At Short Telomeres Tel1 Directs Early Replication and Phosphorylates Rif1

Funding AS was supported by a Cancer Research UK PhD studentship and ORSAS. SK is supported by a Scottish Universities Life Sciences Alliance PhD studentship. This work was supported by Cancer Research UK grant A13356 to ADD (http://www.cancerresearchuk.org). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Convolutional Gated Recurrent Neural Network Based Automatic Detection and Classification of Brain Tumor using Magnetic Resonance Imaging

Magnetic Resonance Imaging (MRI) might be a problematic assignment for tumor fluctuation and complexity because of brain image classification. This work presents the brain tumor classification system using Convolutional Gated Recurrent Neural Network (CGRNN) algorithm based on MRI images. The proposed tumor recognition framework comprises of four stages, to be specific preprocessing, feature extraction, segmentation and classification. Extraction of identified tumor framework features was accomplished utilizing Gray Level Co-occurrence Matrix (GLCM) strategy. At long last, the Convolutional Gated Recurrent Neural Network Classifier has been created to perceive various kinds of brain disease. The proposed framework can be effective in grouping these models and reacting to any variation from the abnormality. The entire framework is isolated into different types of phases: the Learning/Training Phase and the Recognition/Test Phase. A CGRNN classifier under the scholarly ideal separation measurements is utilized to decide the chance of every pixel having a place with the foreground (tumor) and the background. MATLAB software is used in the development of the simulation of the proposed system. The suggested method's simulation results show that the analysis of brain tumours is stable. It shows that the proposed brain tumor classifications are superior to those from brain MRIs than existing brain tumor classifications. The overall accuracy of the proposed system is 98.45%

