NEUROSPORA eNEWS #18
OCTOBER 2011
CONTENTS
Neurospora Policy Committee
Neurospora 2012 Conference
Nominations for Awards at Neurospora 2012
Fungal Genetics Stock Center News
Functional Genomics and Systems Biology Program Project
News
Quantitative Trait Analysis Project News
New Organelle Instructional Video
Neurospora Publication List, April-October 2011
Michael Freitag, Chair
Meritxell Riquelme, past Chair
Matthew Sachs
Stephan Seiler
Kevin McCluskey, Ex officio
NEUROSPORA 2012 CONFERENCE:
The Neurospora Policy Committee invites you and your associates to attend the Neurospora 2012 meeting, to be held March 8th - 11th, 2012 at Asilomar, California. Registration materials and instructions for abstract submission will be found, by the end of October, at the Fungal Genetics Stock Center site: http://www.fgsc.net/asil2012/neurospora_2012.htm
Registration and abstract submission deadlines are December 15, 2011. The overall meeting format will be similar to previous meetings, except that we scheduled more free time during the afternoon hours for networking. While we will have five sessions with invited speakers, all participants are encouraged to present their work as posters and several speakers for each session will be selected from submitted abstracts.
The preliminary schedule includes sessions on:
I. Cell Biology and Morphogenesis
II. Gene Regulation
III. Signalling and Development
IV. Light and Circadian Clock
V. Genomics, Evolution and Technology
Come to Neurospora 2012 to celebrate the leading system for research in the genetics of filamentous fungi!
NOMINATIONS FOR AWARDS AT NEUROSPORA 2012:
We call for nominations, which should be received by the chair of the Neurospora Policy Committee by December 15, 2011. The full rules are available at the
FGSC website.
Beadle and Tatum award. This award is intended for young investigators, whereby the award will help to advance their careers and to give more visibility to Neurospora as a research organism.
B.O. Dodge awards. Two awards are made at each Neurospora meeting in recognition of the fact that a significant part of the success of Neurospora as a model research organism is due to the collaborative nature of its research community. Certain individuals who have made exceptional contributions towards the community will be acknowledged by the awards.
Perkins Fund award. This award supports one outstanding student and one postdoctoral fellow to attend the Neurospora and Fungal Genetics Conferences. Contributions to the Perkins fund may be made via the Genetics Society of America (http://www.genetics-gsa.org/).
FUNGAL GENETICS STOCK CENTER NEWS:
The FGSC has distributed over 1200 individual Neurospora strains as well as 500 96-well plates containing arrayed Neurospora mutants so far in 2011.
The FGSC submitted a Research Coordination Network proposal for the US culture collection community in the past few weeks. People should send citations to recent articles that were only possible because they use materials from culture collections, including the FGSC.
FUNCTIONAL ANALYSIS AND SYSTEMS BIOLOGY PROGRAM PROJECT NEWS:
We have completed our first attempt to knock out every gene in the genome, and most of the mutants have already been deposited at the FGSC. The last 216 mutants are at the final stage of PCR validation or ready to ship. Our latest numbers are 7861 mutated genes (8077, counting the last 216), with 6369 mutants deposited as homokaryons and 1492 as heterokaryons, for 11,301 strains total. New primers have been designed for the failures from the first pass and new genes discovered during the more recent genome annotation, for a total of 1656 genes (9733 total in genome). So far, we have 4 plates of new cassettes and 160 cassettes have been transformed into Neurospora.
A publication summarizing detailed annotation and phenotypes of the Neurospora serine/threonine kinase knockout mutants is in press at Eukaryotic Cell (Park, Servin et al., 2011; see in publication list, below). The mutants are available from the FGSC.
The Filamentous Fungal Gene Expression Database (FFGED), an "active experiment" database that can be used to organize, store, and analyze transcriptomic data pre- or post-publication (Zhang & Townsend, 2010), has been enhanced to accept next-generation transcriptomic data (ChIP-seq and RNA-seq). Support for uploading large raw data fields is provided via FTP. A "template" function for metadata has also been added, facilitating rapid entry of multiple experiments similar to previously submitted experiments.
QUANTITATIVE TRAIT
ANALYSIS PROJECT NEWS
An
NIH R24 grant entitled "The development of genetics and genomics for
analysis of quantitative traits in the model filamentous fungus, Neurospora
crassa" is led by Rachel Brem, Louise Glass and John Taylor (UC Berkeley).
The goal of this project is to develop and distribute tools to identify
genes responsible for any phenotype that can be analyzed in Neurospora.
High-throughput RNA-sequencing on 112 wild isolates from a Louisiana (LA)
population of N. crassa has been
completed. RNA sequencing has also been completed on
19 wild isolates from a Caribbean population of
N. crassa as well as 5 South
American, 4 Panamanian, 1 West African and 4 Texas isolates. Relative
expression levels have been determined for genes from each isolate and each
isolate has been genotyped at approximately 74,000 high-frequency SNP
positions. Within the LA population, a whole-genome association study has
been conducted to associate transcripts with SNPs affecting their expression
both in cis and in
trans. SNPs that are potential master regulators of transcription
have been identified within the LA population. Several statistically
significant transcript sets with common putative regulators that fall into
defined functional categories have been identified.
Current work is ongoing to test for linkage between SNPs and several phenotypes of interest including germling communication and hyphal architecture.
Strains along with expression data and SNP maps will be made available. Please contact Louise Glass (lglass@berkeley.edu) or Charles Hall (charleshall@berkeley.edu) for information.
NEW ORGANELLE INSTRUCTIONAL VIDEO:
Barry Bowman has made an instructional video illustrating the structure and distribution of organelles in Neurospora. The video is five minutes long and is narrated. Photos and time-lapse movies were obtained using confocal microscopy and Red or Green Fluorescent Proteins. The video shows nuclei, the endoplasmic reticulum, golgi, and mitochondria. It also illustrates the different types of structures in which vacuolar proteins are found. The video can be seen on the FGSC website or at http://www.youtube.com/watch?v=Salk9GPWFgg. (The name on Youtube is "Neurospora video.") A version with higher resolution can be obtained from FGSC or from Barry Bowman (bbowman@ucsc.edu).
Submitted by the community or retrieved from
Pubmed using “Neurospora” as the search term.
1: Sun J, Glass NL. Identification of the CRE-1 Cellulolytic Regulon in
Neurospora crassa. PLoS One. 2011;6(9):e25654. Epub 2011 Sep 29. PubMed
PMID: 21980519; PubMed Central PMCID: PMC3183063.
2: Lackey SW, Wideman JG, Kennedy EK, Go NE, Nargang FE. The Neurospora
crassa TOB Complex: Analysis of the Topology and Function of Tob38 and
Tob37. PLoS One. 2011;6(9):e25650. Epub 2011 Sep 28. PubMed PMID: 21980517;
PubMed Central PMCID: PMC3182244.
3: Park G, Servin J, Turner GE, Altamirano L, Colot HV, Collopy P,
Litvinkova L, Li L, Jones CA, Diala FG, Dunlap JC, Borkovich KA. Global
analysis of serine-threonine protein kinase genes in Neurospora crassa.
Eukaryot Cell. 2011 Sep 30. [Epub ahead of print] PubMed PMID: 21965514.
4: Roper M, Ellison C, Taylor JW, Glass NL. Nuclear and genome dynamics in
multinucleate ascomycete fungi. Curr Biol. 2011 Sep 27;21(18):R786-93.
PubMed PMID: 21959169; PubMed Central PMCID: PMC3184236.
5: Summers WA, Wilkins JA, Dwivedi RC, Ezzati P, Court DA. Mitochondrial
dysfunction resulting from the absence of mitochondrial porin in Neurospora
crassa. Mitochondrion. 2011 Sep 18. [Epub ahead of print] PubMed PMID:
21946565.
6: Li C, Wang E, Wang J. Landscape, flux, correlation, resonance, coherence,
stability, and key network wirings of stochastic circadian oscillation.
Biophys J. 2011 Sep 21;101(6):1335-44. Epub 2011 Sep 20. PubMed PMID:
21943414; PubMed Central PMCID: PMC3177066.
7: Gilbert LB, Chae L, Kasuga T, Taylor JW. Array Comparative Genomic
Hybridizations: Assessing the Ability to Recapture Evolutionary
Relationships Using an In Silico Approach. BMC Genomics. 2011 Sep
21;12(1):456. [Epub ahead of print] PubMed PMID: 21936922.
8: Jeon WY, Yoon BH, Ko BS, Shim WY, Kim JH. Xylitol production is increased
by expression of codon-optimized Neurospora crassa xylose reductase gene in
Candida tropicalis. Bioprocess Biosyst Eng. 2011 Sep 16. [Epub ahead of
print] PubMed PMID: 21922311.
