| myosin concentration underlies cell size-dependent scalability of actomyosin ring constriction. | in eukaryotes, cytokinesis is accomplished by an actomyosin-based contractile ring. although in caenorhabditis elegans embryos larger cells divide at a faster rate than smaller cells, it remains unknown whether a similar mode of scalability operates in other cells. we investigated cytokinesis in the filamentous fungus neurospora crassa, which exhibits a wide range of hyphal circumferences. we found that n. crassa cells divide using an actomyosin ring and larger rings constricted faster than smal ... | 2011 | 22123864 |
| a factor in a wild isolated neurospora crassa strain enables a chromosome segment duplication to suppress repeat-induced point mutation. | repeat-induced point mutation (rip) is a sexual stage-specific mutational process of neurospora crassa and other fungi that alters duplicated dna sequences. previous studies from our laboratory showed that chromosome segment duplications (dps) longer than (approx.) 300 kbp can dominantly suppress rip, presumably by titration of the rip machinery, and that although dps less than 200 kbp did not individually suppress rip, they could do so in homozygous and multiply heterozygous crosses, provided t ... | 2011 | 22116279 |
| disruption of alternative nad(p)h dehydrogenases leads to decreased mitochondrial ros in neurospora crassa. | mitochondria are a main providers of high levels of energy, but also a major source of reactive oxygen species (ros) during normal oxidative metabolism. the involvement of neurospora crassa alternative nad(p)h dehydrogenases in mitochondrial ros production was evaluated. the growth responses of a series of respiratory mutants to several stress conditions revealed that disrupting alternative dehydrogenases leads to an increased tolerance to the redox cycler paraquat, with a mutant devoid of the e ... | 2012 | 22100504 |
| diverse interactions mediate asymmetric incompatibility by the het-6 supergene complex in neurospora crassa. | heterokaryon incompatibility (hi) in filamentous fungi is a form of nonself recognition that operates during the vegetative phase of the life cycle. one hi gene complex in neurospora crassa, the het-6 locus, comprises two incompatibility genes, het-6 and un-24, each having two allelic variants, oak ridge (or) and panama (pa). the un-24 gene also encodes the large subunit of ribonucleotide reductase while het-6 appears to be a member of a repetitive gene family with no other known function aside ... | 2012 | 22094057 |
| direct transcriptional control of a p38 mapk pathway by the circadian clock in neurospora crassa. | mapk signal transduction pathways are important regulators of stress responses, cellular growth, and differentiation. in neurospora, the circadian clock controls rhythms in phosphorylation of the p38-like mapk (os-2); however, the mechanism for this regulation is not known. we show that the wcc, a transcription factor and clock component, binds to the os-4 mapkkk promoter in response to light and rhythmically in constant darkness, peaking in the subjective morning. deletion of the wcc binding si ... | 2011 | 22087254 |
| functional characterization and cellular dynamics of the cdc-42 - rac - cdc-24 module in neurospora crassa. | rho-type gtpases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. in this study, we investigate the role of the cdc-42 - rac - cdc-24 module in neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both gtpases share at least one c ... | 2011 | 22087253 |
| illuminating the early signaling pathway of a fungal light-oxygen-voltage photoreceptor. | circadian clocks are molecular timekeepers encountered in a wide variety of organisms, which allow to adapt the cell's metabolism and behavior to the daily and seasonal periods. their function is regulated by light-sensing proteins, among which vivid, a light-oxygen-voltage (lov) sensitive domain of the fungus neurospora crassa, constitutes one of the most prominent examples. although the major photochemical and structural changes during the photocycle of this photosensor have been elucidated th ... | 2012 | 22081493 |
| fine-scale mapping in neurospora crassa by using genome-wide knockout strains. | fine-scale genetic mapping is often hindered by the lack of adequate markers surrounding the locus of interest. in the filamentous ascomycete neurospora crassa, the genome has been sequenced and an effort has been made to generate genome-wide deletion strains for the entire gene set. accordingly, the hygromycin-resistant marker in each deletion strain can be used as a mapping locus in a classical three-point cross, along with the mapping target and a standard marker. we have demonstrated the fea ... | 2016 | 22067301 |
| the neurospora crassa dcc-1 protein, a putative histidine kinase, is required for normal sexual and asexual development and carotenogenesis. | two-component signaling pathways based on phosphoryl group transfer between histidine kinase and response regulator proteins regulate environmental responses in bacteria, archaea, plants, slime molds, and fungi. here we characterize a mutant form of dcc-1, a putative histidine kinase encoded by the ncu00939 gene of the filamentous fungus neurospora crassa. we show that this protein participates in the regulation of processes such as conidiation, perithecial development, and, to a certain degree, ... | 2011 | 22058142 |
| neurospora crassa light signal transduction is affected by ros. | in the ascomycete fungus neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. a major photoreceptor in neurospora cells is wcc, a heterodimeric complex formed by the pas-domain-containing polypeptides wc-1 and wc-2, the products of genes white collar-1 and white collar-2. the photosignal transduction is started by photochemical activity of an exci ... | 2012 | 22046507 |
| cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by neurospora crassa. | the high cost of enzymes for saccharification of lignocellulosic biomass is a major barrier to the production of second generation biofuels. using a combination of genetic and biochemical techniques, we report that filamentous fungi use oxidative enzymes to cleave glycosidic bonds in cellulose. deletion of cdh-1, the gene encoding the major cellobiose dehydrogenase of neurospora crassa, reduced cellulase activity substantially, and addition of purified cellobiose dehydrogenases from m. thermophi ... | 2011 | 22004347 |
| modulation of fungal sensitivity to staurosporine by targeting proteins identified by transcriptional profiling. | an analysis of the time-dependent genetic response to the death-inducer staurosporine was performed in neurospora crassa by transcriptional profiling. staurosporine induced two major genes encoding an abc transporter and a protein with similarity to regulatory subunits of potassium channels. the transcriptional response is dependent on the activity of a novel transcription factor. deletion mutants in differentially expressed genes displayed altered sensitivity to staurosporine, underscoring sign ... | 2011 | 22001288 |
| the neurospora crassa tob complex: analysis of the topology and function of tob38 and tob37. | the tob or sam complex is responsible for assembling several proteins into the mitochondrial outer membrane, including all β-barrel proteins. we have identified several forms of the complex in neurospora crassa. one form contains tob55, tob38, and tob37; another contains these three subunits plus the mdm10 protein; while additional complexes contain only tob55. as previously shown for tob55, both tob37 and tob38 are essential for viability of the organism. mitochondria deficient in tob37 or tob3 ... | 2011 | 21980517 |
