RNA polymerase is poised for activation across the genome

Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter, followed by initiation of RNA synthesis and the transition to productive elongation. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region. To determine the importance of polymerase stalling for transcription regulation, we carried out a genome-wide search for Drosophila melanogaster genes with Pol II stalled within the promoter-proximal region. Our data show that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals. This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues

Maximal Violation of Bell Inequalities using Continuous Variables Measurements

We propose a whole family of physical states that yield a violation of the Bell CHSH inequality arbitrarily close to its maximum value, when using quadrature phase homodyne detection. This result is based on a new binning process called root binning, that is used to transform the continuous variables measurements into binary results needed for the tests of quantum mechanics versus local realistic theories. A physical process in order to produce such states is also suggested. The use of high-efficiency spacelike separated homodyne detections with these states and this binning process would result in a conclusive loophole-free test of quantum mechanics.Comment: 7 pages, 5 figures, to appear in PRA in a slightly different versio

Direct measurement of optical quasidistribution functions: multimode theory and homodyne tests of Bell's inequalities

We develop a multimode theory of direct homodyne measurements of quantum optical quasidistribution functions. We demonstrate that unbalanced homodyning with appropriately shaped auxiliary coherent fields allows one to sample point-by-point different phase space representations of the electromagnetic field. Our analysis includes practical factors that are likely to affect the outcome of a realistic experiment, such as non-unit detection efficiency, imperfect mode matching, and dark counts. We apply the developed theory to discuss feasibility of observing a loophole-free violation of Bell's inequalities by measuring joint two-mode quasidistribution functions under locality conditions by photon counting. We determine the range of parameters of the experimental setup that enable violation of Bell's inequalities for two states exhibiting entanglement in the Fock basis: a one-photon Fock state divided by a 50:50 beam splitter, and a two-mode squeezed vacuum state produced in the process of non-degenerate parametric down-conversion.Comment: 18 pages, 7 figure

Dynamics of entanglement between two trapped atoms

We investigate the dynamics of entanglement between two continuous variable quantum systems. The model system consists of two atoms in a harmonic trap which are interacting by a simplified s-wave scattering. We show, that the dynamically created entanglement changes in a steplike manner. Moreover, we introduce local operators which allow us to violate a Bell-CHSH inequality adapted to the continuous variable case. The correlations show nonclassical behavior and almost reach the maximal quantum mechanical value. This is interesting since the states prepared by this interaction are very different from any EPR-like state.Comment: 9 page

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

PROFIL WISATAWAN MUSEUM RADYA PUSTAKA SURAKARTA

Anggit Margaret, C9407031 2011. Profil Wisatawan Museum Radya Pustaka Surakarta. Program Studi Diploma III Usaha Perjalanan Wisata Fakultas Sastra Dan Seni Rupa Universitas Sebelas Maret Surakarta. Penelitian tugas akhir ini mengkaji tentang Profil Wisatawan di Museum Radya Pustaka Surakarta. Tujuan dari penelitian ini adalah untuk mengetahui dari daerah mana saja wisatawan yang berkunjung ke Museum Radya Pustaka, bagaimana ciri-ciri wisatawan yang berkunjung ke Museum Radya Pustaka serta harapan-harapan yang diinginkan wisatawan terhadap Museum Radya Pustaka. Penelitian dilakukan dengan metode kualitatif. Pengumpulan data dilakukan melalui wawancara dengan narasumber wisatawan yang berkujung di Museum Radya Pustaka Surakarta tempat penulis melakukan penelitian, serta studi pustaka dan studi dokumen guna menambah sumber data. Hasil penelitian menunjukkan bahwa (1) Sebagian besar wisatawan yang datang berasal dari Semarang sebesar 32%. (2) Mayoritas wisatawan yang berkunjung ke Museum Radya Pustaka berusia antara 17-25 tahun dan kebanyakan dari mereka adalah pelajar atau mahasiswa dengan prosentase 52%. (3) Sebagian besar wisatawan yang datang ke Museum Radya Pustaka adalah bertujuan untuk melakukan penelitian yaitu sebesar 34%. (4) Harapan wisatawan yang berkunjung terhadap kelangsungan Museum Radya Pustaka sebagian besar adalah agar ditingkatkan lagi pengelolaan dan keamanan museum, agar kejadian hilangnya benda-benda koleksi museum tidak terulang lagi dikemudian hari. Kesimpulan dari hasil penelitian ini bahwa wisatawan yang berkujung ke Museum Radya Pustaka Surakarta mayoritas berasal dari Semarang, mayoritas berusia 17-25 tahun dan kebanyakan dari mereka adalah berprofesi sebagai pelajar dan mahasiswa. Kebanyakan wisatawan yang datang bertujuan untuk melakukan penelitian, serta harapan wisatawan terhadap Museum Radya Pustaka adalah supaya lebih ditingkatkan lagi pengelolaan dan keamanan museum

Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses

To understand neurological complications of COVID-19 better both acutely and for recovery, we measured markers of brain injury, inflammatory mediators, and autoantibodies in 203 hospitalised participants; 111 with acute sera (1–11 days post-admission) and 92 convalescent sera (56 with COVID-19-associated neurological diagnoses). Here we show that compared to 60 uninfected controls, tTau, GFAP, NfL, and UCH-L1 are increased with COVID-19 infection at acute timepoints and NfL and GFAP are significantly higher in participants with neurological complications. Inflammatory mediators (IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) are associated with both altered consciousness and markers of brain injury. Autoantibodies are more common in COVID-19 than controls and some (including against MYL7, UCH-L1, and GRIN3B) are more frequent with altered consciousness. Additionally, convalescent participants with neurological complications show elevated GFAP and NfL, unrelated to attenuated systemic inflammatory mediators and to autoantibody responses. Overall, neurological complications of COVID-19 are associated with evidence of neuroglial injury in both acute and late disease and these correlate with dysregulated innate and adaptive immune responses acutely