9: Petříčková A, Veselá AB, Kaplan O, Kubáč D, Uhnáková B, Malandra A,
Felsberg J, Rinágelová A, Weyrauch P, Křen V, Bezouška K, Martínková L.
Purification and characterization of heterologously expressed nitrilases
from filamentous fungi. Appl Microbiol Biotechnol. 2011 Sep 3. [Epub ahead
of print] PubMed PMID: 21892598.
10: Ramsey KM, Bass J. Circadian Clocks in Fuel Harvesting and Energy
Homeostasis. Cold Spring Harb Symp Quant Biol. 2011 Sep 2. [Epub ahead of
print] PubMed PMID: 21890641.
11: Gessmann D, Flinner N, Pfannstiel J, Schlösinger A, Schleiff E,
Nussberger S, Mirus O. Structural elements of the mitochondrial preprotein-conducting
channel Tom40 dissolved by bioinformatics and mass spectrometry. Biochim
Biophys Acta. 2011 Aug 23. [Epub ahead of print] PubMed PMID: 21888892.
12: Querfurth C, Diernfellner AC, Gin E, Malzahn E, Höfer T, Brunner M.
Circadian conformational change of the Neurospora clock protein FREQUENCY
triggered by clustered hyperphosphorylation of a basic domain. Mol Cell.
2011 Sep 2;43(5):713-22. PubMed PMID: 21884974.
13: Menet JS, Rosbash M. A new twist on clock protein phosphorylation: a
conformational change leads to protein degradation. Mol Cell. 2011 Sep
2;43(5):695-7. PubMed PMID: 21884970.
14: Sinan S, Yuan X, Russell R. The Azoarcus group I intron ribozyme
misfolds and is accelerated for refolding by ATP-dependent RNA chaperone
proteins. J Biol Chem. 2011 Aug 30. [Epub ahead of print] PubMed PMID:
21878649.
15: Turner E, Jacobson DJ, Taylor JW. Genetic architecture of a reinforced,
postmating, reproductive isolation barrier between Neurospora species
indicates evolution via natural selection. PLoS Genet. 2011
Aug;7(8):e1002204. Epub 2011 Aug 18. PubMed PMID: 21876674; PubMed Central
PMCID: PMC3158040.
16: Gladyshev EA, Arkhipova IR. A widespread class of reverse
transcriptase-related cellular genes. Proc Natl Acad Sci U S A. 2011 Aug 29.
[Epub ahead of print] PubMed PMID: 21876125.
17: Vaidya AT, Chen CH, Dunlap JC, Loros JJ, Crane BR. Structure of a
light-activated LOV protein dimer that regulates transcription. Sci Signal.
2011 Aug 2;4(184):ra50. PubMed PMID: 21868352.
18: Tiwari A, Korripally P, Adhikarla H, Patnala K, Pamarthi MM, Bhanoori M.
Expression and functional characterisation of TNC, a high-affinity nickel
transporter from Neurospora crassa. Fungal Genet Biol. 2011
Nov;48(11):1020-6. Epub 2011 Aug 5. PubMed PMID: 21840412.
19: Kim H, Ridenour JB, Dunkle LD, Bluhm BH. Regulation of stomatal tropism
and infection by light in Cercospora zeae-maydis: evidence for coordinated
host/pathogen responses to photoperiod? PLoS Pathog. 2011 Jul;7(7):e1002113.
Epub 2011 Jul 28. PubMed PMID: 21829344; PubMed Central PMCID: PMC3145785.
20: Crosthwaite SK. Circadian timekeeping in Neurospora crassa and
Synechococcus elongatus. Essays Biochem. 2011 Jun 30;49(1):37-51. doi:
10.1042/BSE0490037. PubMed PMID: 21819383.
21: Díaz-Sánchez V, Estrada AF, Trautmann D, Limón MC, Al-Babili S, Avalos
J. Analysis of al-2 mutations in Neurospora. PLoS One. 2011;6(7):e21948.
Epub 2011 Jul 19. PubMed PMID: 21818281; PubMed Central PMCID: PMC3139582.
22: Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC. CHD1 remodels
chromatin and influences transient DNA methylation at the clock gene
frequency. PLoS Genet. 2011 Jul;7(7):e1002166. Epub 2011 Jul 21. PubMed
PMID: 21811413; PubMed Central PMCID: PMC3140994.
23: Pshennikova ES, Filippovich SY, Bachurina GP, Ponomareva VD, Malygin AG.
[The different effects of carbon dioxide on the toxicity of silver ions for
prokaryotic and eukaryotic microorganisms]. Izv Akad Nauk Ser Biol. 2011
May-Jun;(3):354-7. Russian. PubMed PMID: 21790000.
24: Gonçalves RD, Cupertino FB, Freitas FZ, Luchessi AD, Bertolini MC. A
genome-wide screen for Neurospora crassa transcription factors regulating
glycogen metabolism. Mol Cell Proteomics. 2011 Jul 18. [Epub ahead of print]
PubMed PMID: 21768394.
25: Inoue H. Exploring the processes of DNA repair and homologous
integration in Neurospora. Mutat Res. 2011 Jul-Oct;728(1-2):1-11. Epub 2011
Jul 2. PubMed PMID: 21757027.
26: Ellison CE, Stajich JE, Jacobson DJ, Natvig DO, Lapidus A, Foster B,
Aerts A, Riley R, Lindquist EA, Grigoriev IV, Taylor JW. Massive Changes in
Genome Architecture Accompany the Transition to Self-Fertility in the
Filamentous Fungus Neurospora tetrasperma. Genetics. 2011 Sep;189(1):55-69.
Epub 2011 Jul 12. PubMed PMID: 21750257.
27: Wright SJ, Inchausti R, Eaton CJ, Krystofova S, Borkovich KA. RIC8 Is a
Guanine-Nucleotide Exchange Factor for G{alpha} Subunits That Regulates
Growth and Development in Neurospora crassa. Genetics. 2011
Sep;189(1):165-76. Epub 2011 Jul 12. PubMed PMID: 21750256.
28: Díaz-Sánchez V, Estrada AF, Trautmann D, Al-Babili S, Avalos J. The gene
carD encodes the aldehyde dehydrogenase responsible for neurosporaxanthin
biosynthesis in Fusarium fujikuroi. FEBS J. 2011 Sep;278(17):3164-76. doi:
10.1111/j.1742-4658.2011.08242.x. Epub 2011 Aug 8. PubMed PMID: 21749649.
29: Mallam AL, Jarmoskaite I, Tijerina P, Del Campo M, Seifert S, Guo L,
Russell R, Lambowitz AM. Solution structures of DEAD-box RNA chaperones
reveal conformational changes and nucleic acid tethering by a basic tail.
Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12254-9. Epub 2011 Jul 11.
PubMed PMID: 21746911; PubMed Central PMCID: PMC3145681.
30: Phillips CM, Iavarone AT, Marletta MA. Quantitative proteomic approach
for cellulose degradation by Neurospora crassa. J Proteome Res. 2011 Sep
2;10(9):4177-85. Epub 2011 Aug 1. PubMed PMID: 21744778.
31: Li S, Motavaze K, Kafes E, Suntharalingam S, Lakin-Thomas P. A new
mutation affecting FRQ-less rhythms in the circadian system of Neurospora
crassa. PLoS Genet. 2011 Jun;7(6):e1002151. Epub 2011 Jun 23. PubMed PMID:
21731506; PubMed Central PMCID: PMC3121751.
32: Deka R, Kumar R, Tamuli R. Neurospora crassa homologue of Neuronal
Calcium Sensor-1 has a role in growth, calcium stress tolerance, and
ultraviolet survival. Genetica. 2011 Jul;139(7):885-94. Epub 2011 Jul 5.
PubMed PMID: 21728141.
33: Dang Y, Yang Q, Xue Z, Liu Y. RNA interference in fungi: pathways,
functions, and applications. Eukaryot Cell. 2011 Sep;10(9):1148-55. Epub
2011 Jul 1. PubMed PMID: 21724934.
34: Mager F, Gessmann D, Nussberger S, Zeth K. Functional refolding and
characterization of two Tom40 isoforms from human mitochondria. J Membr
Biol. 2011 Jul;242(1):11-21. Epub 2011 Jun 30. PubMed PMID: 21717124.
35: Baker CL, Loros JJ, Dunlap JC. The circadian clock of Neurospora crassa.
FEMS Microbiol Rev. 2011 Jun 27. doi: 10.1111/j.1574-6976.2011.00288.x. [Epub
ahead of print] PubMed PMID: 21707668.
36: Ha SJ, Wei Q, Kim SR, Galazka JM, Cate J, Jin YS. Cofermentation of
cellobiose and galactose by an engineered Saccharomyces cerevisiae strain.