| global analysis of serine-threonine protein kinase genes in neurospora crassa. | serine/threonine (s/t) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus neurospora crassa. in order to assess the importance of s/t kinases to neurospora biology, we embarked on a global analysis of 86 s/t kinase genes in neurospora. we were able to isolate viable mutants for 77 of the 86 kinase genes. of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing ... | 2011 | 21965514 |
| nuclear and genome dynamics in multinucleate ascomycete fungi. | genetic variation between individuals is essential to evolution and adaptation. however, intra-organismic genetic variation also shapes the life histories of many organisms, including filamentous fungi. a single fungal syncytium can harbor thousands or millions of mobile and potentially genotypically different nuclei, each having the capacity to regenerate a new organism. because the dispersal of asexual or sexual spores propagates individual nuclei in many of these species, selection acting at ... | 2011 | 21959169 |
| mitochondrial dysfunction resulting from the absence of mitochondrial porin in neurospora crassa. | porin, the voltage-dependent anion-selective channel (vdac) in the mitochondrial outer membrane, contributes to metabolism and apoptosis. vdac function was investigated in neurospora, an obligate aerobe with a single porin. porinless strains are viable, with cold-sensitive growth, cytochrome deficiencies and overexpression of alternative oxidase. itraq labeling of mitochondria from a porinless strain and its progenitor revealed a small group of proteins with altered expression levels in the muta ... | 2012 | 21946565 |
| genetic architecture of a reinforced, postmating, reproductive isolation barrier between neurospora species indicates evolution via natural selection. | a role for natural selection in reinforcing premating barriers is recognized, but selection for reinforcement of postmating barriers remains controversial. organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation, but only under restrictive conditions: parental investment in hybrid progeny must inhibit subsequent reproduction, and selected postmating barriers must restore parents' capacity to reproduce successfully. we show that reinforced postmating isolat ... | 2011 | 21876674 |
| structure of a light-activated lov protein dimer that regulates transcription. | light, oxygen, or voltage (lov) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. the lov protein vivid (vvd) of the filamentous fungus neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. here, we determined the crystal structure of the fully light-adapted vvd dimer and reveal the mechanism by which light-driven conformational change alters the o ... | 2011 | 21868352 |
| expression and functional characterisation of tnc, a high-affinity nickel transporter from neurospora crassa. | our previous in silico studies identified a high-affinity nickel transporter, tnc, from the metal transportome of neurospora crassa. a knockout mutant of the tnc gene in n. crassa failed to transport nickel, showed phenotypic growth defects and diminished urease activity under physiological levels of nickel. transport assays conducted in wild type and knockout mutant strains showed that tnc transports nickel with high affinity but exhibits selectivity for other transition metal ions like cobalt. ... | 2011 | 21840412 |
| a genome-wide screen for neurospora crassa transcription factors regulating glycogen metabolism. | transcription factors play a key role in transcription regulation as they recognize and directly bind to defined sites in promoter regions of target genes, and thus modulate differential expression. the overall process is extremely dynamic, as they have to move through the nucleus and transiently bind to chromatin in order to regulate gene transcription. to identify transcription factors that affect glycogen accumulation in neurospora crassa, we performed a systematic screen of a deletion strain ... | 2011 | 21768394 |
| exploring the processes of dna repair and homologous integration in neurospora. | this review offers a personal perspective on historical developments related to our current understanding of dna repair, recombination, and homologous integration in neurospora crassa. previous reviews have summarized and analyzed the characteristics of neurospora dna repair mutants. the early history is reviewed again here as a prelude to a discussion of the molecular cloning, annotation, gene disruption and reverse genetics of neurospora dna repair genes. the classical studies and molecular an ... | 2011 | 21757027 |
| quantitative proteomic approach for cellulose degradation by neurospora crassa. | conversion of plant biomass to soluble sugars is the primary bottleneck associated with production of economically viable cellulosic fuels and chemicals. to better understand the biochemical route that filamentous fungi use to degrade plant biomass, we have taken a quantitative proteomics approach to characterizing the secretome of neurospora crassa during growth on microcrystalline cellulose. thirteen proteins were quantified in the n. crassa secretome using a combination of absolute quantifica ... | 2011 | 21744778 |
| a new mutation affecting frq-less rhythms in the circadian system of neurospora crassa. | we are using the fungus neurospora crassa as a model organism to study the circadian system of eukaryotes. although the frq/wcc feedback loop is said to be central to the circadian system in neurospora, rhythms can still be seen under many conditions in frq-less (frq knockout) strains. to try to identify components of the frq-less oscillator (flo), we carried out a mutagenesis screen in a frq-less strain and selected colonies with altered conidiation (spore-formation) rhythms. a mutation we name ... | 2011 | 21731506 |
| neurospora crassa homologue of neuronal calcium sensor-1 has a role in growth, calcium stress tolerance, and ultraviolet survival. | ncu04379 gene encodes a conserved ca(2+) and/or calmodulin binding protein that possesses a consensus signal for n-terminal myristoylation and four ef-hands, characteristics of neuronal calcium sensor-1proteins. the ncu04379.2 knockout mutant shows slow growth rate, increased sensitivity to calcium and ultraviolet (uv) irradiation, and a wild-type fragment carrying ncu04379 gene complements the mutant. therefore, ncu04379 gene has a role in growth, calcium stress tolerance, and uv survival. cros ... | 2011 | 21728141 |
| the circadian clock of neurospora crassa. | circadian clocks organize our inner physiology with respect to the external world, providing life with the ability to anticipate and thereby better prepare for major fluctuations in its environment. circadian systems are widely represented in nearly all major branches of life, except archaebacteria, and within the eukaryotes, the filamentous fungus neurospora crassa has served for nearly half a century as a durable model organism for uncovering the basic circadian physiology and molecular biolog ... | 2012 | 21707668 |
