(Table S1) Stable isotope record and growth rates of cultured Mytilus edulis

To study the effects of temperature, salinity, and life processes (growth rates, size, metabolic effects, and physiological/genetic effects) on newly precipitated bivalve carbonate, we quantified shell isotopic chemistry of adult and juvenile animals of the intertidal bivalve Mytilus edulis (Blue mussel) collected alive from western Greenland and the central Gulf of Maine and cultured them under controlled conditions. Data for juvenile and adult M. edulis bivalves cultured in this study, and previously by Wanamaker et al. (2006, doi:10.1029/2005GC001189), yielded statistically identical paleotemperature relationships. On the basis of these experiments we have developed a species-specific paleotemperature equation for the bivalve M. edulis [T °C = 16.28 (±0.10) - 4.57 (±0.15) {d18Oc VPBD - d18Ow VSMOW} + 0.06 (±0.06) {d18Oc VPBD - d18Ow VSMOW}**2; r**2 = 0.99; N = 323; p < 0.0001]. Compared to the Kim and O'Neil (1997) inorganic calcite equation, M. edulis deposits its shell in isotope equilibrium (d18Ocalcite) with ambient water. Carbon isotopes (d13Ccalcite) from sampled shells were substantially more negative than predicted values, indicating an uptake of metabolic carbon into shell carbonate, and d13Ccalcite disequilibrium increased with increasing salinity. Sampled shells of M. edulis showed no significant trends in d18Ocalcite based on size, cultured growth rates, or geographic collection location, suggesting that vital effects do not affect d18Ocalcite in M. edulis. The broad modern and paleogeographic distribution of this bivalve, its abundance during the Holocene, and the lack of an intraspecies physiologic isotope effect demonstrated here make it an ideal nearshore paleoceanographic proxy throughout much of the North Atlantic Ocean.

(Table S1) Stable oxygen isotopic values and Mg/Ca ratios of Globigerinoides ruber w from sediment core AAS9_21

Variations in sea surface temperature (SST), d18O of sea water (?18Ow), and salinity were reconstructed for the past 68 ka using a sediment core (AAS9/21) from the eastern Arabian Sea (EAS) in order to understand the changes in evaporation and precipitation associated with the monsoon system. The Mg/Ca-derived SST record varies by ~4°C; it shows that marine isotope stage (MIS) 4 was warmer than MIS 3, that the Last Glacial Maximum was 4°C cooler than the present, and that there was a 2°C increase within the Holocene. MIS 4 records higher d18Ow and salinity values than MIS 2, suggesting variable flow of low-salinity Bay of Bengal flow into the EAS during glacial periods. The transition from MIS 4 to MIS 3 was marked with a conspicuous shift from higher to lower d18Ow values, which reflects a decrease in the evaporation-precipitation budget in the EAS, perhaps due to the strengthening of southwest monsoon. Monsoon reconstructions based on d18Ow reveal that monsoon-driven precipitation was higher during MIS 3 and MIS 1 and was lower during MIS 2 and MIS 4. This is consistent with earlier monsoon reconstructions based on upwelling indices from the western Arabian Sea. However, the amplitude of monsoon fluctuations derived through upwelling indices and d18Ow varies significantly, which may indicate spatial variability of monsoon rainfall.

(Table S1) Age determination ofs ediment cores of the Azores Current System

In order to test the sensitivity of marine primary productivity in the midlatitude open ocean North Atlantic to changes in the Atlantic Meridional Overturning Circulation (AMOC), we investigated two spliced sediment cores from a site south of the Azores Islands at the northern rim of the North Atlantic subtropical gyre. For this purpose we analyzed coccolithophore assemblages, diatom abundances, alkenones and conducted X-ray fluorescence (XRF) core scanning. During times of reduced AMOC, especially during Heinrich event 1 (H1) and the Younger Dryas, we observe a strong increase in productivity as evidenced by high coccolith accumulation rates, high alkenone concentrations/accumulation rates, high Ba/Ti-ratios, high abundances of diatoms and low abundances ofF. profunda. The increased productivity is partly caused by a more southern position of the Azores Front (AzF), and hence by a less northward extension of the subtropical gyre, as deduced from high abundances of the temperate coccolithophore species G. muellerae and low abundances of subtropical species (Oolithotus spp., Umbellosphaera spp., Umbilicosphaeraspp.). However, to explain the full range of the observed productivity increase, other factors like increased westerly winds and advection of nutrient-rich surface waters have also to be considered. Because this pattern can also be observed in other sediment cores from the midlatitude North Atlantic, we propose that during times of reduced AMOC there has been a band of strongly increased productivity across the North Atlantic at the northern rim of the contracted subtropical gyre, which partly counteracts the decreased organic carbon pump in the high northern latitudes.