Appl Environ Microbiol. 2011 Aug 15;77(16):5822-5. Epub 2011 Jun 24. PubMed
PMID: 21705527; PubMed Central PMCID: PMC3165266.
37: Tsumoto K, Kurosawa G, Yoshinaga T, Aihara K. Modeling light adaptation
in circadian clock: prediction of the response that stabilizes entrainment.
PLoS One. 2011;6(6):e20880. Epub 2011 Jun 16. PubMed PMID: 21698191; PubMed
Central PMCID: PMC3116846.
38: Tang X, Dong W, Griffith J, Nilsen R, Matthes A, Cheng KB, Reeves J,
Schuttler HB, Case ME, Arnold J, Logan DA. Systems biology of the qa gene
cluster in Neurospora crassa. PLoS One. 2011;6(6):e20671. Epub 2011 Jun 14.
PubMed PMID: 21695121; PubMed Central PMCID: PMC3114802.
39: Cohen E, Koch L, Thu KM, Rahamim Y, Aluma Y, Ilan M, Yarden O, Carmeli
S. Novel terpenoids of the fungus Aspergillus insuetus isolated from the
Mediterranean sponge Psammocinia sp. collected along the coast of Israel.
Bioorg Med Chem. 2011 May 30. [Epub ahead of print] PubMed PMID: 21676619.
40: Singh S, Korripally P, Vancheeswaran R, Eapen S. Transgenic Nicotiana
tabacum plants expressing a fungal copper transporter gene show enhanced
acquisition of copper. Plant Cell Rep. 2011 Oct;30(10):1929-38. Epub 2011
Jun 14. PubMed PMID: 21671073.
41: Fu C, Iyer P, Herkal A, Abdullah J, Stout A, Free SJ. Identification and
characterization of genes required for cell-to-cell fusion in Neurospora
crassa. Eukaryot Cell. 2011 Aug;10(8):1100-9. Epub 2011 Jun 10. PubMed
PMID: 21666072; PubMed Central PMCID: PMC3165452.
42: Hammond TM, Xiao H, Rehard DG, Boone EC, Perdue TD, Pukkila PJ, Shiu PK.
Fluorescent and bimolecular-fluorescent protein tagging of genes at their
native loci in Neurospora crassa using specialized double-joint PCR
plasmids. Fungal Genet Biol. 2011 Sep;48(9):866-73. Epub 2011 May 31. PubMed
PMID: 21664475.
43: Boland A, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O.
Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein.
Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10466-71. Epub 2011 Jun 6.
PubMed PMID: 21646546; PubMed Central PMCID: PMC3127882.
44: Lew RR. How does a hypha grow? The biophysics of pressurized growth in
fungi. Nat Rev Microbiol. 2011 Jun 6;9(7):509-18. doi: 10.1038/nrmicro2591.
Review. PubMed PMID: 21643041.
45: Held M, Edwards C, Nicolau DV. Probing the growth dynamics of Neurospora
crassa with microfluidic structures. Fungal Biol. 2011 Jun;115(6):493-505.
Epub 2011 Feb 24. PubMed PMID: 21640314.
46: Riquelme M, Yarden O, Bartnicki-Garcia S, Bowman B, Castro-Longoria E,
Free SJ, Fleissner A, Freitag M, Lew RR, Mouriño-Pérez R, Plamann M,
Rasmussen C, Richthammer C, Roberson RW, Sanchez-Leon E, Seiler S, Watters
MK. Architecture and development of the Neurospora crassa hypha -- a model
cell for polarized growth. Fungal Biol. 2011 Jun;115(6):446-74. Epub 2011
Feb 19. Review. PubMed PMID: 21640311.
47: Galazka JM, Cate JH. A new diet for yeast to improve biofuel production.
Bioeng Bugs. 2011 Jul 1;2(4):199-202. doi: 10.4161/bbug.2.4.15624. Epub 2011
Jul 1. PubMed PMID: 21637011.
48: Hasunuma K, Yoshida Y, Haque ME, Wang NY, Fukamatsu Y, Miyoshi O, Lee B.
Global warming, plant paraquat resistance, and light signal transduction
through nucleoside diphosphate kinase as a paradigm for increasing food
supply. Naunyn Schmiedebergs Arch Pharmacol. 2011 May 21. [Epub ahead of
print] PubMed PMID: 21603975.
49: Cotado-Sampayo M, Ortega Pérez R, Ojha M, Seum C, Barja F.
Characterization of Neurospora crassa α-actinin. Curr Microbiol. 2011
Jul;63(1):100-5. Epub 2011 May 20. PubMed PMID: 21598047.
50: Wang TY, He F, Hu QW, Zhang Z. A predicted protein-protein interaction
network of the filamentous fungus Neurospora crassa. Mol Biosyst. 2011
Jul;7(7):2278-85. Epub 2011 May 16. PubMed PMID: 21584303.
51: Schaap IA, Carrasco C, de Pablo PJ, Schmidt CF. Kinesin walks the line:
single motors observed by atomic force microscopy. Biophys J. 2011 May
18;100(10):2450-6. PubMed PMID: 21575579; PubMed Central PMCID: PMC3093571.
52: Hogenesch JB, Ueda HR. Understanding systems-level properties: timely
stories from the study of clocks. Nat Rev Genet. 2011 Jun;12(6):407-16. Epub
2011 May 10. Review. PubMed PMID: 21556016.
53: Moshtaghioun SM, Haghbeen K, Sahebghadam AL, Legge RL, Khoshneviszadeh
R, Farhadi S. Direct spectrophotometric assay of laccase using diazo
derivatives of guaiacol. Anal Chem. 2011 Jun 1;83(11):4200-5. Epub 2011 May
11. PubMed PMID: 21545148.
54: Denisov Y, Freeman S, Yarden O. Inactivation of Snt2, a
BAH/PHD-containing transcription factor, impairs pathogenicity and increases
autophagosome abundance in Fusarium oxysporum. Mol Plant Pathol. 2011
Jun;12(5):449-61. doi: 10.1111/j.1364-3703.2010.00683.x. Epub 2011 Jan 5.
PubMed PMID: 21535351.
55: Jiang J, Yun Y, Fu J, Shim WB, Ma Z. Involvement of a putative response
regulator FgRrg-1 in osmotic stress response, fungicide resistance and
virulence in Fusarium graminearum. Mol Plant Pathol. 2011 Jun;12(5):425-36.
doi: 10.1111/j.1364-3703.2010.00684.x. Epub 2011 Jan 5. PubMed PMID:
21535349.
56: Pomraning KR, Smith KM, Freitag M. 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. Eukaryot Cell.
2011 Jun;10(6):724-33. Epub 2011 Apr 22. PubMed PMID: 21515825; PubMed
Central PMCID: PMC3127673.
57: DeAbreu DM, Olive JE, Collins RA. Additional roles of a peripheral
loop-loop interaction in the Neurospora VS ribozyme. Nucleic Acids Res. 2011
Aug;39(14):6223-8. Epub 2011 Apr 20. PubMed PMID: 21507887; PubMed Central
PMCID: PMC3152364.
58: Smith KM, Phatale PA, Sullivan CM, Pomraning KR, Freitag M.
Heterochromatin is required for normal distribution of Neurospora crassa
CenH3. Mol Cell Biol. 2011 Jun;31(12):2528-42. Epub 2011 Apr 19. PubMed
PMID: 21505064; PubMed Central PMCID: PMC3133421.
59: Gaddameedi RR, Burgula S, Sairam M, Singh SS. Role of insulin in
Cr(VI)-mediated genotoxicity in Neurospora crassa. Lett Appl Microbiol. 2011
Jul;53(1):14-21. doi: 10.1111/j.1472-765X.2011.03058.x. Epub 2011 May 12.
PubMed PMID: 21488912.
60: Kim JD, Kaiser K, Larive CK, Borkovich KA. Use of 1H nuclear magnetic
resonance to measure intracellular metabolite levels during growth and
asexual sporulation in Neurospora crassa. Eukaryot Cell. 2011
Jun;10(6):820-31. Epub 2011 Apr 1. PubMed PMID: 21460191; PubMed Central
PMCID: PMC3127669.
61: Morris VK, Ren Q, Macindoe I, Kwan AH, Byrne N, Sunde M. Recruitment of
class I hydrophobins to the air:water interface initiates a multi-step
process of functional amyloid formation. J Biol Chem. 2011 May
6;286(18):15955-63. Epub 2011 Mar 18. PubMed PMID: 21454575; PubMed Central
PMCID: PMC3091204.
62: Martin SH, Wingfield BD, Wingfield MJ, Steenkamp ET. Structure and
evolution of the Fusarium mating type locus: new insights from the
Gibberellafujikuroi complex. Fungal Genet Biol. 2011 Jul;48(7):731-40. doi:
10.1016/j.fgb.2011.03.005. Epub 2011 Mar 29. PubMed PMID: 21453780.