| fluorescent and bimolecular-fluorescent protein tagging of genes at their native loci in neurospora crassa using specialized double-joint pcr plasmids. | the double-joint polymerase chain reaction (dj-pcr) is a technique that can be used to construct vectors for targeted genome integration without laborious subcloning steps. here we report the availability of plasmids that facilitate dj-pcr-based construction of neurospora crassa tagging vectors. these plasmids allow the creation of green or red fluorescent protein (gfp or rfp) tagging vectors for protein localization studies, as well as split-yellow fluorescent protein (yfp) tagging vectors for ... | 2011 | 21664475 |
| probing the growth dynamics of neurospora crassa with microfluidic structures. | despite occupying physically and chemically heterogeneous natural environments, the growth dynamics of filamentous fungi is typically studied on the surface of homogeneous laboratory media. fungal exploration and exploitation of complex natural environments requires optimal survival and growth strategies at the colony, hyphal, and intra hyphal level, with hyphal space-searching strategies playing a central role. we describe a new methodology for the characterisation and analysis of hyphal space- ... | 2011 | 21640314 |
| architecture and development of the neurospora crassa hypha -- a model cell for polarized growth. | neurospora crassa has been at the forefront of biological research from the early days of biochemical genetics to current progress being made in understanding gene and genetic network function. here, we discuss recent developments in analysis of the fundamental form of fungal growth, development and proliferation -- the hypha. understanding the establishment and maintenance of polarity, hyphal elongation, septation, branching and differentiation are at the core of current research. the advances ... | 2011 | 21640311 |
| characterization of neurospora crassa α-actinin. | α-actinin, an actin-binding protein of the spectrin superfamily, is present in most eukaryotes except plants. it is composed of three domains: n-terminal ch-domains, c-terminal calcium-binding domain (with ef-hand motifs), and a central rod domain. we have cloned and expressed neurospora crassa α-actinin as gst and gfp fusion proteins for biochemical characterization and in vivo localization, respectively. the intracellular localization pattern of α-actinin suggests that this protein is intimate ... | 2011 | 21598047 |
| phenotypic analysis of neurospora crassa gene deletion strains. | phenotypic analysis of neurospora crassa knockout (ko) mutants was used as a vehicle to introduce students to laboratory research. the availability of gene deletion strains was the impetus for the development of a program designed to introduce beginning science students to basic microbiology, genetics, microscopy and beginning bioinformatics. the goal was to provide a research experience, acquire laboratory skills and phenotype hundreds of ko mutants. the data provided by the students was used t ... | 2011 | 21590422 |
| a predicted protein-protein interaction network of the filamentous fungus neurospora crassa. | the filamentous fungus neurospora crassa is a leading model organism for circadian clock studies. computational identification of a protein-protein interaction (ppi) network (also known as an interactome) in n. crassa can provide new insights into the cellular functions of proteins. using two well-established bioinformatics methods (the interolog method and the domain interaction-based method), we predicted 27,588 ppis among 3006 n. crassa proteins. to the best of our knowledge, this is the firs ... | 2011 | 21584303 |
| direct spectrophotometric assay of laccase using diazo derivatives of guaiacol. | laccase (ec 1.10.3.2) is a widespread cuproenzyme able to oxidize various types of phenols and similar aromatic compounds through a one-electron transfer mechanism. the enzyme has already found its way into the market as a biocatalyst. because of its ability to be paired by electron mediators, the expectation for employing laccases in versatile processes is very high. there are a few spectrophotometric methods for assaying the laccase activity; however, all of them are based on the formation of ... | 2011 | 21545148 |
| bulk segregant analysis followed by high-throughput sequencing reveals the neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. | with the advent of high-throughput dna sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (snp) maps. here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. the general map location of a mutation can be identified by a single backcross to a strain enriched in snps compared to a standard wild-type strain. bulk segregant analysis simultaneously increases the likelihood of determining the preci ... | 2011 | 21515825 |
| role of insulin in cr(vi)-mediated genotoxicity in neurospora crassa. | chromium (iii) is an insulinomimetic agent whose biological and/or environmental availability is frequently in the form of cr(vi), which is known to be toxic. wall-less mutant of neurospora crassa (fgsc stock no. 4761) is known to possess insulin receptor in its cell membrane and hence is a good model for cr toxicity studies. this study explores the toxicity of cr(vi) and the possible consequences on simultaneous exposure to insulin in n. crassa. | 2011 | 21488912 |
| use of 1h nuclear magnetic resonance to measure intracellular metabolite levels during growth and asexual sporulation in neurospora crassa. | conidiation is an asexual sporulation pathway that is a response to adverse conditions and is the main mode of dispersal utilized by filamentous fungal pathogens for reestablishment in a more favorable environment. heterotrimeric g proteins (consisting of α, β, and γ subunits) have been shown to regulate conidiation in diverse fungi. previous work has demonstrated that all three of the gα subunits in the filamentous fungus neurospora crassa affect the accumulation of mass on poor carbon sources ... | 2011 | 21460191 |
| phosphorylations: making the neurosporacrassa circadian clock tick. | various post-translational modifications have been identified that play a role in the function of circadian clocks. among these, phosphorylation has been investigated extensively. it was shown that phosphorylation influences half-life, subcellular localisation, transcriptional activity and conformation of clock components over the course of a circadian day. recent observations also indicate that time-of-day specific sequential phosphorylation of the neurospora crassa clock protein frequency is c ... | 2011 | 21453704 |
| light input and processing in the circadian clock of neurospora. | circadian clocks are endogenous oscillators that use zeitgebers as environmental cues to synchronise with the exogenous day-night cycle. the role of light as a zeitgeber has been investigated intensively to date. in neurospora crassa the transcription factor white collar complex (wcc) is directly activated by light, which resets the clock. in addition, a hierarchical cascade of transcription factors activates the light-induced expression of hundreds of genes. disturbance of the clock during the ... | 2011 | 21453703 |
