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Sri, Des Utari - One of the best experts on this subject based on the ideXlab platform.
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PENGARUH PENGGUNAAN CAMPURAN LIMBAH SAWIT DAN DEDAK FERMENTASI DENGAN Phanerochaete chrysosporium DAN Neurospora crassa DALAM RANSUM TERHADAP PERFORMA PUYUH PETELUR DAN INCOME OVER FEED COST
2020Co-Authors: Sri, Des UtariAbstract:Penelitian ini bertujuan untuk mengetahui berapa batasan dan bagaimana pengaruh penggunaan campuran limbah sawit dan dedak yang difermentasi (LSF) dengan Phanerochaete chrysosporium dan Neurospora crassa dalam ransum terhadap performa puyuh petelur. Penelitian ini menggunakan 200 ekor puyuh (Coturnix-coturnix japonica) umur 20 minggu dengan produksi telur 70%. Penelitian ini menggunakan metode eksperimen dengan Rancangan Acak Lengkap (RAL) dengan 4 perlakuan (0%, 8%, 16%, dan 24% LSDF dengan Phanerochaete chrysosporium dan Neurospora crassa) dan 5 kali ulangan. Peubah yang diamati yaitu konsumsi ransum (gr/ekor/hari), produksi telur harian (%), berat telur (g/butir), massa telur (gr/ekor/hari), konversi ransum dan income over feed cost (Rp/kg). Hasil analisis keragaman menunjukkan bahwa penggunaan campuran limbah sawit dan dedak yang difermentasi dengan Phanerochaete chrysosporium dan Neurospora crassa dalam ransum memberikan pengaruh berbeda tidak nyata (P>0.05) terhadap konsumsi ransum, produksi telur harian, berat telur, massa telur, dan konversi ransum. Kesimpulan dari penelitian ini adalah campuran limbah sawit dan dedak yang difermentasi dengan Phanerochaete chrysosporium dan Neurospora crassa dapat digunakan sampai 24% dalam ransum puyuh petelur. Pada kondisi ini diperoleh konsumsi ransum 24,22 gr/ekor/hari, produksi telur 79,93%, berat telur 9,96 gr/butir, massa telur 7,97 gr/ekor/hari, konversi ransum 3,04 dan income over feed cost Rp. 8.510/kg Kata Kunci : Limbah sawit, Neurospora crassa Performa produksi puyuh, Phanerochaete chrysosporium
Michael Brunner - One of the best experts on this subject based on the ideXlab platform.
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phosphorylation timers in the Neurospora crassa circadian clock
Journal of Molecular Biology, 2020Co-Authors: Axel Diernfellner, Michael BrunnerAbstract:Abstract Circadian clocks are self-sustained oscillators that orchestrate metabolism and physiology in synchrony with the 24-h day–night cycle. They are temperature compensated over a wide range and entrained by daily recurring environmental cues. Eukaryotic circadian clocks are governed by cell-based transcriptional–translational feedback loops (TTFLs). The core components of the TTFLs are largely known and their molecular interactions in many cases well established. Although the core clock components are not or only partly conserved, the molecular wiring of TTFLs is rather similar across kingdoms and phylae. In all known systems, circadian timing relies critically on casein kinase 1 (CK1) and CK1-dependent hyperphosphorylation of core clock proteins, in particular of negative elements of the TTFLs. Yet, we lack concepts as to how phosphorylation by CK1a and other kinases relates to timekeeping on the molecular level. Here we summarize what is known about phosphorylation of core components of the circadian clock of Neurospora crassa and speculate about the molecular basis of circadian timekeeping by hyperphosphorylation of intrinsically disordered regions in clock proteins.
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A pathway linking translation stress to checkpoint kinase 2 signaling in Neurospora crassa.
