A systematic analysis of INO80 in DNA replication

ATP-dependent chromatin remodeling has been shown to be critical for transcription and DNA repair. However, the involvement of ATP-dependent chromatin remodeling in DNA replication remains poorly defined. Interestingly, we found that the INO80 chromatin-remodeling complex is directly involved in the DNA damage tolerance pathways activated during DNA replication. DNA damage tolerance is important for genomic stability and is controlled by formation of either mono-ubiquitinated or multi-ubiquitinated PCNA, which respectively induce error prone or error-free replication bypass of the lesions. In addition, homologous recombination (HR) mediated by the Rad51 pathway is also involved in the DNA damage tolerance pathways. ^ We found that INO80 is specifically recruited to replication origins during S phase in a genome-wide fashion. In addition, DNA combing analysis shows INO80 is required for the resumption of replication at stalled forks induced by methyl methane-sulfonate (MMS). Mechanistically, we find that INO80 is required for PCNA ubiquitination as well as for Rad51 mediated processing of replication forks after MMS treatment. Furthermore, chromatin immunoprecipitation at specific ARSs indicates INO80 is necessary for Rad18 and Rad51 recruitment to replication forks after MMS treatment. Moreover, 2D gel analysis shows INO80 is necessary to process Rad51 mediated intermediates at impeded replication forks. ^ In conclusion, our findings establish a novel role of a chromatin-remodeling complex in DNA damage tolerance pathways and suggest that chromatin remodeling is fundamentally important to ensure faithful replication of DNA and genome stability in eukaryotes. ^

Mineral resources in Lower Brule Indian Reservation

On the Lower Brule Indian Reservation in South Dakota, about 3 million tons of metallic manganese are in low-grade deposits in the DeGrey Member of the Pierre Shale on the reservation. The geology and methods of mining and processing this sub-economic mineral resource have been studied extensively; technologically, extraction of manganese is possible. However, an efficient, economical method to separate manganese-bearing nodules from the shale host rocks has yet to be found. The manganiferous nodules occur in the Oacoma zone of the Sully shale member (De-Grey Member) which is a subdivision of the South Dakota Pierre Shale formation. These nodular deposits have an interesting similarity in stratigraphical position, lithology and manganese content to those of the Porcupine Mountain area in Manitoba.

(Table 11-I, page 338) Metal contents (%) of a representative sampling of manganese nodules from the North Pacific high-grade region

Two types of deep-sea dredges are currently under development for the mining of the manganese nodules, a deep-sea hydraulic dredge and a mechanical cable-bucket system. Both systems offer some advantages with the hydraulic system appearing to be advantageous in themining of a specific deposit for which it is designed while the cable-bucket system appears to be somewhat more flexible in working in a variety of deposits, topographic environments, and water depths. Environmental studies conducted in conjunction with deep-sea tests of the two types of mining systems currently indicate that substantially no environmental damage will be done in the mining of the deep-sea nodules. Because of the nature of the deposits and the way in which they can be mined, the manganese nodules appear to be a relatively pollution free and energy-saving source of a number of industrially important metals.

Description and chemical composition of manganese deposits during the deep-sea expedition of the streamer Valdivia in 1898-1899

This monograph forms the fourth part of the tenth volume of the scientific results of the voyage of the German exploring ship Valdivia in the Atlantic and Indian Oceans, made during the years 1898-1899. These volumes are published under the editorship of Prof. Chun, the zoologist of Leipzig, who was leader of the expedition ; and Prof. E. Philippi with the cooperation of Sir John Murray. The nature of the materials brought up at various points during the voyage is well illustrated by a series of plates, similar to those accompanying the Challenger volumes. Among the concretions from the Agulhas Bank were found phosphatic nodules containing 33 per cent, of calcium carbonate, 28 of calcium phosphate, 14.6 of calcium sulphate, and 4.8 of magnesium carbonate, with some ferric oxide, alumina, and silica. These nodules were dredged at a depth of 155 metres. Off the coast of Namibia, a large quantity of manganese nodules were also dredged. Their chemical analysis performed at the Mineralogical Institute of the University Jena show similar composition as the nodules recovered by the "Challenger" at station 253 in the Pacific Ocean.