| neurosporaside, a tetraglycosylated sphingolipid from neurospora crassa. | the new tetraglycosylceramide neurosporaside (1a) has been isolated from the fungus neurospora crassa. neurosporaside is a tetraglycosylated glycosphingolipid characterized by a sugar chain unprecedented among natural glycoconjugates. the structure of neurosporaside was elucidated by extensive spectroscopic analysis and microscale degradation analysis, which allowed full structure elucidation using less than 1 mg of compound. | 2011 | 21425845 |
| problem of interactions between intracellular structures during the neurospora crassa tip growth. | | 2011 | 21369903 |
| a reporter for dsrna response in neurospora crassa. | in the filamentous fungus neurospora, the production of dsrna can elicit a dsrna-induced transcriptional response similar to the interferon response in vertebrates. however, how fungi sense the expression of dsrna and activate gene expression is unknown. in this study, we established a dsrna response reporter system in neurospora crassa. using the dsrna-activated rna-dependent rna polymerase gene rrp-3 promoter, we created an expression construct (prrp-3::myc-al-1) and introduced it into al-1(ko ... | 2011 | 21354420 |
| lilbid-mass spectrometry of the mitochondrial preprotein translocase tom. | in the present work we applied a novel mass spectrometry method termed laser-induced liquid bead ion desorption mass spectrometry (lilbid-ms) to the outer mitochondrial membrane protein translocon tom to analyze its subunit composition and stoichiometry. with tom core complex, purified at high ph, we demonstrate that a tom core complex of neurospora crassa is composed of at least two tom40 and tom22 molecules, respectively, and more than five small tom subunits between 5.5 and 6.4 kda. we show t ... | 2010 | 21339618 |
| traffic of chitin synthase 1 (chs-1) to the spitzenkörper and developing septa in hyphae of neurospora crassa: actin dependence and evidence of distinct microvesicle populations. | we describe the subcellular location of chitin synthase 1 (chs-1), one of seven chitin synthases in neurospora crassa. laser scanning confocal microscopy of growing hyphae showed chs-1-green fluorescent protein (gfp) localized conspicuously in regions of active wall synthesis, namely, the core of the spitzenkörper (spk), the apical cell surface, and developing septa. it was also present in numerous fine particles throughout the cytoplasm plus some large vacuoles in distal hyphal regions. althoug ... | 2011 | 21296914 |
| carrefour mme. gras: a wild-isolated neurospora crassa strain that suppresses meiotic silencing by unpaired dna and uncovers a novel ascospore stability defect. | ordinarily, rip-induced erg-3 mutant neurospora crassa ascospores and their erg(+) siblings do not differ in stability during long-term storage. consequently, the frequency of rip-induced erg-3 mutants remains about constant regardless of the time that has elapsed between ascospore harvest and germination. we found, however, that rip-induced erg-3 mutants were apparently selectively lost with time from among the ascospores stored from a cross with the wild-isolated carrefour mme. gras strain fro ... | 2011 | 21295150 |
| translocations used to generate chromosome segment duplications in neurospora can disrupt genes and create novel open reading frames. | in neurospora crassa, crosses between normal sequence strains and strains bearing some translocations can yield progeny bearing a duplication (dp) of the translocated chromosome segment. here, 30 breakpoint junction sequences of 12 dp-generating translocations were determined. the breakpoints disrupted 13 genes (including predicted genes), and created 10 novel open reading frames. insertion of sequences from lg iii into lg i as translocation t(uk8-18) disrupts the eat-3 gene, which is the orthol ... | 2010 | 21289436 |
| population genomics and local adaptation in wild isolates of a model microbial eukaryote. | elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. here, we have circumvented these issues in the microbial eukaryote n ... | 2011 | 21282627 |
| role of cell wall bound calcium in neurospora crassa. | cell wall bound calcium constitutes a significant fraction (25%) of total mycelia calcium in neurospora crassa. wall bound calcium increases as a function of growth and calcium concentration, while cell wall bound calcium decreases in ca-free medium. removal of wall bound calcium causes its rapid replacement from intracellular pool, inhibited by verapamil, nifedipine, concanamycin a, and wortmanin in a vacuolar mutant (vma-5), but is unaffected by trifluoropyrazine, and calmidizoluim in a calcin ... | 2011 | 21237628 |
| molecular mechanism of the neurospora circadian oscillator. | circadian clocks are the internal time-keeping mechanisms for organisms to synchronize their cellular and physiological processes to the daily light/dark cycles. the molecular mechanisms underlying circadian clocks are remarkably similar in eukaryotes. neurospora crassa, a filamentous fungus, is one of the best understood model organisms for circadian research. in recent years, accumulating data have revealed complex regulation in the neurospora circadian clock at transcriptional, posttranscript ... | 2010 | 21203945 |
| role of individual subunits of the neurospora crassa csn complex in regulation of deneddylation and stability of cullin proteins. | the cop9 signalosome (csn) is an evolutionarily conserved multifunctional complex that controls ubiquitin-dependent protein degradation in eukaryotes. we found seven csn subunits in neurospora crassa in a previous study, but only one subunit, csn-2, was functionally characterized. in this study, we created knockout mutants for the remaining individual csn subunits in n. crassa. by phenotypic observation, we found that loss of csn-1, csn-2, csn-4, csn-5, csn-6, or csn-7 resulted in severe defects ... | 2010 | 21151958 |
| evolution and diversity of a fungal self/nonself recognition locus. | self/nonself discrimination is an essential feature for pathogen recognition and graft rejection and is a ubiquitous phenomenon in many organisms. filamentous fungi, such as neurospora crassa, provide a model for analyses of population genetics/evolution of self/nonself recognition loci due to their haploid nature, small genomes and excellent genetic/genomic resources. in n. crassa, nonself discrimination during vegetative growth is determined by 11 heterokaryon incompatibility (het) loci. cell ... | 2010 | 21124910 |
| biosynthesis of silver, gold and bimetallic nanoparticles using the filamentous fungus neurospora crassa. | the development of production processes that can reduce the environmental impact, offer waste reduction and increase energy efficiency is an important step in the field of application of nanotechnology. in this work the filamentous fungus neurospora crassa was screened and found to be successful for the production of mono and bimetallic au/ag nanoparticles (nps). analysis by scanning electron microscopy (sem), energy dispersive x-ray spectroscopy (eds), and transmission electron microscopy (tem) ... | 2011 | 21087843 |
| dna methylation and normal chromosome behavior in neurospora depend on five components of a histone methyltransferase complex, dcdc. | methylation of dna and of lysine 9 on histone h3 (h3k9) is associated with gene silencing in many animals, plants, and fungi. in neurospora crassa, methylation of h3k9 by dim-5 directs cytosine methylation by recruiting a complex containing heterochromatin protein-1 (hp1) and the dim-2 dna methyltransferase. we report genetic, proteomic, and biochemical investigations into how dim-5 is controlled. these studies revealed dcdc, a previously unknown protein complex including dim-5, dim-7, dim-9, cu ... | 2010 | 21079689 |