(Table S1) Qualitative and semi-quantitative abundance of magnetic particles in Paleocene-Eocene sediments

On the mid-Atlantic Coastal Plain of the United States, Paleocene sands and silts are replaced during the Paleocene-Eocene Thermal Maximum (PETM) by the kaolinite-rich Marlboro Clay. The clay preserves abundant magnetite produced by magnetotactic bacteria and novel, presumptively eukaryotic, iron-biomineralizing microorganisms. Using ferromagnetic resonance spectroscopy and electron microscopy, we map the magnetofossil distribution in the context of stratigraphy and carbon isotope data and identify three magnetic facies in the clay: one characterized by a mix of detrital particles and magnetofossils, a second with a higher magnetofossil-to-detrital ratio, and a third with only transient magnetofossils. The distribution of these facies suggests that suboxic conditions promoting magnetofossil production and preservation occurred throughout inner middle neritic sediments of the Salisbury Embayment but extended only transiently to outer neritic sediments and the flanks of the embayment. Such a distribution is consistent with the development of a system resembling a modern tropical river-dominated shelf.

Pitkittäistutkimus kymmenen S1- ja S2-pojan kirjoitustaidon sujuvuuden, tarkkuuden ja kompleksisuuden kehittymisestä

Olen tutkimuksessani seurannut kymmenen pojan kielitaidon kehittymistä vuodesta 2010 vuoteen 2015. Viisi informanttia puhuu suomea äidinkielenä ja viisi suomea toisena kielenä. Tutkimus on pragmaattis-funktionaalinen ja laadullinen pitkittäistutkimus. Kielitaidon mittareina käytän sujuvuutta, tarkkuutta ja kompleksisuutta. Näiden kolmen mittarin alle sijoitan kielen ainekset, joita ovat seuraavat: sähköpostin tervehdys ja lopetus sekä tekstilajinomaisuus (sujuvuus), possessiivisuffiksin käyttö (tarkkuus), direktiivin valinta ja pyynnön vahvistaminen (syväkompleksisuus) sekä sanamäärä ja lauseen osien lukumäärä (pintakompleksisuus). Tutkin lisäksi, miten hyvän osaamisen kuvaukset ja eurooppalaisen viitekehyksen taitotasoasteikot toimivat käytännön arvioinnissa. Informantit kirjoittivat kukin neljä tekstiä: sähköpostin verkkokauppaan vuosina 2010 ja 2015 sekä vapaan tarinan pelottavasta tai hauskasta tapahtumasta vuosina 2011 ja 2015. Informantit olivat tutkimuksen alkaessa 4.-luokkalaisia ja päättyessä 9.-luokkalaisia. Tuloksista selviää, että sekä S1-pojat että S2-pojat osaavat suhteellisen hyvin tekstilajien piirteet, esittävät pyynnön konditionaalissa kohteliaasti ja vahvistavat pyynnön eri keinoin. S1-pojat käyttävät S2-poikia enemmän possessiivisuffiksia, mutta S2-poikien oppivat käyttämään sitä tutkimusjakson aikana. S1-pojat kirjoittavat sanamäärissä laskettuna aluksi pidempiä tekstejä, mutta 9. luokalla S2-pojat kirjoittavat pidemmät vapaatekstit kuin S1-pojat. Virkkeiden jakaantumisessa eri osiin ei ole suurta eroa. Pojista on muodostettavissa viisi erilaista kirjoittajaprofiilia: varovainen kirjoittaja, vaihteleva kirjoittaja, sujuva kirjoittaja (S1) / kehittyvä sujuva kirjoittaja (S2), motivoitumaton kirjoittaja ja taitava kirjoittaja. Tutkimuksen perusteella ehdotan, että koulujen kirjoitusaiheissa olisi enemmän pojille suunnattuja aiheita. Arvioinnin oikeudenmukaisuuden toteutumiseksi voi harkita tekstinkäsittelyohjelmien käyttämistä merkityksellisissä kokeissa. Opettajat tarvitsevat enemmän konkreettisia mittareita kirjoitusten arviointiin. Kirjoitusprofiilin ja kohdennetun tuen antaminen saattaisi olla hyödyllistä. S2-opetuksessa on järkevää säilyttää nykyiset pienryhmät tai tehdä S1- ja S2-oppilaita sisältävät yhdistelmäryhmät riittävän pieniksi yksilöllisen ohjauksen varmistamiseksi erityisesti kirjoitustehtävissä. S2-oppijoille tulee tarjota oman kielitasonsa mukainen opetusryhmä, jotta heidän kielitaitonsa kehittyy riittävästi. Toisen polven S2-oppijoiden kannattaa opiskella eri ryhmässä kuin juuri maahan tulleiden S2-oppijoiden.

