than oceanic mantle peridotites, and can be modeled by 1.5 GPa melting at fO2's as high as FMQ. However, the majority of arc-related peridotites have V-MgO systematics overlapping that of oceanic mantle peridotites, suggesting that although some arc mantle may melt under slightly oxidizing conditions, most arc mantle does not. The fact that thermobarometrically determined fO2's in arc peridotites and lavas can be significantly higher than that inferred from V systematics, suggests that V retains a record of the fO2 during partial melting, whereas the activity of Fe3+ in arc peridotitic minerals and lavas reflect subsequent metasomatic overprints and magmatic differentiation/emplacement processes, respectively. Peridotites associated with middle to late Archean cratonic mantle are characterized by highly variable V-MgO systematics. Tanzanian cratonic peridotites have V systematics indistinguishable from post-Archean oceanic mantle and can be modeled by 3 GPa partial melting at ~FMQ - 3. In contrast, many South African and Siberian cratonic peridotites have much lower V contents for a given degree of melting, suggesting at first glance that partial melting occurred at high fO2's. More likely, however, their unusually low V contents for a given degree of melting may be artifacts of excess orthopyroxene, a feature that pervades many South African and Siberian peridotites but not the Tanzanian peridotites. This is indicated by the fact that the V contents of South African and Siberian peridotites are correlated with increases in SiO2 content, generating data arrays that cannot be modeled by partial melting but can instead be generated by the addition of orthopyroxene through processes unrelated to primary melt depletion. Correction for orthopyroxene addition suggests that the South African and Siberian peridotites have V-MgO systematics similar to those of Tanzanian peridotites. Thus, if the Tanzanian peridotites represent the original partial melting residues, and if the South African and Siberian peridotites have been modified by orthopyroxene addition, then there is no indication that Archean cratonic mantle formed under fO2's significantly greater than that of modern oceanic mantle. Instead, the fO2's inferred from the V systematics in these three cratonic peridotite suites are within range of modern oceanic mantle. This also suggests that the transition from a highly reducing mantle in equilibrium with a metallic core to the present oxidized state must have occurred by late Archean times.

Chemical composition of waters from the Black Sea

Concentrations of sulfate ions at three depths in the water column of the Black Sea were studied during cruises of the GOIN (State Oceanographic Institute) Sevastopol' Division in 1983 and 1985. Results were compared with data from earlier studies. Obtained data indicate pronounced lateral and temporal variation in the SO4/Cl ratio.