New vs. Given

This squib begins with an argument emphasizing that the grammar of English makes a distinction between constituents that are focused and those that are merely new, hence not given. If the distinction is made via features, we need two features: one indicating focus and one indicating either given or new information. Which one of the two? Semantically, the choice doesn’t matter: whatever information is given is not new and the other way round. For the phonology, there is a difference, however. If the prosody of all-new constituents is default prosody, but the prosody of given constituents is special, we would want to indicate givenness, rather than newness

Fungal Planet description sheets: 1042–1111

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.)from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.)on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.)from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes

Fungal Planet description sheets: 1042–1111

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.)from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.)on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.)from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes

The 3’-Jα Region of the TCRα Locus Bears Gene Regulatory Activity in Thymic and Peripheral T Cells

<div><p>Much progress has been made in understanding the important <i>cis</i>-mediated controls on mouse TCRα gene function, including identification of the Eα enhancer and TCRα locus control region (LCR). Nevertheless, previous data have suggested that other <i>cis</i>-regulatory elements may reside in the locus outside of the Eα/LCR. Based on prior findings, we hypothesized the existence of gene regulatory elements in a 3.9-kb region 5’ of the Cα exons. Using DNase hypersensitivity assays and TCRα BAC reporter transgenes in mice, we detected gene regulatory activity within this 3.9-kb region. This region is active in both thymic and peripheral T cells, and selectively affects upstream, but not downstream, gene expression. Together, these data indicate the existence of a novel <i>cis</i>-acting regulatory complex that contributes to TCRα transgene expression <i>in vivo</i>. The active chromatin sites we discovered within this region would remain in the locus after TCRα gene rearrangement, and thus may contribute to endogenous TCRα gene activity, particularly in peripheral T cells, where the Eα element has been found to be inactive.</p></div

Effects of diapause conditions on gut-related structures in <i>Canton S</i> flies.

<p><b>A</b> The intestinal epithelium appears to age more slowly during diapause. The epithelial cells (EC) were marked with NP1-Gal4 driven expression of GFP (green) in combination with nuclear staining with Hoechst 33342 (blue). The insets display enlarged view of nuclear staining. The flies tested were kept under control and diapause conditions as described earlier for 3 h (3 h N) or 3 days normal conditions (3 dN), 3–9 weeks normal conditions (3–9 w N), 3 days (3 d D) or 3–9 weeks diapause conditions (3–9 w D) and finally for 1–9 weeks recovery conditions after 6 weeks of diapause (1–9 w R). The age-associated changes in growth of EC size and disruption of the EC monolayer in the midgut are delayed by at least 3 weeks in diapausing flies. The yellow asterisks indicate small polyploid cells (sign of intestinal dysplasia). <b>B</b> The length of the midgut was measured during diapause (conditions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113051#pone-0113051-g002" target="_blank">Fig. 2A</a>). The midgut is significantly longer in flies kept 1-week at normal conditions (C1), know to feed properly, than in 3–6 h old flies (C0). In diapausing flies (D1–D12) the midgut is shorter than in C1 controls and then becomes significantly longer after recovery from diapause (R1′, R1–2). Data are presented as means ± S.E.M, <i>n</i> = 6–9 randomly selected flies for each sample point. Significance of differences from the 1-week control (C1) is indicated, as well as between groups indicated by connectors, * <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001, N.S. not significantly different (ANOVA followed with Tukey test). <b>C</b> The width of the midgut did not change much during diapause, except a significant increase after 1-week recovery from diapause (R1′, R1). Data are presented as means ± S.E.M, <i>n</i> = 5–8 randomly selected flies for each sample point. Significance of differences from the 1-week control (C1) is indicated, as well as between groups indicated by connectors, ^#<i>p</i><0.05 (Kruskal–Wallis test followed by pairwise comparisons using Wilcoxon rank sum test).</p

Diapause conditions affect circulating and stored carbohydrates and proteins as well as stored lipids in <i>Canton S</i>.

<p>Flies were kept under the same conditions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113051#pone-0113051-g002" target="_blank">Fig. 2A</a>. In the panels data are presented as means ± S.E.M, <i>n</i> = 5–6 independent replicates with 10–15 flies in each replicate. Data significantly different from the flies kept for one week at normal conditions (C1) are indicated * <i>p</i><0.05, ** <i>p</i><0.01, ***<i>p</i><0.001, N.S. not significantly different (ANOVA followed with Tukey test) or with ^#<i>p</i><0.05, ^##<i>p</i><0.01 or ^####<i>p</i><0.01 (Kruskal–Wallis test followed by pairwise comparisons using Wilcoxon rank sum test). <b>A</b> Glucose concentrations in hemolymph (mM) are significantly increased throughout diapause as compared to the flies kept at normal conditions for one week (C1). After recovery from diapause (R1′–R2) glucose levels remain high. <b>B</b> Trehalose levels in hemolymph increase to a peak at three weeks of diapause (D3) and then return to the control level (C1). Recovery conditions have no effect on trehalose. <b>C</b> Whole body glucose also increases significantly during diapause, but falls after recovery compared to controls (C1). <b>D</b> Whole body trehalose stores increase significantly to a peak at three weeks diapause (D3) and drop thereafter to very low levels, similar to one week controls (C1). <b>E</b> Compared to the 1 week controls (C1) glycogen stores first drop (D1) and then increase with a peak at three weeks of diapause (D3). During recovery (R1′, R1 and R2) flies restore glycogen to the control (C1) value. <b>F</b> Triacylglycerid (TAG) contents increase significantly and also peak after three weeks of diapause (D3) and remain elevated compared to C1. <b>G</b> The total protein in the hemolymph is elevated during 1–3 weeks of diapause (D1–D3) compared to 1 week control flies (C1). After recovery from three weeks of diapause protein levels remain reduced, but after 2 weeks of recovery from 6 weeks of diapause proteins are elevated in the hemolymph. <b>H</b> The total body protein is similar to the one week non-diapausing controls (C1) throughout diapause. See also Fig. S5, S6 and S7E–L in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113051#pone.0113051.s002" target="_blank">File S1</a> for comparisons of metabolite levels in <i>dilp</i> mutants and <i>w¹¹¹⁸</i>.</p

Comparison of metabolic phenotypes in four strains of <i>D. melanogaster</i>: <i>Canton S</i>, <i>dilp5</i> and <i>dilp2-3</i> mutants and <i>w¹¹¹⁸</i> kept under normal conditions.

<p>The parameters were investigated in 3–6 h old flies <i>D. melanogaster</i>, kept for 1 week (7 days) at 25°C and normal photoperiod 12L:12D, light/dark, which correspond to the standard (normal) conditions in most studies with <i>D. melanogaster</i>. Significantly different from the wild line <i>Canton S</i> with *<i>p</i><0.05, **<i>p</i><0.01, ***<i>p</i><0.001 as assessed by unpaired Students' <i>t</i>-test or ^##<i>p</i>>0.01 as assessed by Mann-Whitney-Wilcoxon rank sum test. N.S. – values are not significantly different.</p><p>Comparison of metabolic phenotypes in four strains of <i>D. melanogaster</i>: <i>Canton S</i>, <i>dilp5</i> and <i>dilp2-3</i> mutants and <i>w¹¹¹⁸</i> kept under normal conditions.</p