| activation and localization of protein kinase c in neurospora crassa. | the neurosporacrassa protein kinase c (npkc) is reported to be a regulator of light responsive genes. it phosphorylates the light receptor wc-1 and regulates the levels of the circadian clock protein frq and transcription of the light-induced albino-2 gene. in mammals, the conventional and novel isoforms of pkc are activated by diacylglycerol (dag), which induces pkc translocation from the cytoplasm to membranes. to investigate the interaction of npkc and dag in neurospora, we constructed a stra ... | 2011 | 21070858 |
| the de novo cytosine methyltransferase drm2 requires intact uba domains and a catalytically mutated paralog drm3 during rna-directed dna methylation in arabidopsis thaliana. | eukaryotic dna cytosine methylation can be used to transcriptionally silence repetitive sequences, including transposons and retroviruses. this silencing is stable between cell generations as cytosine methylation is maintained epigenetically through dna replication. the arabidopsis thaliana dnmt3 cytosine methyltransferase ortholog domains rearranged methyltransferase2 (drm2) is required for establishment of small interfering rna (sirna) directed dna methylation. in mammals piwi proteins and pir ... | 2010 | 21060858 |
| of switches and hourglasses: regulation of subcellular traffic in circadian clocks by phosphorylation. | investigation of the phosphorylation of circadian clock proteins has shown that this modification contributes to circadian timing in all model organisms. phosphorylation alters the stability, transcriptional activity and subcellular localization of clock proteins during the course of a day, such that time-of-day-specific phosphorylation encodes information for measuring time and is crucial for the establishment of an approximately 24-h period. one main feature of molecular timekeeping is the day ... | 2010 | 21052092 |
| degradation of carbohydrate moieties of arabinogalactan-proteins by glycoside hydrolases from neurospora crassa. | arabinogalactan-proteins (agps) are a family of plant proteoglycans having large carbohydrate moieties attached to core-proteins. the carbohydrate moieties of agps commonly have β-(1→3)(1→6)-galactan as the backbone, to which other auxiliary sugars such as l-ara and glca are attached. for the present study, an α-l-arabinofuranosidase belonging to glycoside hydrolase family (ghf) 54, ncaraf1, and an endo-β-(1→6)-galactanase of ghf 5, nc6gal, were identified in neurospora crassa. recombinant ncara ... | 2010 | 20932514 |
| dcaf26, an adaptor protein of cul4-based e3, is essential for dna methylation in neurospora crassa. | dna methylation is involved in gene silencing and genome stability in organisms from fungi to mammals. genetic studies in neurospora crassa previously showed that the cul4-ddb1 e3 ubiquitin ligase regulates dna methylation via histone h3k9 trimethylation. however, the substrate-specific adaptors of this ligase that are involved in the process were not known. here, we show that, among the 16 ddb1- and cul4-associated factors (dcafs) encoded in the n. crassa genome, three interacted strongly with ... | 2010 | 20885793 |
| sequence requirements for ribosome stalling by the arginine attenuator peptide. | the 5' regions of eukaryotic mrnas often contain upstream open reading frames (uorfs). the neurospora crassa arg-2 uorf encodes the 24-residue arginine attenuator peptide (aap). this regulatory uorf-encoded peptide, which is evolutionarily conserved in fungal transcripts specifying an arginine biosynthetic enzyme, functions as a nascent peptide within the ribosomal tunnel and negatively regulates gene expression. the nascent aap causes ribosomes to stall at the uorf stop codon in response to arg ... | 2010 | 20884617 |
| modeling a circadian surface. | experiments that systematically varied t, τ, and photoperiod in neurospora crassa revealed that the traditional nonparametric and parametric approaches could not explain entrainment for all of the tested conditions. the authors have developed a new approach to understanding entrainment that incorporates several features of the old paradigms but allows exploration of the underlying mechanisms in synchronized clocks, making extrapolations from constant conditions to entrained state unnecessary. it ... | 2010 | 20876814 |
| a circadian surface of entrainment: varying t, τ, and photoperiod in neurospora crassa. | the two major prerequisites for a functional circadian system are the generation of an internal day (circadian cycle) and adjusting its length-and phase-to that of the external day (zeitgeber cycle). the generation of circadian cycles can be observed in constant conditions where organisms show a self-sustained, free-running rhythm. their expression depends on the nature of the constant conditions (e.g., constant darkness, dd, or constant light, ll). the mechanism that synchronizes the circadian ... | 2010 | 20876812 |
| temporal and spatial regulation of gene expression during asexual development of neurospora crassa. | in this study we profiled spatial and temporal transcriptional changes during asexual sporulation in the filamentous fungus neurospora crassa. aerial tissue was separated from the mycelium to allow detection of genes specific to each tissue. we identified 2641 genes that were differentially expressed during development, which represents ∼25% of the predicted genes in the genome of this model fungus. on the basis of the distribution of functional annotations of 1102 of these genes, we identified ... | 2010 | 20876563 |
| h2b- and h3-specific histone deacetylases are required for dna methylation in neurospora crassa. | neurospora crassa utilizes dna methylation to inhibit transcription of heterochromatin. dna methylation is controlled by the histone methyltransferase dim-5, which trimethylates histone h3 lysine 9, leading to recruitment of the dna methyltransferase dim-2. previous work demonstrated that the histone deacetylase (hdac) inhibitor trichostatin a caused a reduction in dna methylation, suggesting involvement of histone deacetylation in dna methylation. we therefore created mutants of each of the fou ... | 2010 | 20876559 |
| α-1,6-mannosylation of n-linked oligosaccharide present on cell wall proteins is required for their incorporation into the cell wall in the filamentous fungus neurospora crassa. | the enzyme α-1,6-mannosyltransferase (och-1) is required for the synthesis of galactomannans attached to the n-linked oligosaccharides of neurospora crassa cell wall proteins. the neurospora crassa och-1 mutant has a tight colonial phenotype and a defective cell wall. a carbohydrate analysis of the och-1 mutant cell wall revealed a 10-fold reduction in the levels of mannose and galactose and a total lack of 1,6-linked mannose residues. analysis of the integral cell wall protein from wild-type an ... | 2010 | 20870880 |
| circadian oscillators in eukaryotes. | the biological clock, present in nearly all eukaryotes, has evolved such that organisms can adapt to our planet's rotation in order to anticipate the coming day or night as well as unfavorable seasons. as all modern high-precision chronometers, the biological clock uses oscillation as a timekeeping element. in this review, we describe briefly the discovery, historical development, and general properties of circadian oscillators. the issue of temperature compensation (tc) is discussed, and our pr ... | 2010 | 20836046 |