Description and chemical and mineral composition of iron oxide samples from two Finnish lakes

Fifteen iron oxide accumulations from the bottoms of two Finnish lakes ("lake ores") were found to contain as much as 50% Fe. Differential X-ray powder diffraction and selective dissolution by oxalate showed that the samples consisted of poorly crystallized goethite and ferrihydrite. The crust ores of one lake had higher ferrihydrite to goethite ratios than the nodular ores of the other lake. The higher ferrihydrite proportion was attributed to a higher rate of Fe2+ supply from the ground water and/or a higher rate of oxidation as a function of water depth and bottom-sediment permeability. Values of Al-for-Fe substitution of the goethites determined from unit-cell dimensions agreed with those obtained from chemical extraction if the unit-cell volume rather than the c dimension was used. In very small goethite crystals a slight expansion of the a unit-cell dimension is probaby compensated by a corresponding contraction of the c dimension, so that a contraction of the c dimension need not necessarily be caused by Al substitution. The goethites of the two lakes differed significantly in their Al-for-Fe substitutions and hence in their unit-cell sizes, OH-bending characteristics, dehydroxylation temperatures, dissolution kinetics, and Mössbauer parameters. The difference in Al substitution (0 vs. 7 mole %) is attributed to the Al-supplying power of the bottom sediments: the silty-clayey sediments in one lake appear to have supplied A1 during goethite formation, whereas the gravelly-sandy sediments in the other lake did not. The compositions of the goethites thus reflect their environments of formation.

Permian manganese nodules near Dillon, Montana

Concentrically ringed manganese nodules, similar in form to many found on modern ocean and sea floors, occur in a very fine grained argillaceous sandstone bed of the Permian Park City Formation near Dillon, Montana. They are enriched in many rare elements and contain us much as 2.5 percent zinc, l.3 percent nickel, and 0.22 percent cobalt. The manganese minerals are chalcophanite and todorokite. The nodules probably formed in a shallow marine oxidizing environment on the western side of the Permian sedimentary basin. The occurrence of an appreciable amount of fluorite in the bed suggests that the water was saline.

Geochemistry on sediments in Lake Biwa

Thirty sediment cores (30-40 cm in length), 47 Ekman dredge sediments, and Mn concretions were collected from Lake Biwa. The concentrations of 36 elements in the samples were determined by instrumental neutron activation, X-ray fluorescence, atomic absorption, and colorimetric analyses. The elements determined included Mn, P, As, Sb, Fe, Ni, Co, Zn, Cu, Pb, Hg, Cr, Ti, Na, K, Rb, Cs, Mg, Ca, Sr, Ba, Sc, Hf, La, Ce, Sm, Eu, Yb, Lu, U, Th, Au, Ta, Nd, Br and N. Based on statistical considerations and calculation of the concentration factors of the elements, the features of the elemental distribution in Lake Biwa sediment were determined. The main results are summarized as follows : (1) Concentrations of Mn and As were very high in the uppermost oxidized layer of the offshore sediment and Mn concretions. This resulted from the dissolution-deposition cycles of these elements within the sedimentary column and the bottom water. The fixation of As at the sediment surface is mainly attributed to the adsorption of arsenate onto Mn (II) -rich hydrous Mn (IV) oxide. (2) There were high concentrations of Zn, Cu, Pb and Hg in the recent sediments. Although the source of these elements is attributed to human activities, the individual distributions of Zn and Cu in the sediment may result from the deposition of metal-rich planktonic debris and subsequent degradation of the debris. (3) The orders of increasing concentrations of alkali metals and lanthanides in the sediment from the central region compared with the nearshore pediment were identical to the orders of increasing atomic numbers from Na to Cs and from La to Lu, respectively.

Annotated record and chemical composition of iron-manganese nodules from the Baltic Sea

Iron-manganese concretions, closely related to lacustrine ores and deep sea manganese nodules, are presently forming in different parts of Gulfs of Bothnia and Finland. They can be divided according to physical form into three distinct groups: (1) round pea-shaped concretions, (2) ring-shaped concrections, and (3) flat sheets and crusts of concretionary material. A definite correlation was found to exist between the form i.e. type of concretions and their chemical composition (Mn/Fe ratio). Trace element concentrations were generally rather high, although not as high as in deep sea manganese nodules. X-ray and DTA was used to study the mineralogy and crystal structure of the concretions. Surface concentrations and geographical distribution of the concretions were estimated on the basis of samples, diving observations and echo-grams.

Description and chemical composition of ferromanganese encrustations and deposits in the Atlantic Ocean from R/V Atlantis II cruises 20, 42, 60, 85; R/V Chain cruise 35; R/V Knorr cruise 61 and RRS Shackleton cruise 75/1 stations

Chemical and mineralogical compositions of ferromanganese oxide coatings on rocks dredged from the New England Seamounts, the Sierra Leone Rise and the Mid-Atlantic Ridge near the Equator have been determined in an investigation of regional differences in Atlantic ferromanganese deposits. Most encrustations are clearly of hydrogenous origin, consisting mainly of todorokite and delta MnO2, but several recovered from the equatorial fracture zones may be hydrothermal accumulations. Differences in the chemistry of the water column and in growth rates of the ferromanganese coatings may be important in producing this regional contrast in composition. Fine-scale changes in element abundances within the encrustations indicate that the nature of the substrate has little influence on compositional variations.