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex

Peer reviewedPublisher PD

The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation

Peer reviewedPublisher PD

Fungal Planet description sheets: 1284-1382

Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii fromagrassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis oncalcareoussoil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceousdebris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica) , Inocybe corsica onwetground. France (French Guiana) , Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. [...]P.R. Johnston thanks J. Sullivan (Lincoln University) for the habitat image of Kowai Bush, Duckchul Park (Manaaki Whenua – Landcare Research) for the DNA sequencing, and the New Zealand Department of Conservation for permission to collect the specimens; this research was supported through the Manaaki Whenua – Landcare Research Biota Portfolio with funding from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment. V. Hubka was supported by the Czech Ministry of Health (grant number NU21-05-00681), and is grateful for the support from the Japan Society for the Promotion of Science – grant-in-aid for JSPS research fellow (grant no. 20F20772). K. Glässnerová was supported by the Charles University Grant Agency (grant No. GAUK 140520). J. Trovão and colleagues were financed by FEDERFundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), and by Portuguese funds through FCT – Fundação para a Ciência e a Tecnologia in the framework of the project POCI-01-0145-FEDER-PTDC/ EPH-PAT/3345/2014. This work was carried out at the R&D Unit Centre for Functional Ecology – Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). J. Trovão was also supported by POCH – Programa Operacional Capital Humano (co-funding by the European Social Fund and national funding by MCTES), through a ‘FCT – Fundação para a Ciência e Tecnologia’ PhD research grant (SFRH/BD/132523/2017). D. Haelewaters acknowledges support from the Research Foundation – Flanders (Junior Postdoctoral Fellowship 1206620N). M. Loizides and colleagues are grateful to Y. Cherniavsky for contributing collections AB A12-058-1 and AB A12- 058-2, and Á. Kovács and B. Kiss for their help with molecular studies of these specimens. C. Zmuda is thanked for assisting with the collection of ladybird specimens infected with Hesperomyces parexochomi. A.V. Kachalkin and colleagues were supported by the Russian Science Foundation (grant No. 19-74-10002). The study of A.M. Glushakova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121040800174-6. S. Nanu acknowledges the Kerala State Council for Science, Technology and Environment (KSCSTE) for granting a research fellowship and is grateful to the Chief Conservator of Forests and Wildlife for giving permission to collect fungal samples. A. Bañares and colleagues thank L. Monje and A. Pueblas of the Department of Drawing and Scientific Photography at the University of Alcalá for their help in the digital preparation of the photographs, and J. Rejos, curator of the AH herbarium for his assistance with the specimens examined in the present study. The research of V. Antonín received institutional support for long-term conceptual development of research institutions provided by the Ministry of Culture (Moravian Museum, ref. MK000094862). The studies of E.F. Malysheva, V.F. Malysheva, O.V. Morozova, and S.V. Volobuev were carried out within the framework of a research project of the Komarov Botanical Institute RAS, St Petersburg, Russia (АААА-А18-118022090078-2) using equipment of its Core Facility Centre ‘Cell and Molecular Technologies in Plant Science’.The study of A.V. Alexandrova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121032300081-7. The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits van Waveren, Leiden, Netherlands) contributed substantially to the costs of sequencing and travelling expenses for M.E. Noordeloos. The work of B. Dima was partly supported by the ÚNKP- 20-4 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund. The work of L. Nagy was supported by the ‘Momentum’ program of the Hungarian Academy of Sciences (contract No. LP2019- 13/2019 to L.G.N.). G.A. Kochkina and colleagues acknowledge N. Demidov for the background photograph, and N. Suzina for the SEM photomicrograph. The research of C.M. Visagie and W.J. Nel was supported by the National Research Foundation grant no 118924 and SFH170610239162. C. Gil-Durán acknowledges Agencia Nacional de Investigación y Desarrollo, Ministerio de Ciencia, Tecnología, Conocimiento e Innovación, Gobierno de Chile, for grant ANID – Fondecyt de Postdoctorado 2021 – N° 3210135. R. Chávez and G. Levicán thank DICYT-USACH and acknowledges the grants INACH RG_03-14 and INACH RT_31-16 from the Chilean Antarctic Institute, respectively. S. Tiwari and A. Baghela would like to acknowledge R. Avchar and K. Balasubramanian from the Agharkar Research Institute, Pune, Maharashtra for helping with the termite collection. S. Tiwari is also thankful to the University Grants Commission, Delhi (India) for a junior research fellowship (827/(CSIR-UGC NET DEC.2017)). R. Lebeuf and I. Saar thank D. and H. Spencer for collecting and photographing the holotype of C. bondii, and R. Smith for photographing the habitat. A. Voitk is thanked for helping with the colour plate and review of the manuscript, and the Foray Newfoundland and Labrador for providing the paratype material. I. Saar was supported by the Estonian Research Council (grant PRG1170) and the European Regional Development Fund (Centre of Excellence EcolChange). M.P.S. Câmara acknowledges the ‘Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq’ for the research productivity fellowship, and financial support (Universal number 408724/2018-8). W.A.S. Vieira acknowledges the ‘Coordenação de Aperfeiçoamento Pessoal de Ensino Superior – CAPES’ and the ‘Programa Nacional de Pós-Doutorado/CAPES – PNPD/CAPES’ for the postdoctoral fellowship. A.G.G. Amaral acknowledges CNPq, and A.F. Lima and I.G. Duarte acknowledge CAPES for the doctorate fellowships. F. Esteve-Raventós and colleagues were financially supported by FEDER/ Ministerio de Ciencia, Innovación y Universidades – Agencia Estatal de Investigación (Spain)/ Project CGL2017-86540-P. The authors would like to thank L. Hugot and N. Suberbielle (Conservatoire Botanique National de Corse, Office de l’Environnement de la Corse, Corti) for their help. The research of E. Larsson is supported by The Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala. Financial support was provided to R.J. Ferreira by the National Council for Scientific and Technological Development (CNPq), and to I.G. Baseia, P.S.M. Lúcio and M.P. Martín by the National Council for Scientific and Technological Development (CNPq) under CNPq-Universal 2016 (409960/2016-0) and CNPq-visiting researcher (407474/2013-7). J. Cabero and colleagues wish to acknowledge A. Rodríguez for his help to describe Genea zamorana, as well as H. Hernández for sharing information about the vegetation of the type locality. S. McMullan-Fisher and colleagues acknowledge K. Syme (assistance with illustrations), J. Kellermann (translations), M. Barrett (collection, images and sequences), T. Lohmeyer (collection and images) and N. Karunajeewa (for prompt accessioning). This research was supported through funding from Australian Biological Resources Study grant (TTC217-06) to the Royal Botanic Gardens Victoria. The research of M. Spetik and co-authors was supported by project No. CZ.02.1.01/0.0/0.0 /16_017/0002334. N. Wangsawat and colleagues were partially supported by NRCT and the Royal Golden Jubilee Ph.D. programme, grant number PHD/0218/2559. They are thankful to M. Kamsook for the photograph of the Phu Khiao Wildlife Sanctuary and P. Thamvithayakorn for phylogenetic illustrations. The study by N.T. Tran and colleagues was funded by Hort Innovation (Grant TU19000). They also thank the turf growers who supported their surveys and specimen collection. N. Matočec, I. Kušan, A. Pošta, Z. Tkalčec and A. Mešić thank the Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). A. Pošta thanks the Croatian Science Foundation for their support under the grant HRZZ-2018-09-7081. A. Morte is grateful to Fundación Séneca – Agencia de Ciencia y Tecnología de la Región de Murcia (20866/ PI/18) for financial support. The research of G. Akhmetova, G.M. Kovács, B. Dima and D.G. Knapp was supported by the National Research, Development and Innovation Office, Hungary (NKFIH KH-130401 and K-139026), the ELTE Thematic Excellence Program 2020 supported by the National Research, Development and Innovation Office (TKP2020-IKA-05) and the Stipendium Hungaricum Programme. The support of the János Bolyai Research Scholarship of the Hungarian Academy of Sciences and the Bolyai+ New National Excellence Program of the Ministry for Innovation and Technology to D.G. Knapp is highly appreciated. F.E. Guard and colleagues are grateful to the traditional owners, the Jirrbal and Warungu people, as well as L. and P. Hales, Reserve Managers, of the Yourka Bush Heritage Reserve. Their generosity, guidance, and the opportunity to explore the Bush Heritage Reserve on the Einasleigh Uplands in far north Queensland is greatly appreciated. The National Science Foundation (USA) provided funds (DBI#1828479) to the New York Botanical Garden for a scanning electron microscope used for imaging the spores. V. Papp was supported by the ÚNKP-21-5 New National Excellence Program of the Ministry for Innovation and Technology from the National Research, Development and Innovation Fund of Hungary. A.N. Miller thanks the WM Keck Center at the University of Illinois Urbana – Champaign for sequencing Lasiosphaeria deviata. J. Pawłowska acknowledges support form National Science Centre, Poland (grant Opus 13 no 2017/25/B/NZ8/00473). The research of T.S. Bulgakov was carried out as part of the State Research Task of the Subtropical Scientific Centre of the Russian Academy of Sciences (Theme No. 0492-2021- 0007). K. Bensch (Westerdijk Fungal Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various Latin epithets.Peer reviewe