| vivid interacts with the white collar complex and frequency-interacting rna helicase to alter light and clock responses in neurospora. | the photoreceptor and pas/lov protein vivid (vvd) modulates blue-light signaling and influences light and temperature responses of the circadian clock in neurospora crassa. one of the main actions of vvd on the circadian clock is to influence circadian clock phase by regulating levels of the transcripts encoded by the central clock gene frequency (frq). how this regulation is achieved is unknown. here we show that vvd interacts with complexes central for circadian clock and blue-light signaling, ... | 2010 | 20807745 |
| new insights into the circadian clock in chlamydomonas. | the unicellular green alga chlamydomonas reinhardtii has long been used in research on circadian rhythm. various circadian rhythms in behavior and physiology including phototaxis, chemotaxis, the cell division cycle, uv sensitivity, stickiness to glass (changes in properties of the cell surface), and starch content are observed in this alga. soon after the isolation of clock mutants in drosophila melanogaster and neurospora crassa, clock mutants were also isolated in chlamydomonas. whereas genes ... | 2010 | 20797685 |
| entrainment elicits period aftereffects in neurospora crassa. | circadian clocks continue to oscillate in constant conditions with their own period (tau) and entrain to a cyclic environment by adjusting their intrinsic period to that of the zeitgeber. when circadian clocks are released from entrained to constant conditions, the tau of their initial free-run often depends on the nature of the prior zeitgeber. these postentrainment effects on period (tau-aftereffects) have predominantly been reported for animals but, so far, not fungi. the authors therefore in ... | 2010 | 20795879 |
| physical interaction between vivid and white collar complex regulates photoadaptation in neurospora. | photoadaptation, the ability to attenuate a light response on prolonged light exposure while remaining sensitive to escalating changes in light intensity, is essential for organisms to decipher time information appropriately, yet the underlying molecular mechanisms are poorly understood. in neurospora crassa, vivid (vvd), a small lov domain containing blue-light photoreceptor protein, affects photoadaptation for most if not all light-responsive genes. we report that there is a physical interacti ... | 2010 | 20733070 |
| a proteomic approach towards the identification of the matrix protein content of the two types of microbodies in neurospora crassa. | microbodies (peroxisomes) comprise a class of organelles with a similar biogenesis but remarkable biochemical heterogeneity. here, we purified the two distinct microbody family members of filamentous fungi, glyoxysomes and woronin bodies, from neurospora crassa and analyzed their protein content by hplc/esi-ms/ms. in the purified woronin bodies, we unambiguously identified only hexagonal 1 (hex1), suggesting that the matrix is probably exclusively filled with the hex1 hexagonal crystal. the prot ... | 2010 | 20707002 |
| transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex. | light signaling pathways and circadian clocks are inextricably linked and have profound effects on behavior in most organisms. here, we used chromatin immunoprecipitation (chip) sequencing to uncover direct targets of the neurospora crassa circadian regulator white collar complex (wcc). the wcc is a blue-light receptor and the key transcription factor of the circadian oscillator. it controls a transcriptional network that regulates ∼20% of all genes, generating daily rhythms and responses to lig ... | 2010 | 20675579 |
| cr(vi) removal on fungal biomass of neurospora crassa: the importance of dissolved organic carbons derived from the biomass to cr(vi) reduction. | interactions of toxic cr(vi) with renewable biomaterials are considered an important pathway for cr(vi) removal in ecosystems. biomaterials are susceptible to dissolution, and their dissolved derivatives may provide an alternative to surface-involved pathway for scavenging of cr(vi). in this study, dissolved organic carbon (doc) derived from neurospora crassa biomass was investigated. the proportion of cr(vi) reduction by doc to that on biomass was determined to evaluate the importance of doc to ... | 2010 | 20669959 |
| structure and engineering of l-arabinitol 4-dehydrogenase from neurospora crassa. | l-arabinitol 4-dehydrogenase (lad) catalyzes the conversion of l-arabinitol into l-xylulose with concomitant nad(+) reduction. it is an essential enzyme in the development of recombinant organisms that convert l-arabinose into fuels and chemicals using the fungal l-arabinose catabolic pathway. here we report the crystal structure of lad from the filamentous fungus neurospora crassa at 2.6 a resolution. in addition, we created a number of site-directed variants of n. crassa lad that are capable o ... | 2010 | 20655316 |
| in vitro activities of the multifunctional rna silencing polymerase qde-1 of neurospora crassa. | qde-1 is an rna- and dna-dependent rna polymerase that has functions in the rna silencing and dna repair pathways of the filamentous fungus neurospora crassa. the crystal structure of the dimeric enzyme has been solved, and the fold of its catalytic core is related closely to that of eukaryotic dna-dependent rna polymerases. however, the specific activities of this multifunctional enzyme are still largely unknown. in this study, we characterized the in vitro activities of the n-terminally trunca ... | 2010 | 20647305 |
| neurospora illuminates fungal photoreception. | light not only is indispensable as an energy source for life on earth but also serves as an essential environmental cue conveying the information of daily and seasonal time to organisms across different kingdoms. although the molecular mechanisms underlying light responses are actively explored in various light-sensitive organisms, these studies are either hindered by the complexity of the systems or an incomplete familiarity with the light signaling components involved in the scheme. therefore, ... | 2010 | 20637887 |
| qip, a component of the vegetative rna silencing pathway, is essential for meiosis and suppresses meiotic silencing in neurospora crassa. | among the processes that play essential roles in both genome defense and organism survival are those involved in chromosome comparison. they are acutely active in the meiotic cells of neurospora crassa, where they evaluate the mutual identity of homologs by a process we call trans-sensing. when nonsymmetrical regions are found, they are silenced. the known molecular components of this meiotic silencing machinery are related to rna-dependent rna polymerases, argonautes and dicers, suggesting that ... | 2010 | 20592262 |
| real-time fluorescence lifetime imaging system with a 32 x 32 0.13microm cmos low dark-count single-photon avalanche diode array. | a compact real-time fluorescence lifetime imaging microscopy (flim) system based on an array of low dark count 0.13microm cmos single-photon avalanche diodes (spads) is demonstrated. fast background-insensitive fluorescence lifetime determination is achieved by use of a recently proposed algorithm called 'integration for extraction method' (iem) [j. opt. soc. am. a 25, 1190 (2008)]. here, iem is modified for a wider resolvability range and implemented on the fpga of the new spad array imager. we ... | 2010 | 20588879 |