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Axel Diernfellner, Linda Lauinger, Anton Shostak, Michael BrunnerAbstract:Checkpoint kinase 2 (CHK-2) is a key component of the DNA damage response (DDR). CHK-2 is activated by the PIP3-kinase-like kinases (PI3KKs) ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related protein (ATR), and in metazoan also by DNA-dependent protein kinase catalytic subunit (DNA-PKcs). These DNA damage-dependent activation pathways are conserved and additional activation pathways of CHK-2 are not known. Here we show that PERIOD-4 (PRD-4), the CHK-2 ortholog of Neurospora crassa, is part of a signaling pathway that is activated when protein translation is compromised. Translation stress induces phosphorylation of PRD-4 by a PI3KK distinct from ATM and ATR. Our data indicate that the activating PI3KK is mechanistic target of rapamycin (mTOR). We provide evidence that translation stress is sensed by unbalancing the expression levels of an unstable protein phosphatase that antagonizes phosphorylation of PRD-4 by mTOR complex 1 (TORC1). Hence, Neurospora mTOR and PRD-4 appear to coordinate metabolic state and cell cycle progression.
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the coding and noncoding transcriptome of Neurospora crassa
BMC Genomics, 2017Co-Authors: Ibrahim Avi Cemel, Nati Ha, Geza Schermann, Shusuke Yonekawa, Michael BrunnerAbstract:Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete. We have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species. Our transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs.
Sandi Arfi - One of the best experts on this subject based on the ideXlab platform.
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Pengaruh Penggunaan Campuran Limbah Sawit Dan Dedak Yang Difermentasi Dengan Phanerochaete chrysosporyum dan Neurospora crassa Dalam Ransum Terhadap Kualitas Telur Ayam Ras
2020Co-Authors: Sandi ArfiAbstract:ABSTRAK Penelitian ini bertujuan untuk mengetahui berapa batasan level dan bagaimana pengaruh penggunaan campuran limbah sawit dan dedak yang difermentasi (LSDF) dengan Phanerochaete chrysosporium dan Neurospora crassa dalam ransum terhadap kualitas telur ayam ras petelur. Penelitian ini menggunakan 200 ekor ayam ras petelur strain Isa Brown yang berumur 56 minggu dengan produksi 70%, kandang yang digunakan adalah kandang baterai dengan ukuran 45x40x30 cm terbuat dari kawat sebanyak 20 unit yang ditempati 10 ekor ayam per unit. Metode penelitian ini menggunakan Rancangan Acak Lengkap (RAL) dengan 5 perlakuan (0%, 10%, 15%, 20%, dan 25% LSDF dengan Phanerochaete chrysosporium dan Neurospora crassa) dan 4 ulangan. Peubah yang diamati yaitu kolesterol kuning telur (mg/100g), lemak kuning telur (%), dan warna kuning telur. Hasil analisis keragaman menunjukkan bahwa penggunaan campuran limbah sawit dan dedak yang difermentasi dengan Phanerochaete chrysosporium dan Neurospora crassa berpengaruh sangat nyata (P0,05) terhadap kandungan lemak kuning telur. Kesimpulan dari penelitian ini adalah penggunaan campuran limbah sawit dan dedak yang difermentasi dengan Phanerochaete chrysosporium dan Neurospora crassa (1:1) sampai level 25% dalam ransum dapat meningkatkan kualitas telur ayam (menurunkan kolesterol dan meningkatkan warna kuning telur). Pada kondisi ini diperoleh kolesterol sebanyak 370,95 (mg/100g), lemak kuning telur 25,42%, dan skor warna kuning telur sebanyak 9,50. Kata Kunci : Fermentasi, kualitas telur, limbah sawit, Phanerochaete chrysosporium, Neurospora crass
Jeffrey P Townsend - One of the best experts on this subject based on the ideXlab platform.