Tel1 is required for early replication of short telomeres.

<p>(A) Telomere length analysis in wild-type (<i>YKU70 TEL1</i>), <i>tel1</i>Δ, <i>yku70</i>Δ, and <i>yku70</i>Δ<i> tel1</i>Δ strains. Terminal chromosome fragments were detected by probing a Southern blot of XhoI-digested genomic DNA for TG_1–3 sequence. Smear represents average length of Y′ telomeres. (B) Replication kinetics of various genomic sequences in wild-type and short telomere mutants <i>yku70</i>Δ, <i>tel1</i>Δ and <i>yku70</i>Δ<i> tel1</i>Δ. Telomere-proximal sequences shown are Y′ (solid line with filled circles), ARS522 (solid line with filled diamonds), and proARS1202 (solid line with filled triangles). Non-telomeric marker sequences (dashed lines) are early origins ARS305 (open squares), late origin ARS1412 (open circles), and Chr XIV-internal sequences (open diamonds). Strains were released from α-factor block at 30°C. (C) Replication indices (RI) values from experiments in B, where replication times are normalized to early origin ARS305 (RI = 0) and Chr.XIV-int (RI = 1). Strains are BB14-3a (wild-type), ASY5 (<i>tel1</i>Δ), AW99 (<i>yku70</i>Δ) and ASY13 (<i>yku70</i>Δ<i> tel1</i>Δ; corresponding to second isolate in part A); all are in A364a background as listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen.1004691.s015" target="_blank">Table S1</a>.</p

Rif1 acts downstream of Tel1 in regulating telomere replication time.