63: Diernfellner AC, Schafmeier T. Phosphorylations: Making the Neurospora
crassa circadian clock tick. FEBS Lett. 2011 May 20;585(10):1461-6. Epub
2011 Mar 29. Review. PubMed PMID: 21453704.
64: Schafmeier T, Diernfellner AC. Light input and processing in the
circadian clock of Neurospora. FEBS Lett. 2011 May 20;585(10):1467-73. Epub
2011 Mar 29. Review. PubMed PMID: 21453703.
65: Nygren K, Strandberg R, Wallberg A, Nabholz B, Gustafsson T, García D,
Cano J, Guarro J, Johannesson H. A comprehensive phylogeny of Neurospora
reveals a link between reproductive mode and molecular evolution in fungi.
Mol Phylogenet Evol. 2011 Jun;59(3):649-63. Epub 2011 Mar 23. PubMed PMID:
21439389.
66: Paukstelis PJ, Chari N, Lambowitz AM, Hoffman D. NMR Structure of the
C-terminal domain of a tyrosyl-tRNA synthetase that functions in group I
intron splicing. Biochemistry. 2011 May 10;50(18):3816-26. Epub 2011 Apr 12.
PubMed PMID: 21438536; PubMed Central PMCID: PMC3092736.
67: Zhang L, Weng W, Guo J. Posttranscriptional mechanisms in controlling
eukaryotic circadian rhythms. FEBS Lett. 2011 May 20;585(10):1400-5. Epub
2011 Mar 14. Review. PubMed PMID: 21414314.
68: Keeping AJ, Collins RA. Evidence for the phenotypic neutrality of the
Neurospora Varkud (V) and Varkud satellite (VS) plasmids. Fungal Genet Biol.
2011 Jul;48(7):741-6. doi: 10.1016/j.fgb.2011.02.007. Epub 2011 Mar 21.
PubMed PMID: 21397711.
69: Whittle CA, Johannesson H. Evidence of the accumulation of
allele-specific non-synonymous substitutions in the young region of
recombination suppression within the mating-type chromosomes of Neurospora
tetrasperma. Heredity. 2011 Oct;107(4):305-14. doi: 10.1038/hdy.2011.11.
Epub 2011 Mar 9. PubMed PMID: 21386869.
70: Matei E, Louis JM, Jee J, Gronenborn AM. NMR solution structure of a
cyanovirin homolog from wheat head blight fungus. Proteins. 2011
May;79(5):1538-49. doi: 10.1002/prot.22981. Epub 2011 Mar 1. PubMed PMID:
21365681; PubMed Central PMCID: PMC3076533.
71: Cavinder B, Hamam A, Lew RR, Trail F. Mid1, a mechanosensitive calcium
ion channel, affects growth, development, and ascospore discharge in the
filamentous fungus Gibberella zeae. Eukaryot Cell. 2011 Jun;10(6):832-41.
Epub 2011 Feb 25. PubMed PMID: 21357477; PubMed Central PMCID: PMC3127676.
72: Bowman BJ, Abreu S, Margolles-Clark E, Draskovic M, Bowman EJ. Role of
four calcium transport proteins, encoded by nca-1, nca-2, nca-3, and cax, in
maintaining intracellular calcium levels in Neurospora crassa. Eukaryot
Cell. 2011 May;10(5):654-61. Epub 2011 Feb 18. PubMed PMID: 21335528; PubMed
Central PMCID: PMC3127652.
73: de Freitas CD, Nogueira FC, Vasconcelos IM, Oliveira JT, Domont GB,
Ramos MV. Osmotin purified from the latex of Calotropis procera: biochemical
characterization, biological activity and role in plant defense. Plant
Physiol Biochem. 2011 Jul;49(7):738-43. Epub 2011 Feb 4. PubMed PMID:
21334906.
74: Sánchez-León E, Verdín J, Freitag M, Roberson RW, Bartnicki-Garcia S,
Riquelme M. 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. Eukaryot Cell. 2011
May;10(5):683-95. Epub 2011 Feb 4. PubMed PMID: 21296914; PubMed Central
PMCID: PMC3127655.
75: Kasbekar DP, Singh PK, Ramakrishnan M, Raj KB. Carrefour Mme. Gras: a
wild-isolated Neurospora crassa strain that suppresses meiotic silencing by
unpaired DNA and uncovers a novel ascospore stability defect. Fungal Genet
Biol. 2011 Jun;48(6):612-20. Epub 2011 Feb 2. PubMed PMID: 21295150.
76: Desjardins G, Bonneau E, Girard N, Boisbouvier J, Legault P. NMR
structure of the A730 loop of the Neurospora VS ribozyme: insights into the
formation of the active site. Nucleic Acids Res. 2011 May;39(10):4427-37.
Epub 2011 Jan 25. PubMed PMID: 21266483; PubMed Central PMCID: PMC3105416.
77: Naveena Lavanya Latha J, Maruthi Mohan P. Role of cell wall bound
calcium in Neurospora crassa. Microbiol Res. 2011 Jul 20;166(5):419-29. Epub
2011 Jan 15. PubMed PMID: 21237628.
78: Keeping A, Deabreu D, Dibernardo M, Collins RA. Gel-based mass
spectrometric and computational approaches to the mitochondrial proteome of
Neurospora. Fungal Genet Biol. 2011 May;48(5):526-36. Epub 2010 Dec 7.
PubMed PMID: 21145408.
79: Frederick, Lafayette, W. Lena Austin, Alice Walker, Cecilia Stewart and
Monde Imoh. 2011. Observations on wall surface topography and development in
ascospores of the genera Neurospora, Gelasinospora and Sordaria.
Southeastern Biology 58: 41-71.
Neurospora E-News #17 May 2010
Contents
Neurospora 2010
Awards 2010
Nominations for 2011 Awards and Funding
Neurospora Policy Committee
Planning for Neurospora 2012
News from the Fungal Genetics Stock Center
News from the Functional Genomics and Systems Biology program project
News from Quantitative Trait Analysis project
Neurospora Mauriceville SNPs for mapping
Summary of Pan-Fungal Genome Database Meeting
Neurospora 2010 was held at Asilomar from April 8 – 11, the seventh Neurospora-specific meeting in the spirit of the former “Neurospora Information Conference”. We hope that you all had a good time and enjoyed the excellent talks and poster presentations. Our community is strong and very international, with several new labs starting up in 2010.
The updated meeting schedule and abstracts are now available on the FGSC website (http://www.fgsc.net/asil2010/neurospora_2010.htm).
This year’s logo was designed by Diego Delgado-Alvarez, a PhD student in the Mourino-Perez lab at CICESE (Ensenada, Mexico) and the photograph of participants was taken by Matt Sachs (Texas A&M University).
Awards 2010.
Beadle and Tatum award. This award is intended for young independent investigators and will both help advance their careers and give more visibility to Neurospora as a research organism.
Our warmest congratulations to Dr. Stephan Seiler of the Georg-August Universität Göttingen, the winner of this year’s Beadle and Tatum Award. The award recognizes Stephan’s groundbreaking work on the regulation of hyphal morphology, most recently revolving around the kinases involved.
B.O. Dodge awards. Two awards are made at each Neurospora meeting in recognition of the fact that a significant part of the success of Neurospora as a model research organism is due to the collaborative nature of its research community.
This year awards went to Kathy Borkovich (University of California at Riverside) and Kevin McCluskey (FGSC, University of Missouri, Kansas City). Kathy has spearheaded large group efforts to organize and present to a wide scientific audience lessons learned from the Neurospora genome and - most recently - information on the molecular biology of filamentous fungi. She has been involved in the Neurospora sequencing, functional genomics and now systems biology program project grants. Kevin has used his position at the FGSC to increase the visibility of Neurospora as a preferred organism for basic research. He has completely redefined the role of the FGSC curator and through his initiative the FGSC is a wholly modern stock center. We all owe these two individuals many thanks!!
A special Dodge award was presented to Mary Case (University of Georgia). Mary developed the first practical transformation protocol for Neurospora. Without this important advance Neurospora would not have retained its preeminence as a model organism in the era of molecular genetics. The whole Neurospora community is indebted to Mary for her pioneering work.
Perkins fund award. This award supports outstanding students and postdocs to attend both the Neurospora and Fungal Genetics Conferences.
As there were – surprisingly – no nominations for graduate students, two post-doctoral researchers were awarded for their hard work and both gave outstanding talks at the meeting: Shinji Honda (University of Oregon, Mentor: Eric Selker), who works on the control of heterochromatin formation and DNA methylation and Renato DePaula (Texas A&M University, Mentor: Deborah Bell-Pedersen), who works on oscillators that drive circadian rhythms. Congratulations!!