| [comparative analysis of respiratory activity in the wild type strain of neurospora crassa and its photoreceptor complex mutants]. | cell respiratory activity of protoplasts obtained from the wild type of neurospora crassa and photoreceptor complex wcc--white collar 1 (wc-1) and white collar 2 (wc-2)--mutants of neurospora crassa strains was investigated. respiration inhibition by kcn in the presence of 25 mm succinate was similar in all strains and did not exceed 83-85% against control. the significant induction of kcn-resistant respiratory pathway occurred under 1% glucose oxidation in wc-1 and wc-2 mutants if compared with ... | 2013 | 20586289 |
| robustness from flexibility in the fungal circadian clock. | robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. a key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. in all organisms, the clock circuits typically comprise multiple interloc ... | 2010 | 20576110 |
| atm and atr homologes of neurospora crassa are essential for normal cell growth and maintenance of chromosome integrity. | genome integrity is maintained by many cellular mechanisms in eukaryotes. one such mechanism functions during the cell cycle and is known as the dna damage checkpoint. in the filamentous fungus neurospora crassa, mus-9 and mus-21 are homologes of two key factors of the mammalian dna damage checkpoint, atr and atm, respectively. we previously showed that mus-9 and mus-21 mutants are sensitive to dna damage and that each mutant shows a characteristic growth defect: conidia from the mus-9 mutant ha ... | 2010 | 20553930 |
| qip, a protein that converts duplex sirna into single strands, is required for meiotic silencing by unpaired dna. | rna interference (rnai) depends on the production of small rna to regulate gene expression in eukaryotes. two rnai systems exist to control repetitive selfish elements in neurospora crassa. quelling targets transgenes during vegetative growth, whereas meiotic silencing by unpaired dna (msud) silences unpaired genes during meiosis. the two mechanisms require common rnai proteins, such as rna-directed rna polymerases, dicers, and argonaute slicers. we have previously demonstrated that, while quell ... | 2010 | 20551436 |
| turgor and net ion flux responses to activation of the osmotic map kinase cascade by fludioxonil in the filamentous fungus neurospora crassa. | the internal hydrostatic pressure (turgor) of the filamentous fungus neurospora crassa is regulated at about 400-500 kilopascals, primarily by an osmotic map kinase cascade which activates ion uptake from the extracellular medium and glycerol synthesis. in the absence of hyperosmotic stress, the phenylpyrrole fungicide fludioxonil activates the osmotic map kinase cascade, resulting in cell death. turgor, the electrical potential and net ion fluxes were measured after treatment with fludioxonil. ... | 2010 | 20546911 |
| reinforced postmating reproductive isolation barriers in neurospora, an ascomycete microfungus. | maladaptive hybridization promotes reinforcement, selection for stringent reproductive isolation barriers during speciation. reinforcement is suspected when barriers between sympatric populations are stronger than allopatric barriers, and particularly when stronger barriers evolve in the species and sex suffering the greatest costs of hybridization. canonically, reinforcement involves premating barriers. selection for postmating barriers is controversial, but theoretically possible. we examined ... | 2010 | 20546092 |
| deletion of a novel f-box protein, mus-10, in neurospora crassa leads to altered mitochondrial morphology, instability of mtdna and senescence. | while mitochondria are renowned for their role in energy production, they also perform several other integral functions within the cell. thus, it is not surprising that mitochondrial dysfunction can negatively impact cell viability. although mitochondria have received an increasing amount of attention in recent years, there is still relatively little information about how proper maintenance of mitochondria and its genomes is achieved. the neurospora crassa mus-10 mutant was first identified thro ... | 2010 | 20516500 |
| characterization of the temperature-sensitive mutations un-7 and png-1 in neurospora crassa. | the model filamentous fungus neurospora crassa has been studied for over fifty years and many temperature-sensitive mutants have been generated. while most of these have been mapped genetically, many remain anonymous. the mutation in the n. crassa temperature-sensitive lethal mutant un-7 was identified by a complementation based approach as being in the open reading frame designated ncu00651 on linkage group i. other mutations in this gene have been identified that lead to a temperature-sensitiv ... | 2010 | 20502699 |
| catalase evolved to concentrate h2o2 at its active site. | catalase is a homo-tetrameric enzyme that has its heme active site deeply buried inside the protein. its only substrate, hydrogen peroxide (h2o2), reaches the heme through a 45 a-long channel. large-subunit catalases, but not small-subunit catalases, have a loop (gate loop) that interrupts the major channel. two accesses lead to a gate that opens the final section of the channel to the heme; gates from the r-related subunits are interconnected. using molecular dynamic simulations of the neurospo ... | 2010 | 20494646 |
| membrane fluidity determines sensitivity of filamentous fungi to chitosan. | the antifungal mode of action of chitosan has been studied for the last 30 years, but is still little understood. we have found that the plasma membrane forms a barrier to chitosan in chitosan-resistant but not chitosan-sensitive fungi. the plasma membranes of chitosan-sensitive fungi were shown to have more polyunsaturated fatty acids than chitosan-resistant fungi, suggesting that their permeabilization by chitosan may be dependent on membrane fluidity. a fatty acid desaturase mutant of neurosp ... | 2010 | 20487294 |
| functional characterization of mat1-1-specific mating-type genes in the homothallic ascomycete sordaria macrospora provides new insights into essential and nonessential sexual regulators. | mating-type genes in fungi encode regulators of mating and sexual development. heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. to analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted eac ... | 2010 | 20435701 |
| mapping of lysine methylation and acetylation in core histones of neurospora crassa. | core histones are susceptible to a variety of post-translational modifications (ptms), among which methylation and acetylation play critical roles in various chromatin-dependent processes. the nature and biological functions of these ptms have been extensively studied in plants, animals, and yeasts. in contrast, the histone modifications in neurospora crassa, a convenient model organism for multicellular eukaryotes, remained largely undefined. in this study, we used several mass spectrometric te ... | 2010 | 20433192 |