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Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa
2016Co-Authors: Nina A. Lehr, Zheng Wang, Frances Trail, David A. Hewitt, Jeffrey P TownsendAbstract:Many fungi form complex three-dimensional fruiting bodies, within which the meiotic machinery for sexual spore production has been considered to be largely conserved over evolutionary time. Indeed, much of what we know about meiosis in plant and animal taxa has been deeply informed by studies of meiosis in Saccharomyces and Neurospora. Nevertheless, the genetic basis of fruiting body development and its regulation in relation to meiosis in fungi is barely known, even within the best studied multicellular fungal model Neurospora crassa. We characterized morphological development and genome-wide transcriptomics in the closely related species Neurospora crassa, Neurospora tetrasperma, and Neurospora discreta, across eight stages of sexual development. Despite diverse life histories within the genus, all three species produce vase-shaped perithecia. Transcriptome sequencing provided gene expression levels of orthologous genes among all three species. Expression of key meiosis genes and sporulation genes corresponded to known phenotypic and developmental differences among these Neurospora species during sexual development. We assembled a list of genes putatively relevant to the recent evolution of fruiting body development by sorting genes whose relative expression acros
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Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa.
PLOS ONE, 2014Co-Authors: Nina A. Lehr, David Hewitt, Francesc López-giráldez, Zheng Wang, Ning Li, Frances Trail, Jeffrey P TownsendAbstract:Many fungi form complex three-dimensional fruiting bodies, within which the meiotic machinery for sexual spore production has been considered to be largely conserved over evolutionary time. Indeed, much of what we know about meiosis in plant and animal taxa has been deeply informed by studies of meiosis in Saccharomyces and Neurospora. Nevertheless, the genetic basis of fruiting body development and its regulation in relation to meiosis in fungi is barely known, even within the best studied multicellular fungal model Neurospora crassa. We characterized morphological development and genome-wide transcriptomics in the closely related species Neurospora crassa, Neurospora tetrasperma, and Neurospora discreta, across eight stages of sexual development. Despite diverse life histories within the genus, all three species produce vase-shaped perithecia. Transcriptome sequencing provided gene expression levels of orthologous genes among all three species. Expression of key meiosis genes and sporulation genes corresponded to known phenotypic and developmental differences among these Neurospora species during sexual development. We assembled a list of genes putatively relevant to the recent evolution of fruiting body development by sorting genes whose relative expression across developmental stages increased more in N. crassa relative to the other species. Then, in N. crassa, we characterized the phenotypes of fruiting bodies arising from crosses of homozygous knockout strains of the top genes. Eight N. crassa genes were found to be critical for the successful formation of perithecia. The absence of these genes in these crosses resulted in either no perithecium formation or in arrested development at an early stage. Our results provide insight into the genetic basis of Neurospora sexual reproduction, which is also of great importance with regard to other multicellular ascomycetes, including perithecium-forming pathogens, such as Claviceps purpurea, Ophiostoma ulmi, and Glomerella graminicola.
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rna extraction probe preparation and competitive hybridization for transcriptional profiling using Neurospora crassa long oligomer dna microarrays
Fungal Genetics Reports, 2008Co-Authors: Travis A Clark, Julie M Guilmette, Daniel Renstrom, Jeffrey P TownsendAbstract:We developed protocols optimized for the performance of experiments assaying genomic gene expression using Neurospora crassa long-oligomer microarrays. We present methods for sample growth and harvesting, total RNA extraction, poly(A) mRNA selection, preparation of NH3-Allyl Cy3/Cy5 labeled probes, and microarray hybridization. The quality of the data obtained with these protocols is demonstrated by the comparative transcriptional profiling of basal and apical zones of vegetative growth of N. crassa.
Christian I Hong - One of the best experts on this subject based on the ideXlab platform.
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efficient gene editing in Neurospora crassa with crispr technology
Fungal biology and biotechnology, 2015Co-Authors: Toru Matsuura, Jungin Kwon, Mokryun Baek, Christian I HongAbstract:Efficient gene editing is a critical tool for investigating molecular mechanisms of cellular processes and engineering organisms for numerous purposes ranging from biotechnology to medicine. Recently developed RNA-guided CRISPR/Cas9 technology has been used for efficient gene editing in various organisms, but has not been tested in a model filamentous fungus, Neurospora crassa. In this report, we demonstrate efficient gene replacement in a model filamentous fungus, Neurospora crassa, with the CRISPR/Cas9 system. We utilize Cas9 endonuclease and single crRNA:tracrRNA chimeric guide RNA (gRNA) to: (1) replace the endogenous promoter of clr-2 with the β-tubulin promoter, and (2) introduce a codon optimized fire fly luciferase under the control of the gsy-1 promoter at the csr-1 locus. CLR-2 is one of the core transcription factors that regulate the expression of cellulases, and GSY-1 regulates the conversion of glucose into glycogen. We show that the β-tubulin promoter driven clr-2 strain shows increased expression of cellulases, and gsy-1-luciferase reporter strain can be easily screened with a bioluminescence assay. CRISPR/Cas9 system works efficiently in Neurospora crassa, which may be adapted to Neurospora natural isolates and other filamentous fungi. It will be beneficial for the filamentous fungal research community to take advantage of CRISPR/Cas9 tool kits that enable genetic perturbations including gene replacement and insertions.