Nominations for 2011 Awards and Funding
While it seems early, please consider nominations for the Perkins Awards for the Fungal Genetics Conference in 2011. Nominations should be send to any of the NPC members by December 1, 2010.
Note: Contributions to the Perkins fund may be made at any time via the Genetics Society of America or via the FGSC e-commerce page (please use "Perkins Award" as the invoice number).
Neurospora Policy Committee. We would like to thank David Catcheside and Yi Liu for their service on the NPC over the past four years. At the Neurospora meeting the community elected two new NPC members, Stephan Seiler (Universität Göttingen) and Matt Sachs (Texas A&M University) to four-year terms.
Below the contact information for all current NPC members:
Meritxell Riquelme
riquelme@cicese.mx
Michael Freitag
freitagm@cgrb.oregonstate.edu
Matthew Sachs
msachs@mail.bio.tamu.edu
Stephan Seiler
sseiler@gwdg.de
Kevin Mc Cluskey
mccluskeyk@umkc.edu (ex officio)
Planning for Neurospora 2012. Matt Sachs and Stephan Seiler will serve as Program Chairs for the next Neurospora meeting to be held in 2012 at Asilomar, while the remaining NPC members - Kevin McCluskey, Meritxell Riquelme and Michael Freitag - will be responsible for general meeting arrangements. Our preferred dates for Neurospora 2012 are currently in early March (1-4, 8-11 or 15-18) to separate the meeting from the European Conference on Fungal Genetics in Marburg (first week of April). Final decisions are always made by the Asilomar Conference Center and will be communicated in the next edition of the e-news. (mf)
News from the stock center. Now in its 50th year, the FGSC is enjoying unprecedented growth and use of their collections. The total number of strains housed at FGSC has doubled in the last five years while the number of genes for which mutants are available has grown from around 1,200 to nearly over 9,000. Arrayed mutant sets include the nearly complete set for Neurospora as well as growing numbers of Cryptococcus and Candida mutants. The FGSC has also agreed to provide genomic DNA to the JGI for a growing number of fungal species being sequenced. (kmc)
Neurospora Functional Genomics and Systems Biology program project grant. At the Neurospora meeting summaries of the P01 program project grant - led by Jay Dunlap (Dartmouth Medical School) were presented by Kathy Borkovich (UC Riverside), Jeremy Zucker (Broad Institute) and Matt Sachs (Texas A&M University). This grant involves 11 institutions and 14 PIs and the biological focus is on two key triggers of asexual development: light and desiccation. There are three ongoing projects: Project 1 will complete the Neurospora gene knockouts, extend the systematic disruption of genes to Aspergillus and develop general tools for analysis of protein-protein interactions in Neurospora. Project 2 is focused on bioinformatics and the development of a Systems Biology approach to genetic and metabolic regulation of growth and development. This includes refinement of gene model annotation in the current Neurospora genome database, and further development of genome browsers to accommodate the anticipated flood of genomics-based data generated in Project 3. Project 3 makes use of high throughput sequencing technology to identify and characterize DNA elements and proteins that influence gene expression. This is done in the context of chromatin, by making use of chromatin immunoprecipitation (ChIP), methyl-DNA immunoprecipitation (MeDIP) and bisulfite sequencing, and transcriptome analyses by RNA-seq. (mf)
Quantitative Trait Analysis in Neurospora. An NIH R24 grant entitled "The development of genetics and genomics for analysis of quantitative traits in the model filamentous fungus, Neurospora crassa" is led by Rachel Brem, Louise Glass and John Taylor (UC Berkeley). The goal of this project is to develop and distribute tools to identify genes responsible for any phenotype that can be analyzed in Neurospora. Such tools will allow for mass annotation of uncharacterized genes and identification of genes contributing to phenotypes of interest, all at high resolution. Further, high-throughput RNA-sequencing on wild isolates of N. crassa, grown on Bird's media is being conducted, with a final goal of 100 strains. This should allow the determination of relative expression levels for genes from each strain. So far, high-density SNP maps from sequence data have been generated and linkage of SNPs to expression level and phenotypes are being analyzed. In the long run, this work will allow the community to associate phenotype, genotype and gene expression to understand the path from genotype to phenotype at the locus, gene and nucleotide level. Strains along with expression data and SNP maps will be made available. Please contact Louise Glass (lglass@berkeley.edu) or Charles Hall (charleshall@berkeley.edu) for information. (ch)
Neurospora Mauriceville SNPs. A preliminary high-density set of SNPs that are part of common restriction endonuclease sites was derived from a genome sequence of FGSC2225 and is now available at the FGSC (http://www.fgsc.net/Neurospora/SNPs/SNP_map.htm). We hope that this pre-publication release will be useful for the community in mapping specific mutations by RFLP while we are putting the last touches on the paper we are preparing. Please contact Kyle Pomraning (pomranosaurus@gmail.com) or Michael Freitag (freitagm@cgrb.oregonstate.edu) at Oregon State University for additional information and/or feedback. (mf)
Pan-Fungal Genome Database Meeting. On February 22 and 23, the Burroughs Wellcome Fund sponsored a strategy meeting to discuss and plan the future of fungal databases. Over the past couple of years it has become apparent that the sequencing center and NCBI databases cannot accommodate all wishes and needs of the wider fungal research communities. With easily thousands of fungal strains and species being sequenced and analyzed over the next couple of years, it seems necessary to plan for meaningful organization of the data. The meeting featured speakers in two introductory sessions on Biological Applications of Bioinformatic Tools and Data Resources Today. Breakout sessions put together smaller groups to discuss Needs Across Organisms, the accumulation of Information and Integration of databases, and Emerging Tools. The final breakout session addressed Immediate Opportunities and Priorities and Strategies for Moving Forward. Neurospora was well represented at this meeting, with five PIs present. Gavin Sherlock (Stanford University) from the Saccharomyces Genome Database suggested that their model can be successfully transferred to other organisms, as has been done already with Candida and Aspergillus. The need for curation under this model was stressed by several researchers. David Roos (University of Pennsylvania) presented the impressive interface and search capabilities of the Eukaryotic Pathogen Genome Database (http://EuPathDB.org). This may be an excellent model to follow for a taxon-driven database. Most audience members felt that it was premature to talk about specific database architecture (always a moving target), instead interconnectivity by direct stable links and exchange of data formats between existing genome center databases was repeatedly mentioned. The final To Do List included the realization that databases need to strive for standardization, that curated annotation needs to be increased as data acquisition already outstrips our ability to annotate data expertly, that data sharing needs to happen in a timely fashion and that thus nimble interactions between databases should be sought. One way to accomplish this is by designing a “portal” for all fungal databases. While there are several candidate sites, most everybody agreed that Jason Stajich’s (University of California Riverside) site (http://fungalgenomes.org) has all the characteristics necessary for success in the near future. (mf)
Michael Freitag on behalf of the NPC
Neurospora E-News (#16); November 2009
Contents
• Neurospora 2010
• Call for nominations for Perkins, Beadle and Tatum, and Dodge awards.
• News from the Genome Project
• News from the Stock Centre
Neurospora 2010 will be held April 8th – 11th, 2010 at Asilomar, California.
Registration and abstract submission deadlines are January 15, 2010.
Registration materials, instructions for abstract submission and further information on the program should be found on the FGSC web page from the end of November 2009. The meeting schedule will be similar to that of previous meetings but with additional free time during the afternoon hours for networking. There will be five sessions of invited talks, including speakers selected from abstracts of submitted posters. All participants are encouraged to present their work as posters.
The preliminary schedule includes sessions on:
i. Cell Signalling and Development
ii. Cell Biology and Morphogenesis
iii. Gene Regulation
iv. Light and Circadian Clock
v. Evolution and Genomics
Come to Neurospora 2010 to celebrate the leading system for research in the
genetics of filamentous fungi!
Call for nominations for the Beadle and Tatum, Dodge and Perkins awards
for presentation at Neurospora 2010.
The Neurospora Policy Committee strongly encourages nominations for these
awards which should be received by the current chair of the committee (David.Catcheside@flinders.edu.au)
by December 1, 2009.
Beadle and Tatum award. This award is intended for young investigators
whereby the award will help to advance their careers and to give more
visibility to Neurospora as a research organism.
B.O. Dodge awards. Two awards are made at each Neurospora meeting in
recognition of the fact that a significant part of the success of Neurospora
as a model research organism is due to the collaborative nature of its
research community. Certain individuals who have made exceptional
contributions towards the community will be acknowledged by the awards.
Perkins fund award. This award supports outstanding students and postdocs to
attend the Neurospora and Fungal Genetics Conferences. Contributions to the
Perkins fund may be made via the Genetics Society of America.
Additional details of the awards can be found at the FGSC web page.