Specific serology for emerging human coronaviruses by protein microarray

We present a serological assay for the specific detection of IgM and IgG antibodies against the emerging human coronavirus hCoV-EMC and the SARS-CoV based on protein microarray technology. The assay uses the S1 receptor-binding subunit of the spike protein of hCoV-EMC and SARS-CoV as antigens. The assay has been validated extensively using putative cross-reacting sera of patient cohorts exposed to the four common hCoVs and sera from convalescent patients infected with hCoV-EMC or SARS-CoV.

RESPONSE OF LOCALLY ADAPTED PEARL MILLET POPULATIONS TO S1 PROGENY RECURRENT SELECTION FOR GRAIN YIELD AND RESISTANCE TO RUST

In the semi-arid zones of Uganda, pearl millet ( Pennisetum glaucum (L.) R. Br.) is mainly grown for food and income; but rust (Puccinia substriata var indica (L.) R. Br.) is the main foliar constraint lowering yield. The objective of the study was to genetically improve grain yield and rust resistance of two locally adapted populations (Lam and Omoda), through two cycles of modified phenotypic S1 progeny recurrent selection. Treatments included three cycles of two locally adapted pearl millet populations, evaluated at three locations. Significant net genetic gain for grain yield (72 and 36%) were achieved in Lam and Omoda populations, respectively. This led to grain yield of 1,047 from 611 kg ha-1 in Lam population and 943 from 693 kg ha-1 in Omoda population. Significant improvement in rust resistance was achieved in the two populations, with a net genetic gain of -55 and -71% in Lam and Omoda populations, respectively. Rust severity reduced from 30 to 14% in Lam population and from 57 to 17% in Omoda population. Net positive genetic gains of 68 and 8% were also achieved for 1000-grain weight in Lam and Omoda, respectively. Traits with a net negative genetic gain in both populations were days to 50% flowering, days to 50% anthesis, days to 50% physiological maturity, flower-anthesis interval, plant height and leaf area.

Isolation of a potential anticancer agent with protein phosphatase inhibitory activity from soil-derived Penicillium sp strain H9318

Purpose: To determine the effect of the secondary metabolites from Penicillium sp. H9318 on cytotoxicity and cell cycle progression. Methods: A yeast PP1 inhibitory screening system was carried out to confirm the presence of anti- PP1c activity in crude acetone extracts of strain H9318. The extracts were fractionated and identified as Fraction S1 and Citrinin 9318 (CTN9318). Various cancer cell lines were used to test for the toxicity of the crude acetone extracts, Fraction S1 and Citrinin 9318, using MTT viability assay. Results: It was found that a colorectal cancer cell line, HT-29, was susceptible to Fraction S1 and Citrinin 9318. A propidium iodide (PI)-incorporated DNA assay was used to show that there was G2/M arrest in HT-29 by Citrinin 9318. Conclusion: Citrinin 9318 inhibits the viability of HT-29 via mitotic block. The results suggest that Citrinin 9318 is capable of exerting cytotoxicity and mitotic arrest in a colon cancer cell line, HT29

Antibody Recognition Of Plasmodium Falciparum Infected Red Blood Cells By Symptomatic And Asymptomatic Individuals In The Brazilian Amazon.