Geochemistry of manganese nodules from a British Columbia fjord

Concretions of iron and manganese oxides and hydrous oxidesóobjects commonly called manganese nodulesóare widely distributed not only on the deep-sea floor but also in shallow marine environments1. Such concretions were not known to occur north of Cape Mendocino in the shallow water zones bordering the North-East Pacific Ocean until the summer of 1966 when they were recovered by one of us (J. W. M.) in dredge samples from Jervis Inlet, a fjord approximately 50 miles north-west of Vancouver, British Columbia.

Description and chemical composition of the fossil manganese nodules of the Cambrian manganese deposits of Conception and Trinity bays, Newfoundland

This paper is based upon data collected during the summers of 1912 and 1913. Mr. A. O. Hayes and Prof. van Ingen of Princeton University, while making a study of the general geology, stratigraphy, and palaeontology of the shores of Conception Bay, Newfoundland, came upon the manganiferous rocks of the Lower Cambrian exposed at Manuels, Topsail, Brigus, and other places. The following summer, of 1913, the writer as a member of the Princeton Newfoundland Expedition undertook a more detailed study of these deposits. In this paper therefore there has been an attempt to present as comprehensive a study of the manganese of southeastern Newfoundland. It is primarily chemical in its nature and the analyses herewith presented are from samples taken from the principal manganese-bearing beds.

Description and chemical composition of ferromanganese deposits from Trout Lake, northern Wisconsin

Sediments were collected with Eckman and Petersen dredges from the bottom of Trout Lake, northern Wisconsin, at 221 stations. Sampling was done with a spud sampler at 32 stations, and core samples were obtained with a Jenkins and Mortimer and a Twenhofel sampler at 17 stations. The shore and offshore deposits of the shores of Trout Lake and the shores of the islands are described. Megascopic descriptions are given of the samples collected with the Eckman and Petersen dredges. Sediments on bottoms of about 10 meters or deeper are mainly gyttja, or crusts composed of mixtures of organic matter, ferric hydroxide, and some form of manganese oxide. The latter deposits are extensive. Detailed descriptions of some of the samples of sands are given, and generalizations respecting size and distribution are made. Tables showing quartiles, medians, and coefficients of sorting and skewness of the coarse sediments collected from the bottom are given in tables. Mechanical analyses of all fine sediments, mainly gyttja, were not made, as previous experience seems to have demonstrated that results have no sedimentational value. Organic matter of the gyttja was determined and also the percentages of lignin in the organic matter. Core samples are composed almost entirely of fine materials, mainly gyttja, and determinations were made on these samples in the same way as on the samples obtained with the Eckman and Petersen dredges. Studies of the core samples show that the fine sediments usually contain in excess of 90 per cent moisture and there is very little change in the moisture content from top to bottom of cores. A map shows the distribution of the iron and manganese deposits. These deposits were found to contain 10 to 20 per cent of organic matter, 11 to 16 per cent of metallic iron, and 12 to 30 per cent of metallic manganese. No stratification of any kind was found in any of the deep-water sediments of Trout Lake except in the iron and manganese crusts. Absence of stratification is considered to be due to the slow rate of deposition and the mixing of sediments by organisms which dwell in them. The data indicate that the rate of deposition in the deep waters of Trout Lake is of the order of 1 foot in 15,000 years.

Geochemical composition of a representative collection of manganese nodules and slabs collected in the Western Pacific

Chemical analyses were performed on seveteen manganese nodules collected from the Pacific Ocean floor. The results were discussed compared with the previous data on the manganese nodules. Minerals were found to be todorokite, delta-MnO2 and other silicates, montmorillonite, illite, phillipsite and alpha-SiO2. Average composition shows that copper is concentrated on the deep sea nodules more than the shallow ones, and that the todorokite rich nodules contain more copper and nickel than the delta-MnO2 rich ones.

Annotated record and chemical composition of manganese nodules from station VITYAZ 4575, Indian Ocean

Analyses are given for the core and outer colliform shell of a manganese nodule collected at a depth of 5000 m in the Indian Ocean, and for the red clay that encloses the nodules. Trace elements determined include rare earths, Nb, Ta, Th, and V. The cores of the nodules were once composed of basaltic rock, but now are phillipsite and nontronite. The outer shell is composed of manganite, with admixed quartz, phillipsite, and some geothite. The correlations established between the redox potentials and the concentration coefficients for 12 elements indicate that Eh plays a greater role in the formation of the manganiferous shells than coprecipitation properties.