News from the Neurospora Genome Project
The Neurospora Genome Project has been renewed and investigators now include
Townsend, Sachs, Bell-Pedersen, Freitag, Borkovich, Galagan, Selker, Plamann,
McKluskey, Osmani, and Dunlap. The chief focus of the renewal is on
developing a comprehensive view of how the genome responds to developmental
changes elicited by light. There are many facets to the work; several of the
investigators are still looking to fill positions and interested individuals
should contact individual investigators directly. Beyond this, efforts
continue to complete the full set of Neurospora gene knockouts. Completed
knockouts can be requested from the FGSC, and if a gene has not yet been
deleted, investigators can still request that the new knockouts be made by
emailing knockouts@dartmouth.edu.
News from the Fungal Genetics Stock Center.
We would like to welcome Ms. Bobbie Burgee as our newest employee at the
FGSC.
Bobbie will handle most of the orders.
David Catcheside
On behalf of the Neurospora Policy Committee
Neurospora E-News #15 May 2009
Contents
•Neurospora 2010 and call for suggestions
•Awards 2010, call for nomination
•Awards 2009
•News from the stock centre
•News from the genome project
Neurospora 2010 will be held at Asilomar from April 8 – 11, the seventh
Neurospora-specific meeting in the spirit of the former “Neurospora
Information Conference”. We hope that you can join us even though next
year’s meeting is unusually late. Based on the previous six Neurospora
conferences, next year’s gathering promises to be a fine meeting!
The website for the meeting will be at http://www.fgsc.net/asil2010/neurospora_2010.htm.
The program will be announced in mid-November.
The scientific program chairs, Meritxell Riquelme and Michael Freitag, ask
for your suggestions on specific sessions, topics and the meeting format.
The schedule will roughly follow previous outlines, running from Thursday to
Sunday and we will attempt to schedule more free time during the afternoon
hours for networking. It is anticipated that there will be five sessions
(last year’s topics are listed below). All participants are encouraged to
present their work as posters and speakers for short talks that will be
selected from the submitted poster abstracts. Please send your suggestions
to any member of the Neurospora Policy Committee:
David Catcheside david.catcheside@flinders.edu.au
Yi Liu Yi.Liu@UTSouthwestern.edu
Meritxell Riquleme riquelme@cicese.mx
Michael Freitag freitagm@cgrb.oregonstate.edu
Kevin Mc Cluskey mccluskeyk@umkc.edu
Neurospora 2010 sessions: I: Gene Silencing, Sex, Repair and
Recombination. II: Clocks and Light. III: Cell Growth, Morphogenesis and
Populations. IV: Gene Regulation and Cell Signaling V: Genomics and
Methodology.
Awards 2010:
Call for nominations which should be received by the chair of the Neurospora
Policy Committee (David.Catcheside@flinders.edu.au) by December 1 2009. The
full rules are available at the FGSC web site.
Beadle and Tatum award: This award is intended for young investigators
whereby the award will help to advance their careers and to give more
visibility to Neurospora as a research organism.
B.O. Dodge awards: Two awards are made at each Neurospora meeting in
recognition of the fact that a significant part of the success of Neurospora
as a model research organism is due to the collaborative nature of its
research community. Certain individuals who have made exceptional
contributions towards the community will be acknowledged by the awards.
Perkins fund award: This award supports outstanding students and postdocs to
attend the Neurospora and Fungal Genetics Conferences. Contributions to the
Perkins fund may be made via the Genetics Society of America.
Awards 2009
Our warmest congratulations to Dr. Jay C. Dunlap of Dartmouth Medical School
for his election to the National Academy of Sciences, one of the highest
honors that can be accorded to a U.S. scientist.
2009 Robert Metzenberg award: Dr. Hirokazu Inoue of Saitama University for
his lifetime contributions to our understanding of DNA repair and his
discovery of near 100% homologous recombination in Neurospora by deleting
the ku70/ku80 gene, key to the success of making knockouts for the
Neurospora genome project.
2009 Perkins Awards: for support of graduate students and postdoctoral
fellows to attend the 2009 Fungal Genetics Conference: William Alexander,
graduate student (Mentor: Patrick Shiu). Keyur Adhvaryu, Postdoctoral fellow
(Mentor: Eric Selker). Kristina Smith, Postdoctoral fellow (Mentor: Michael
Freitag)
News from the stock center:
The FGSC has now arrayed Neurospora crassa Knock Out mutants in 107 96-well
plates. Additional sets include transcription factor knock outs, hyphal
growth related knock outs and kinase knock outs. Microarray slides for
Neurospora are available in two formats. The N. discreta and N. tetrasperma
genome sequences are available at the JGI.
News from the Neurospora genome project.
We are delighted to note that the project grant led by Jay Dunlap has been
renewed and will complete the Neurospora gene knockouts, extend the
systematic disruption of genes to Aspergillus and develop tools for analysis
of protein-protein interactions in Neurospora. A primary goal, targeted
through molecular, cell biological, genomic and computational approaches,
will be to understand how N. crassa transitions from mycelial growth to
complete asexual spore development. 11 institutions and 14 PIs will focus on
two key triggers of asexual development: light and desiccation.
David Catcheside on behalf of the NPC
Neurospora E-News (#14) ; January 2007
Contents:
1. Memorial and Funds dedicated to David and Dorothy Perkins
2. The Neurospora methods book
3. Neurospora business lunch (Thursday March 22nd) at Asilomar 2007
1. Memorial and Funds dedicated to David and Dorothy Perkins
The Fungal Genetics Community was shocked by the deaths this month, just
four days apart, of both David Perkins and his wife Dorothy Newmeyer Perkins
who both significantly contributed to fungal genetics. The Neurospora Policy
Committee along with the Perkins family have formalized plans for a Memorial
Celebration and lasting tributes to these wonderful friends and colleagues.
The celebration of David’s and Dot’s lives will take place at the
forthcoming 24th Fungal Genetics Meeting in Asilomar on the evening of 20
March 2007. Friends and colleagues are most welcome to attend.
Memorial contributions in David’s and Dot’s name can be made to two funds
designed to provide lasting support for Neurospora and fungal genetic
research: The Perkins Award Fund and The FGSC Endowment Fund.
Rededication of the Perkins Award
The Perkins Award was established in 1995 to honour the enormous
contributions made by David Perkins to fungal genetics, Neurospora genetics
and to nurturing young scientists in these fields. Since 1997 when the first
awards were made, 21 promising graduate students and postdocs have been
supported to attend the Neurospora and Fungal Genetics Conferences held at
that venue in alternate years.
The Neurospora Policy Committee has taken this opportunity to rededicate the
Perkins Award to honour both David and Dot and to seek additional funds to
strengthen the endowment to keep the value and number of the David and
Dorothy Newmeyer Perkins Awards in line with the rising cost of conference
attendance and the increasing number of young scientists who should be
there. The purpose and rules for the award are otherwise unchanged: to
recognize outstanding graduate students and postdoctoral scientists that
utilize Neurospora as an experimental system and provide monetary support to
attend one of the Asilomar meetings.
Contributions
Both funds are managed by the Genetics Society of America. Checks should be
made payable to The Genetics Society of America with the fund name (Perkins
Award or the FGSC Endowment) written in the lower left corner of the check,
and mailed c/o Elaine Strass, Executive Director, Genetics Society of
America 9650 Rockville Pike, Bethesda, MD 20814.
More History
When the Perkins Award was established, those were happier times! As a
reminder and to make us smile, we have included below the original
solicitation for contributions to the Perkins Award, sent out by Jay Dunlap
and Jennifer Loros on behalf of the Neuropora Policy Committee. The many
contributors proffered tributes to David that are all the more touching
because the writers knew that they were never destined for David's eyes.
Some of these appreciations will now be revealed and can accessed at
http://www.stanford.edu/group/neurospora/PerkinsAward.html <http://www.stanford.edu/group/neurospora/PerkinsAward.html>
. Other outpourings from the Neurospora and Fungal Genetics Communities
following David’s and Dot’s deaths can be found at
http://www.stanford.edu/group/neurospora.
“- Stream of consciousness-
"So, anyway", says Dorsey Stuart, "Look, David's been so enormously helpful
to
so many of us for so long, we really ought to do something".
"Yeah", we said, "Well, he gave the after dinner address at Asilomar a few
years ago, . . . But somehow that doesn't communicate the appropriate level
of
appreciation, does it."
Silence.
" It really ought to be something a little more permanent"
"The Neurospora Policy Committee is the right group to organize this,"
Dorsey says. "How about a David Perkins Scholarship Fund to support travel
for a student to the Fungal Genetics meeting or a similar meeting where
people will be talking about Neurospora. I could kick it off with a
contribution from my company."
***
A few months later, after some gestation, this was discussed with the August
Director of the Fungal Genetics Stock Center, Prof. Dr. John Kinsey:
"So, Jack, this seems like a good idea. The FGSC could help to administrate
this, right?"
