Organic geochemistry of late Cenozoic sediments from the subtropical South Atlantic Ocean

Organic matter has been characterized in samples of Pleistocene, Pliocene, and Miocene sediments from seven Deep Sea Drilling Project sites in the subtropical South Atlantic Ocean. Organic carbon concentrations average 0.3% for most samples, and n-alkanoic acid, n-alkanol, and alkane biomarkers indicate extensive microbial reworking of organic matter in these organic-carbon-lean sediments. Samples from the easternmost parts of the South Atlantic contain an average of 4.1% organic carbon and reflect the high productivity associated with the Benguela Current. Lipid biomarkers show less microbial reworking in these sediments. Eolian transport of land-derived hydrocarbons is evident at most of these oceanic locations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24671/1/0000090.pd

Organic geochemistry of Cretaceous black shales from the Galicia Margin, Ocean Drilling Program Leg 103

Organic-carbon-rich "black shales" from three different Cretaceous episodes sampled during Ocean Drilling Program Leg 103 have been studied by organic geochemical methods. Rock-Eval analysis, carbon isotope data, and lipid biomarkers show organic matter to contain varying proportions of marine and continental materials. In Hauterivian-Barremian organic-carbon-rich turbiditic marlstones, major amounts of land-derived organic matter are found. Aptian-Albian black-colored shales are interspersed within green claystones, from which they differ by containing more marine organic matter. An abbreviated layer of black shale from the Cenomanian-Turonian boundary is dominated by well-preserved marine organic matter. Downslope transport and rapid reburial within a predominantly oxygenated deepwater setting created most of these examples of black shales, except for the Cenomanian-Turonian deposits in which deepwater anoxia may have been involved.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27474/1/0000515.pd

Oil generation in the michigan basin: A biological marker and carbon isotope approach

Palaeozoic strata in the Michigan Basin produced crude oils which, despite their rather small volume and economic value, are interesting because of the considerable age of the basin and because of the opportunity to study generation and migration of oils within a relatively simple but ancient geological setting.Based on n-alkane profiles, biological marker distributions and carbon isotope ratios, the oils belong to three main families of different genetic origin and a few less important mixed types. Silurian oils from Salina and Niagara Limestones have broad n-alkane distributions and abundant isoprenoid hydrocarbons. A strong phytane-over-pristane predominance and the lack of diasteranes indicate a carbonate source for these oils. Chemical maturity parameters show that they are more mature than the oils from the other main families from which they are also clearly distinguished by carbon isotope ratios of hydrocarbon fractions and single n-alkanes.Oils found in the calcareous Ordovician Trenton formation contain n-alkane, cyclohexylalkane and alkyl phenanthrene distributions typical of immature oils. Many oils from the Devonian Dundee reservoirs are very similar in overall composition to the Trenton oils.Devonian Traverse oils are considered to be mainly from a Devonian source with some contribution of Ordovician-type oil and are of intermediate maturity. Based on calculations using kinetic parameters of biological marker reactions, considerably deeper subsidence of the Devonian source rock in the past is implied.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26406/1/0000493.pd

1997 Wild Blueberry Progress Reports

The 1997 edition of the Wild Blueberry Progress Reports was prepared for the Wild Blueberry Commission of Maine and the Wild Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include: 1. Investigation of processing damage of IQF blueberries 2. Use of sorter rejects and wild blueberry puree to prevent warmed over flavor in processed beef patties 3. Factors affecting the quality of IQF wild blueberries 4. Determination of pesticide residue levels in fresh and processed wild blueberries 5. Pollination ecology of wild blueberries in Maine 6. Control tactics for wild blueberry pest insects 7. IPM Strategies 8. Pest Biology 9. Effect of antidessication treatments on wild blueberry cold temperature tolerance 10. Phosphorus/nitrogen fertilizer ratio 11. Effect of boron application methods on boron uptake in wild blueberries 12. Effect of foliar zinc application on growth and yield of wild blueberries 13. Effect of soil pH on nutrient uptake 14. Crop year fertilization of wild blueberry 15. Effect of Photomag® on growth and yield of wild blueberries 16. Evaluation of Pronone MG® spot treatments for control of St. Johnswort, dogbane, bracken fern, witch grass/fall panicum and bunchberry 17. Effect of hexazinone formulation on movement through the soil profile 18. Effect of time of fall pruning on wild blueberry fruit set and yield 19. Effect of pre and postemergence herbicide applications on control of grasses 20. Hexazinone groundwater survey 21. Effect of plant source and density on spread of wild blueberry 22. Effect of surfactant and ammonium sulfate on glyphosate activity 23. Effect of crop year application of hexazinone on weed control, yield and hexazinone residue. 24. Long term effects of tribenuron methyl on wild blueberries and weed species composition 25. Effect of Velpar® DF/MAP on wild blueberry fruit set and yield. 26. Effect of reduced volume lmidan® 2.5 EC UL V applications on wild blueberry residue and efficacy 27. Wild blueberry extension education progra

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution

It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

Sediment descriptions, stage, calcium carbonate, organic carbon, delta 13C and geolipids at DSDP Hole 93-603B

Organic matter contents of black shales from the Cretaceous Hatteras and Blake-Bahama formations have been compared to those from surrounding organic-poor strata using C/N ratios, d13C values, and distributions of extractable and nonsolvent-extractable, long-chain hydrocarbons, acids, and alcohols. The proportion of marine and land-derived organic matter varies considerably among all samples, although terrigenous components generally dominate. Most black shales are hydrocarbon-poor relative to their organic-carbon concentrations. Deposition of the black shales in Hole 603B evidently occurred through turbiditic relocation from shallower landward sites and rapid reburial at this outer continental rise location under generally oxygenated bottom-water conditions