In the Amazon Region, there is a virtual absence of severe malaria and few fatal cases of naturally occurring Plasmodium falciparum infections; this presents an intriguing and underexplored area of research. In addition to the rapid access of infected persons to effective treatment, one cause of this phenomenon might be the recognition of cytoadherent variant proteins on the infected red blood cell (IRBC) surface, including the var gene encoded P. falciparum erythrocyte membrane protein 1. In order to establish a link between cytoadherence, IRBC surface antibody recognition and the presence or absence of malaria symptoms, we phenotype-selected four Amazonian P. falciparum isolates and the laboratory strain 3D7 for their cytoadherence to CD36 and ICAM1 expressed on CHO cells. We then mapped the dominantly expressed var transcripts and tested whether antibodies from symptomatic or asymptomatic infections showed a differential recognition of the IRBC surface. As controls, the 3D7 lineages expressing severe disease-associated phenotypes were used. We showed that there was no profound difference between the frequency and intensity of antibody recognition of the IRBC-exposed P. falciparum proteins in symptomatic vs. asymptomatic infections. The 3D7 lineages, which expressed severe malaria-associated phenotypes, were strongly recognised by most, but not all plasmas, meaning that the recognition of these phenotypes is frequent in asymptomatic carriers, but is not necessarily a prerequisite to staying free of symptoms.

Digestive Peptidase Evolution In Holometabolous Insects Led To A Divergent Group Of Enzymes In Lepidoptera.

Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic l-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three primary processes regulate the activity of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. Here, we present a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects and reveal divergent characteristics of Lepidoptera enzymes in comparison with those of Coleoptera and Diptera. In particular, trypsin subsite S1 was more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 were more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a lineage-specific trypsin group belonging only to the Noctuidae family. Evidence for facilitated trypsin auto-activation events were also observed in all the insect orders studied, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to their mammal counterparts. Overall, our findings suggest that the need for fast digestion allowed holometabolous insects to evolve divergent groups of peptidases with high auto-activation rates, and highlight that the evolution of trypsins led to a most diverse group of enzymes in Lepidoptera.

Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition

Background: A family of hydrophilic acylated surface (HASP) proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic) and intracellular (amastigote) stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia) have lost HASP genes from their genomes. Methods/Principal Findings: We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia) species, L. (V.) braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L.) mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o) HASPs) are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family. Conclusions/Significance: These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are surface-exposed on amastigotes (although L. (L.) major parasites also express HASPB on the metacyclic plasma membrane). The central repetitive domains of the HASPs are highly variant in their amino acid sequences, both within and between species, consistent with a role in immune recognition in the host.

Identification of protein coding regions using the modified Gabor-wavelet transform

An important topic in genomic sequence analysis is the identification of protein coding regions. In this context, several coding DNA model-independent methods based on the occurrence of specific patterns of nucleotides at coding regions have been proposed. Nonetheless, these methods have not been completely suitable due to their dependence on an empirically predefined window length required for a local analysis of a DNA region. We introduce a method based on a modified Gabor-wavelet transform (MGWT) for the identification of protein coding regions. This novel transform is tuned to analyze periodic signal components and presents the advantage of being independent of the window length. We compared the performance of the MGWT with other methods by using eukaryote data sets. The results show that MGWT outperforms all assessed model-independent methods with respect to identification accuracy. These results indicate that the source of at least part of the identification errors produced by the previous methods is the fixed working scale. The new method not only avoids this source of errors but also makes a tool available for detailed exploration of the nucleotide occurrence.