<p>(A) Telomere length analysis in wild-type, <i>tel1</i>Δ, <i>rif1</i>Δ and <i>rif1</i>Δ<i> tel1</i>Δ strains. Southern blot analysis carried out as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g001" target="_blank">Fig. 1A</a>. (B) Replication kinetics of various genomic sequences in <i>rif1</i>Δ and <i>rif1</i>Δ<i> tel1</i>Δ strains. Plots and symbols as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g001" target="_blank">Fig. 1B</a>. (C) Replication indices from experiments in B, along with values from wild-type and <i>tel1</i>Δ experiments from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g001" target="_blank">Fig. 1</a>. Strains are HYLS44 (<i>rif1</i>Δ) and ASY14 (<i>rif1</i>Δ<i> tel1</i>Δ; corresponding to first isolate in part A).</p

Non-phosphorylatable <i>rif1-7S</i>→<i>A</i> does not delay early replication of short <i>yku70</i>Δ telomeres.

<p>(A) Telomere length analysis of Rif1 phospho-site mutants. Genomic DNA was extracted from the indicated strains and telomere length analyses performed as described. Smear indicates average length of Y′ telomeres. <i>rif1</i>Δ<i>scd</i> represents an internal deletion within the <i>RIF1</i> C-terminal region made as a strain construction intermediate (see Supplementary Materials & Methods). <i>RIF1-7S</i>→<i>S</i> represents a <i>RIF1</i> reconstruction, where wild-type sequence was re-inserted into <i>rif1</i>Δ<i>scd</i> to control for telomere length recovery. (B) Replication program of <i>yku70</i>Δ <i>rif1-7S</i>→<i>A</i>, released from an α-factor block at 30°C. Sequences analyzed are as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g001" target="_blank">Fig. 1</a>. (C) Replication indices from <i>yku70</i>Δ<i> rif1-7S</i>→<i>A</i> experiment shown in B, along with values from wild-type and <i>yku70</i>Δ experiments from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g001" target="_blank">Fig. 1B&C</a>. Strains in part A are BB14-3a (wild-type), HYLS44 (<i>rif1</i>Δ), ASY5 (<i>tel1</i>Δ), AW99 (<i>yku70</i>Δ), ASY51 (<i>rif1</i>Δ<i>scd</i>); ASY81 (<i>RIF1-7S→S</i>). For <i>rif1-7S</i>→<i>A</i> asterisk indicates ASY69, used for replication timing in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen.1004691.s013" target="_blank">Fig. S11</a>; for <i>rif1-7S</i>→<i>E</i> asterisk indicates ASY73, used for replication timing in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen.1004691.s014" target="_blank">Fig. S12</a>; for <i>yku70</i>Δ<i> rif1-7S</i>→<i>A</i> asterisk indicates ASY76, used for replication timing in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen-1004691-g006" target="_blank">Fig. 6 B&C</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004691#pgen.1004691.s012" target="_blank">S10</a>; for <i>yku70</i>Δ<i> rif1-7S</i>→<i>E</i> asterisk indicates ASY78.</p

Phosphorylation of Rif1 Serine-1308 depends on Tel1.

<p>(A) Plots shows relative levels of the S-1308 phosphorylated peptide [KVDS(ph)QDIQVPATQGM(ox)K] in <i>yku70</i>Δ (Light-labeled R0K0) and <i>yku70</i>Δ<i> tel1</i>Δ (Heavy-labeled R10K8) strains. H/L ratio is 0.10. (B) Equivalent plot for S-1351 phosphorylated peptide NTAIM(ox)NSSQQESHANR. H/L ratio is 0.97048. Strains used are ASY30 (<i>yku70</i>Δ<i> RIF1-13Myc</i>), and ASY46 (<i>yku70</i>Δ<i> tel1</i>Δ <i>RIF1-13Myc</i>).</p