Jack says, "Yup. We'd be happy to. Now, in order to be able to provide a
scholarship of, say, $500 every two years, we need to generate interest of
$250 per year, which at a yield of 5% on the principal, means that we need a
principal of at least $5000. "
"No problem", we say, "Given the selfless manner in which David has given
his time to the community over the years, people will be stumbling over
themselves to show their gratitude."
And, we hope that you, dear fellow Neurosporologist, will.
Would you be willing to contribute to the David Perkins Scholarship Fund?
When we conducted a straw survey on the Internet to determine the level of
support, we suggested that a good rule of thumb might be to consider a gift
to the Fund of whatever you make, gross, for a morning's work. Be honest
with yourself; you work hard, around 50 hrs a week and 50 weeks a year, so
just take your annual salary, divide by 2500, and multiply by the number of
hours between when you arrive and when you eat lunch. Then get out your
checkbook.
Time wise, our goal will be to have the scholarship money in hand and the
Fund established by the time of the Fungal Genetics Meeting at Asilomar.
We will keep, and give to David, a list of the names of contributors, but
will not list the amounts given. We, along with Dorsey and Jack, compiled
the mailing list, but suspect that some people who should have been
approached were inadvertently left off the list. Please feel free to ask
them!
Please make checks payable to ….
Please send your contribution to …
**And, please, keep it a SECRET FROM DAVID for now.**
Thanks and best wishes,
for the Neurospora Policy Committee……………”
This will always be a secret now from David and Dot so we can communicate
and donate freely.
The FGSC Endowment
David Perkins encouraged the Fungal Genetics Stock Center (FGSC) to
establish an endowment fund recently to provide a basis for achieving
permanent financial sustainability for the FGSC. The endowment money also
will be available as emergency funds, but only if necessary. David and Dot
both were enthusiastic supporters of the FGSC from its inception through its
continuing expansions into this genomic era. Contribution made in the
Perkins’ name will help FGSC reach their goal and provide permanent service,
support, and outreach to the Fungal Genetics Community.
The way to contribute to the Perkins Award/FGSC Endowment again:
Checks made payable to The Genetics Society of America with the fund name
(Perkins Award or the FGSC Endowment) written in the lower left corner of
the check, and mailed c/o Elaine Strass, Executive Director, Genetics
Society of America 9650 Rockville Pike, Bethesda, MD 20814.
2. The Neurospora methods book
A call for sending in protocols in order to complete the methods book has
been recently sent out by Deb Bell-Pedersen. Your contributions towards the
completion of this book is another fine way to honor the memory of Dave and
Dot. Please chose a topic from the distributed list (or an experimental
procedure on any additional topic) and forward your working protocol to Deb
(dpedersen@mail.bio.tamu.edu).
3. Neurospora business lunch at Asilomar 2007.
The Neurospora business lunch has been scheduled for Thursday March 22nd. A
separate dining area has been reserved for the entire Neurospora community
and we hope all will attend.
The Neurospora Policy Committee
Neurospora E-News (#12) ; July 2006
Sequencing of Neurospora discreta and N. tetrasperma has been approved.
As a result of the continued efforts invested by Don Natvig, Dave Jacobson, Louise Glass and John Taylor, along with the support provided by members of the Neurospora community, the DOE Joint Genomes Institute (JGI) has approved the full-genome sequencing of one individual each of Neurospora discreta and Neurospora tetrasperma. These individuals will be sequenced at 5X coverage and the genome of a second N. tetrasperma individual of the opposite mating type, will be sequenced at 0.5X coverage. These sequences, combined with the existing N. crassa sequence, near outgroup sequences from Podospora anserina and Chaetomium globosum, and the more distant outgroup species, Magnaporthe grisea will create an environment for genomic comparative biology that will be unsurpassed for studies of genome evolution. Given the existing N. crassa genome sequence and improvements in sequencing fidelity since the completion of that genome, the requested coverage will give full genomes for N. discreta and N. tetrasperma, and useful coverage of both N. tetrasperma mating-type chromosomes. Adaptation of fungi that interact with forest trees, genome defense against mobile elements, evolution and genetic consequences of the widespread fungal mating strategy, pseudohomothallism, and fungal mutation and selection are just examples of the many research projects that will be enabled by access to these sequences.
Neurospora KO project news.
The long-awaited anchor paper for the Knockout Project within the Neurospora Genome Project has been published in PNAS. It is available online through Open Access and the reference is Colot et al., (2006) PNAS 103, pp. 10352–10357. This is the paper that should be cited in subsequent publications that use any of the strains generated or the technologies developed for making knockouts.
The project has completed more than 1,100 knockout strains representing close to 800 genes. Overall about 20% of the deleted genes result in an ascospore lethal phenotype and those strains have been submitted to the FGSC as heterokaryons. For an up-to-date list of completed strains as well as those in process, go to http://www.dartmouth.edu/~neurosporagenome/knockouts_completed.html
The Knockout Project continues to accept nominations for genes to be disrupted. Simply email "knockouts@dartmouth.edu" with your NCU #s and they will be put into the queue.
The third Neurospora Genetics & Genomics Summer Research Institute at UCLA is in the process of analyzing 268 KO mutant strains. This work will be completed by the end of August. To view the data for these and for previously phenotyped KO mutants go to http://www.broad.mit.edu/annotation/genome/neurospora/Home.html, select Alleles and a summary page listing phenotypes will allow you to view phenotypic data by selecting a phenotype category. Then selecting KO1 will display all the data for a given knockout strain.
A web-based community annotation resource for the Neurospora genome is now maintained at the Broad Institute; go to
http://www.broad.mit.edu/annotation/genome/neurospora/CAHome.html. We thank all who have participated thus far and strongly encourage additional participation from the community. This resource, built at community request, needs community input for it to be most useful.
The FGSC have prepared the available Neurospora mutants in 96-well plates and they are available within the US as frozen conidial stocks and to foreign addresses as conidia spotted on filter paper (in 96 well plates).
The cost involved is $100 per plate, with a cap of $3000 for labs that want the whole set of plates (The cost of shipping is above the fee for the plates).
The FGSC have also arrayed special sets, like the transcription factor strains and a hyphal growth set.
Individual KO strains are also available under the same terms as other strains. http://www.fgsc.net/newship.html
SNP project news.
As part of a joint effort conducted at Dartmouth medical school and the Broad institute, 273 cleaved amplified polymorphic sequence (CAPS) markers between OakRidge 74A and Mauriceville randomly distributed over the entire genome with an average density of one every 100-200 kb have been confirmed. The majority of digests for CAPS analysis were performed with one of twelve well-established four-cutter enzymes. To ensure maximal coverage in regions with poor EST data, additional enzymes with longer, more degenerate recognition sequences have been used. Current work also includes the mapping and cloning of a couple of genes as "proof of principle" for submitting a manuscript this fall, and the designing of an evenly distributed set of 96 oligomer pairs to be ordered as a master plate that can be diluted and distributed upon request through the FGSC. The Mauriceville strain FGSC 2226 (mt a) was found, not surprisingly, to not be isogenic with 2225 (mtA) used for the sequencing and CAPS selection, so work is being performed to replace the large A idiomorph with the small a idiomorph to facilitate the CAPS map usage.
The Neurospora crassa e-Compendium.
The e-Compendium (also called "Gene
List")
http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/gene_list.htm
provides an unparalleled resource. It is a compilation of genes, products,
phenotypes, references, and genetic and physical mapping data initiated by
Alan Radford in 2000 with the help of
Masters' students in Bioinformatics
at the University of Leeds. It continues the tradition of gene compilations
established by "Map Construction in Neurospora crassa" by Barratt,
Newmeyer, Perkins, and Garnjobst (Adv. Genet. 1954),
"Chromosomal Loci of
Neurospora crassa
" by Perkins, Radford,
Newmeyer, and Bjorkman (Microbiol.. Revs. 1982) and
" The Neurospora
Compendium
" by Perkins, Radford, and
Sachs (2001) on line at the
Fungal
Genetics Stock Center (FGSC).
The e-Compendium has been continuously updated and expanded. It now contains
over 2,500 gene entries including mitochondrial genes, physical mapping and
sequence data from the
Neurospora genome project
at the Broad Institute, MIT, new genes from
"Lessons from the Genome Sequence of
Neurospora crassa
: Tracing the Path from Genomic Blueprint to Multicellular Organism."
by Borkovich et al., Microbiol. Mol. Biol. Revs. (2004), sequence
links to PDB, and images of many morphological mutants.
Functionality has been improved in this platform-independent version,
including a new search function for the gene database, links from genes to
sequences at the Neurospora genome project and elsewhere, to clone and
strain catalogs at FGSC, to metabolic maps, and to cross-links from
"redundant" gene synonyms to the main gene entry; also links from cited
references to reference details, Pubmed abstracts and full articles where
available. The bibliography of over 2,400 references is also independently
browsable and searchable.