| biotransformation of alpha-cedrol and caryophyllene oxide by the fungus neurospora crassa. | incubation of alpha-cedrol and caryophyllene oxide with neurospora crassa afforded 12beta-hydroxy cedrol, 10alpha-hydroxy cedrol, and 3beta-hydroxy cedrol, and 12beta-hydroxy caryophyllene oxide as major metabolites, respectively. the antibacterial and radical scavenging activities of the metabolites were evaluated in vitro using broth microdilution and bioauthographic techniques. however, no significant antibacterial and antioxidant activities were observed when compared with those of standard ... | 2010 | 20433062 |
| dna methylation and the formation of heterochromatin in neurospora crassa. | studies of the control and function of dna methylation in neurospora crassa have led to a greater understanding of heterochromatin formation. dna methylation in neurospora is dependent on trimethylation of histone h3 lysine 9 (h3k9me3) by the histone methyltransferase, dim-5. the linkage between these two methyl marks is facilitated by heterochromatin protein 1 (hp1), which serves as an adapter protein. hp1 binds to the h3k9me3 and recruits the dna methyltransferase, dim-2. although hp1 links h3 ... | 2010 | 20407471 |
| high efficient gene targeting on the agamous gene in an arabidopsisatlig4 mutant. | gene targeting induced by homologous integration of a foreign dna segment into a chromosomal target sequence enables precise disruption or replacement of genes of interest and provides an effective means to analyze gene function, and also becomes an useful technique for breeding. but, integration of introduced dna fragments is predominantly non-homologous in most species. however, we presented high-efficient homologous integration in disruptants of non-homologous end joining (nhej), that is, the ... | 2010 | 20406622 |
| identification of dim-7, a protein required to target the dim-5 h3 methyltransferase to chromatin. | functionally distinct chromatin domains are delineated by distinct posttranslational modifications of histones, and in some organisms by differences in dna methylation. proper establishment and maintenance of chromatin domains is critical but not well understood. we previously demonstrated that heterochromatin in the filamentous fungus neurospora crassa is marked by cytosine methylation directed by trimethylated lysine 9 on histone h3 (h3k9me3). h3k9me3 is the product of the dim-5 lysine methylt ... | 2010 | 20404183 |
| de novo assembly of a 40 mb eukaryotic genome from short sequence reads: sordaria macrospora, a model organism for fungal morphogenesis. | filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by sanger sequencing. while next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and chip analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size an ... | 2010 | 20386741 |
| effects of prd circadian clock mutations on frq-less rhythms in neurospora. | rhythmic conidiation (spore formation) in neurospora crassa provides a model system for investigating the molecular mechanisms of circadian rhythmicity. a feedback loop involving the frq, wc-1, and wc-2 gene products (frq/ wcc) is an important component of the mechanism; however, rhythmic conidiation can still be observed when these gene products are absent. the nature of the oscillator(s) that drives this frq-less rhythmicity (flo) is an important question in neurospora circadian biology. we ha ... | 2010 | 20348458 |
| marker fusion tagging, a new method for production of chromosomally encoded fusion proteins. | a new gene-tagging method (marker fusion tagging [mft]) is demonstrated for neurospora crassa and magnaporthe oryzae. translational fusions between the hygromycin b resistance gene and various markers are inserted into genes of interest by homologous recombination to produce chromosomally encoded fusion proteins. this method can produce tags at any position and create deletion alleles that maintain n- and c-terminal sequences. we show the utility of mft by producing enhanced green fluorescent pr ... | 2010 | 20348390 |
| live-cell imaging of microtubule dynamics in hyphae of neurospora crassa. | due to the large number of microtubules in the wild-type strain, total internal reflection fluorescence (tirf) microscopy was used to study cortical microtubule dynamics in leading hyphae of neurospora crassa expressing beta-tubulin-gfp. detection of plus-end dynamics of individual microtubule was much improved with this approach compared to the other commonly used methods such as confocal and widefield fluorescence microscopy. in order to address the roles of motor proteins in microtubule dynam ... | 2010 | 20238275 |
| biochemical methods used to study the gene expression and protein complexes in the filamentous fungus neurospora crassa. | biochemical approaches are powerful tools for investigating mechanisms of biological processes. here, we describe several biochemical approaches that have been successfully in our laboratory to study the filamentous fungus neurospora crassa. these approaches include protein extraction and western blot analysis, protein purification using epitope-tagged fusion protein, protein immunoprecipitation (ip) and chromatin immunoprecipitation (chip) assays. these methods can also be modified for use in o ... | 2010 | 20238270 |
| gene silencing for functional analysis: assessing rnai as a tool for manipulation of gene expression. | the availability of a large number of gene-disrupted mutants (either from natural mutants' collections or from knockout projects) is a great advantage for functional analysis studies. however, disfunction of many fungal genes, involved in key developmental processes, leads to dramatic and pleotropic changes in cell morphology, conferring a major difficulty in studying null mutants. therefore, obtaining variable levels of reduction in gene expression, especially of essential genes or genes whose ... | 2010 | 20238262 |
| the dmm complex prevents spreading of dna methylation from transposons to nearby genes in neurospora crassa. | transposable elements are common in genomes and must be controlled. many organisms use dna methylation to silence such selfish dna, but the mechanisms that restrict the methylation to appropriate regions are largely unknown. we identified a jmjc domain protein in neurospora, dna methylation modulator-1 (dmm-1), that prevents aberrant spreading of dna and histone h3k9 methylation from inactivated transposons into nearby genes. mutation of a conserved residue within the jmjc fe(ii)-binding site ab ... | 2010 | 20139222 |
| systematic overrepresentation of dna termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear dna molecules. | analysis of fungal genome sequence assemblies reveals that telomeres are poorly represented even though telomeric reads tend to be superabundant. we surmised that the problem might lie in the dna shearing conditions used to create clone libraries for genome sequencing. | 2010 | 20122283 |
| circadian rhythms in neurospora crassa: dynamics of the clock component frequency visualized using a fluorescent reporter. | the frequency (frq) gene of neurospora crassa has long been considered essential to the function of this organism's circadian rhythm. increasingly, deciphering the coupling of core oscillator genes such as frq to the output pathways of the circadian rhythm has become a major focus of circadian research. to address this coupling it is critical to have a reporter of circadian activity that can deliver high resolution spatial and temporal information about the dynamics of core oscillatory proteins ... | 2010 | 20051268 |