Data report: early Pleistocene calcareous nannofossils, IODP Expedition 339, Site U1387

We present a revision and refinement of semiquantitative analyses of calcareous nannofossil assemblages in early Pleistocene samples from Holes U1387A and U1387C recovered toward the eastern end of the Faro Drift (36°48.3210N, 7°43.1321W) during Integrated Ocean Drilling Program Expedition 339, Mediterranean Outflow (November 2011–January 2012). The record is characterized by intervals very rich in calcareous nannofossils that are in general moderately to well preserved. On the other hand, the record contains an interval directly above the youngest dolomite layer in Section 339-U1387C-19R-4 (~0.7 m) where no coccoliths were preserved. The new stratigraphic constraints of events such as the lowest occurrence (LO) of large Gephyrocapsa, the highest occurrence (HO) of Calcidiscus macintyrei (1.66 Ma), the LO of medium-sized Gephyrocapsa group, and the HO of Discoaster brouweri (1.95 Ma) allow better interpretation of the isotope stratigraphy applied to this interval.FCT Portugal projects CCMAR:UID/Multi/04326/2019info:eu-repo/semantics/publishedVersio

Expand+Functional selection and systematic analysis of intronic splicing elements identify active sequence motifs and associated splicing factors

Despite the critical role of pre-mRNA splicing in generating proteomic diversity and regulating gene expression, the sequence composition and function of intronic splicing regulatory elements (ISREs) have not been well elucidated. Here, we employed a high-throughput in vivo Screening PLatform for Intronic Control Elements (SPLICE) to identify 125 unique ISRE sequences from a random nucleotide library in human cells. Bioinformatic analyses reveal consensus motifs that resemble splicing regulatory elements and binding sites for characterized splicing factors and that are enriched in the introns of naturally occurring spliced genes, supporting their biological relevance. In vivo characterization, including an RNAi silencing study, demonstrate that ISRE sequences can exhibit combinatorial regulatory activity and that multiple trans-acting factors are involved in the regulatory effect of a single ISRE. Our work provides an initial examination into the sequence characteristics and function of ISREs, providing an important contribution to the splicing code

Silage Additives

SummaryThrough the years a number of materials have been suggested for incorporation into silage to improve the preservation of nutrients, nutritive value or palatability of the silage. In addition to being called additives, some of these materials are referred to as preservatives or conditioners. Especially during recent years, many commercial preparations have been made available to the farmer, who naturally wonders whether their use will be economically sound. Thorough testing of these materials would require that each be used at several levels, with forages at various moisture contents, under different storage conditions and with many kinds of silage. Therefore, it is highly impractical, if not impossible, to attempt thorough testing of each. However, there is sufficient understanding of the process of silage formation, the requirements for preservation of its nutrients, and the principle of action of the ingredients used in the various additives to make sound decisions as to whether they might be economically worth-while. There is, in addition to this understanding, a rather large amount of research which has been done and reported, and this in its summation justifies the use of what is already known to make judgments. In order to make an appropriate judgment, one should be able to answer certain questions, as follows:1.What happens during the process of silage formation? 2. What does the additive being considered contain and what do its ingredients do?3. What is the value of the silage and what is the cost of the additive?4. How much preservation beyond that afforded by good ensiling procedures can one logically expect from the additive?5.Can one expect to improve the feeding value of a silage by using a particular additive?The discussion that follows deals with these questions

The transient IDEMIX model as a nonorographic gravity wave parameterization in an atmospheric circulation model

The Internal wave Dissipation, Energy and Mixing (IDEMIX) model presents a novel way of parameterizing internal gravity waves in the atmosphere. Using a continuous full wave spectrum in the energy balance equation and integrating over all vertical wavenumbers and frequencies results in prognostic equations for the energy density of gravity waves in multiple azimuthal compartments. It includes their non-dissipative interaction with the mean flow, allowing for an evolving and local description of momentum flux and gravity wave drag. A saturation mechanism maintains the wave field within convective stability limits, and an energetically consistent closure for critical-layer effects controls how much wave flux propagates from the troposphere into the middle atmosphere. IDEMIX can simulate zonal gravity wave drag around the mesopause, similar to a traditional gravity wave parameterization and to a state-of-the-art wave ray tracing model in an atmospheric circulation model. In addition, IDEMIX shows a reversal of the gravity wave drag around the mesopause region due to changes in the momentum flux there. When compared to empirical model data, IDEMIX captures well the summer hemisphere flow reversal, the cold summer mesospheric pole and the alternate positive and negative structures in the meridional mean flow.Comment: 21 pages, 19 figure

Primary productivity evolution during the latest Holocene (2,000 yr) off Oporto (Portuguese Margin)

European Geosciences Union General Assembly 2008 (EGU 2008), Vienna, Austria, April 13-18, 200

Molecular Electroporation and the Transduction of Oligoarginines

Certain short polycations, such as TAT and polyarginine, rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction as well as by endocytosis and macropinocytosis. These cell-penetrating peptides (CPPs) promise to be medically useful when fused to biologically active peptides. I offer a simple model in which one or more CPPs and the phosphatidylserines of the inner leaflet form a kind of capacitor with a voltage in excess of 180 mV, high enough to create a molecular electropore. The model is consistent with an empirical upper limit on the cargo peptide of 40--60 amino acids and with experimental data on how the transduction of a polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of arginines in the CPP and on the CPP concentration. The model makes three testable predictions.Comment: 15 pages, 5 figure

MBNL1 binds GC motifs embedded in pyrimidines to regulate alternative splicing

Muscleblind-like 1 (MBNL1) regulates alternative splicing and is a key player in the disease mechanism of myotonic dystrophy (DM). In DM, MBNL1 becomes sequestered to expanded CUG/CCUG repeat RNAs resulting in splicing defects, which lead to disease symptoms. In order to understand MBNL1’s role in both the disease mechanism of DM and alternative splicing regulation, we sought to identify its RNA-binding motif. A doped SELEX was performed on a known MBNL1-binding site. After five rounds of SELEX, MBNL1 selected pyrimidine-rich RNAs containing YGCY motifs. Insertion of multiple YGCY motifs into a normally MBNL1-independent splicing reporter was sufficient to promote regulation by MBNL1. MBNL1 was also shown to regulate the splicing of exon 22 in the ATP2A1 pre-mRNA, an exon mis-spliced in DM, via YGCY motifs. A search for YGCY motifs in 24 pre-mRNA transcripts that are mis-spliced in DM1 patients revealed an interesting pattern relative to the regulated exon. The intronic regions upstream of exons that are excluded in normal tissues relative to DM1, are enriched in YGCY motifs. Meanwhile, the intronic regions downstream of exons that are included in normal tissues relative to DM1, are enriched in YGCY motifs

Precipitation Maxima and upwelling trends at the NAO Southern Pole during the last millenium

European Geosciences Union General Assembly 2009 (EGU 2009), Vienna, Austria, April 19-24, 200

Millennial-scale deep ocean ventilation and sea-surface variability during the last four glacial cycles : a new assessment for the Northern Hemisphere ice-sheet growth

AGU Fall Meeting, S. Francisco (USA), 19-14 December 2007, Suppl., Abstract PP44B-0