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efficient gene editing in Neurospora crassa with crispr technology
Fungal biology and biotechnology, 2015Co-Authors: Toru Matsuura, Jungin Kwon, Mokryun Baek, Christian I HongAbstract:Efficient gene editing is a critical tool for investigating molecular mechanisms of cellular processes and engineering organisms for numerous purposes ranging from biotechnology to medicine. Recently developed RNA-guided CRISPR/Cas9 technology has been used for efficient gene editing in various organisms, but has not been tested in a model filamentous fungus, Neurospora crassa. In this report, we demonstrate efficient gene replacement in a model filamentous fungus, Neurospora crassa, with the CRISPR/Cas9 system. We utilize Cas9 endonuclease and single crRNA:tracrRNA chimeric guide RNA (gRNA) to: (1) replace the endogenous promoter of clr-2 with the β-tubulin promoter, and (2) introduce a codon optimized fire fly luciferase under the control of the gsy-1 promoter at the csr-1 locus. CLR-2 is one of the core transcription factors that regulate the expression of cellulases, and GSY-1 regulates the conversion of glucose into glycogen. We show that the β-tubulin promoter driven clr-2 strain shows increased expression of cellulases, and gsy-1-luciferase reporter strain can be easily screened with a bioluminescence assay. CRISPR/Cas9 system works efficiently in Neurospora crassa, which may be adapted to Neurospora natural isolates and other filamentous fungi. It will be beneficial for the filamentous fungal research community to take advantage of CRISPR/Cas9 tool kits that enable genetic perturbations including gene replacement and insertions.
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circadian rhythms synchronize mitosis in Neurospora crassa
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Christian I Hong, Mokryun Baek, Judit Zamborszky, Laszlo Labiscsak, Kyungsu Ju, Luis F Larrondo, Alejandra Goity, Hin Siong Chong, William J Belden, Attila CsikasznagyAbstract:The cell cycle and the circadian clock communicate with each other, resulting in circadian-gated cell division cycles. Alterations in this network may lead to diseases such as cancer. Therefore, it is critical to identify molecular components that connect these two oscillators. However, molecular mechanisms between the clock and the cell cycle remain largely unknown. A model filamentous fungus, Neurospora crassa, is a multinucleate system used to elucidate molecular mechanisms of circadian rhythms, but not used to investigate the molecular coupling between these two oscillators. In this report, we show that a conserved coupling between the circadian clock and the cell cycle exists via serine/threonine protein kinase-29 (STK-29), the Neurospora homolog of mammalian WEE1 kinase. Based on this finding, we established a mathematical model that predicts circadian oscillations of cell cycle components and circadian clock-dependent synchronized nuclear divisions. We experimentally demonstrate that G1 and G2 cyclins, CLN-1 and CLB-1, respectively, oscillate in a circadian manner with bioluminescence reporters. The oscillations of clb-1 and stk-29 gene expression are abolished in a circadian arrhythmic frqko mutant. Additionally, we show the light-induced phase shifts of a core circadian component, frq, as well as the gene expression of the cell cycle components clb-1 and stk-29, which may alter the timing of divisions. We then used a histone hH1-GFP reporter to observe nuclear divisions over time, and show that a large number of nuclear divisions occur in the evening. Our findings demonstrate the circadian clock-dependent molecular dynamics of cell cycle components that result in synchronized nuclear divisions in Neurospora.