A new addition is the physical maps,
http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/physical_maps.htm
, with >2000 named genes assigned to positions with nucleotide coordinates
(based on the Broad Institute 7th release).
Neurospora meetings.
About 125 participants attended the Neurospora meeting in late March (http://www.fgsc.net/asil2006/MeetingAnnounc06.htm). The next meeting is scheduled for spring of 2008 (dates will be announced when they are set). Our next meeting’s program chairs will be David Catcheside and Yi Liu.
Shortly after the Asilomar meeting, thirty scientists from twelve countries attended the first European Neurospora meeting, which was held as a one day satellite meeting of the 8th European Conference on Fungal Genetics in Vienna. Luis M. Corrochano was responsible for the scientific content. The meeting increased the interaction of European Neurospora scientists and the visibility of the growing Neurospora community in Europe. This meeting is the first of a series of European Neurospora meetings that will take place in coordination with the European Conference on Fungal Genetics, and the organizers propose that a member of the organizing committee of each ECFG together with a member of the Neurospora community will coordinate the efforts to organize the next European Neurospora meeting.
Methods Book update.
Under the leadership of Deb Bell-Pedersen, continuous progress is being made on the Neurospora methods book. Currently, there are over 80 methods write ups available on the Neurospora home page (http://www.fgsc.net/Neurospora/NeurosporaProtocolGuide.htm) with more continuously being added. So, keep checking the web site for new additions. We want to thank the contributors, particularly David Perkins, for all of their efforts. If you would like to contribute a method or have comments/additions/modifications to existing methods, please contact Deborah Bell-Pedersen at dpedersen@bio.tamu.edu. We are particularly in need of methods involving molecular and biochemical techniques.
Neurospora awards.
Even though the next Fungal Genetics Meeting is 9 months away, this would be a good time to start thinking of potential candidates for the various Neurospora community awards which have been established to recognize achievements of Neursopora community members at all career levels. Briefly, these include (i) The Beadle and Tatum Award in recognition of outstanding and original research using Neurospora as a model organism. This award is intended for young investigators whereby the award will help to advance their careers and to give more visibility to Neurospora as a research organism. The award is given to one researcher every two years at the Neurospora conference in Asilomar. The recipient is asked to give the Beadle and Tatum award lecture at the meeting; (ii) The Perkins Fund Award, established in honor of our colleague, Dr. David Perkins, to support outstanding students and postdocs attending the Neurospora and Fungal Genetics Conferences. The award will be presented at either the Fungal Genetics Conference or the Neurospora Conference. Each awardee will be asked to present their research findings at the meeting.
Two additional awards, to be awarded next in 2008 (at the next Neurospora meeting) and in 2009 (at the following Fungal Genetics Meeting), are The B.O. Dodge Community Award and The Metzenberg Award, respectively.
For complete details concerning all the mentioned awards, please visit the Neursopora website - http://www.fgsc.net/Neurospora/Awards.htm.
From the Neurospora Policy Committee
Neurospora E-News; September 2005
1. Neurospora Theses
David Perkins has pointed out that much valuable information remains locked up in unpublished theses. In the five years 2000 -2005, for example, there were 43 Ph.D. and 8 Masters theses that used Neurospora (see http://wwwlib.umi.com/dissertations). PDFs of these can be obtained from Dissertation Abstracts for $18. The Policy Committee will also take steps to have these listed in the Neurospora bibliography and perhaps also in a future E-news.
2. The Metzenberg Award Fund.
Following up the successful presentation of the first Metzaward to Jay Dunlap at this year’s Asilomar meeting, the NPC would like to re-issue the call for financial contributions to this fund. The main purpose is to assist with travel costs for award recipients, when needed. The original plan was to attempt to bring the fund up to 10 or 15 K, but so far this has not been reached. Donations should be sent to Elaine Strass at the GSA. The GSA only wants checks, no credit cards, made out to the GSA but clearly marked for the Metz award. The address is Elaine Strass, Genetics Society of America, 9650 Rockville Pike, Bethesda MD 20814; they are deductible for tax purposes in the US and possibly elsewhere too. Also, two anonymous donors are willing to match donations up to a total of 5 K.
3. Asilomar 06
A reminder that the next Neurospora meeting will be March 30 – April 2 at Asilomar. The registration deadline will probably be in December. Suggestions for symposia and speakers should be addressed to program chairs Nora Plesofsky or Oded Yarden (nora@cbs.umn.edu, yardeno@agri3.agri.huji.ac.il).
4. Call for nominations for the 2006 Beadle and Tatum Award.
Nominations should include a letter of nomination and a CV of the candidate and be sent to the NPC chair (Tony Griffiths) by Dec 1. The NPC will review the nominations and forward these to the Selection Committee (a group of up to 8 distinguished scientists) by Jan1.
5. Call for nominations for the Perkins Award for student and postdoc travel
Nominations should be made in the form of a one-page letter from the candidate’s research advisor. This letter should include a 200 word or less description of why the individual’s work is exceptional. Up to two re-prints or pre-prints of published research may also be included with the nomination. Nominations need to be received by Dec 1. Evaluation of the nominations are overseen by the NPC. Award decisions will be made by Feb 1. The awardees will be notified prior to the meeting.
6. Call for nominees for the new Neurospora Community Awards.
These awards will made in recognition of the fact that a significant part of the success of Neurospora as a model research organism is due to the collaborative nature of its research community. Certain individuals have made exceptional contributions towards community. These are the people who will be acknowledged by the awards, which will be an appropriate presentation piece. Please include a letter explaining your rationale. Deadline for nominations, Dec 1.
7. Alan Radford' s new brainchild "mapping on the fly"
This is a new feature for the "gene list"; it is a Java-based utility which takes the current linkage data from the gene list source files and calculates the best (longest unambiguous) map of a user-selected linkage group. This does away with a pencil and a lot of scrap paper! It will also recalculate and show the limits of location on the map of any other user-selected gene, and as a final step recalculate the map with the specified gene in the backbone. As some of the present map is based on rearrangement breakpoints and duplication coverage, the mapping utility needed the creation of a new XML data file of rearrangement breakpoint data. The mapping URL is
http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/linkagefront.html
Another addition to the “gene list” e-Compendium is a Java utility to extract into a tab-delimited text file data contig data on all sequenced genes. This can be imported into spreadsheet software and sorted to create and analyse physical maps, and also to zero in on candidate ORFs for well-mapped but currently unsequenced genes. The URL is http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/contigfront.html
For convenience, both mapping and contig extraction utilities are indexed at the “gene list” e-Compendium front page at http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/
8. Now available
i) The current "gene list" e-Compendium contains all of the 2001 Compendium data and much more, including sophisticated search functions. It has over the summer been updated to bring sequences and contig data into line with genome assembly v7.
ii) Neurospora micro-array slides are now available: check the FGSC website.
9. New FGSC tech.
Mrs. Stewart has left and the new technician is Rachel Yedlin who joins us after obtaining a BA in biological sciences at the University of Texas, Austin. Prior to joining the FGSC Rachel worked in the safety office and most recently developed a comprehensive inventory of all Lasers on campus at UT.
10. FGN.
The first group of articles for FGN52 are now online and additional submissions are solicited for the FGN.
11. Knockout project news
The Neurospora Genome Project is pleased to announce that an initial group of strains resulting from the deletion of 80 genes will be available from the FGSC shortly after September 26, 2005. A list of strains is posted on our website at http://www.dartmouth.edu/~neurosporagenome/knockouts_completed.html or at the FGSC at http://www.fgsc.net/ncrassa.html. You may request strains from the FGSC by NCU number and desired mating type (if both mating types are available) or by FGSC number (when designated). To date, about 300 genes have been mutated. Some were created in a pilot study in which we mutated 100 transcription factors – these will be described in a publication that is in preparation, but they will not be made available until the paper nears publication. You can view a separate list of them on our website. The other approximately 100 knockouts (including some transcription factors that are not the focus of the first publication) will be submitted to the FGSC within the next few weeks. Their NCU numbers will also be listed on our website soon, in advance of their availability.
12. Methods Book Reminder
Deb Bell-Pedersen would like to remind people who promised to write method reviews and/or new methods to send them to her as soon as possible. They will start appearing on the Neurospora Home Page soon.
From the Neurospora Policy Committee
4/19/05
THE NEUROSPORA E-NEWS
Prepared by the Neurospora Policy Committee (NPC) : Deb Bell-Pedersen, Tony Griffiths (Chair), Nora Plesofsky, and Oded Yarden.1. Fungal Genetics (FG) Asilomar Meeting, March 2005
The FG meeting at Asilomar went off well, with a great scientific programme and a full house of delegates. The excess of demand over supply re accommodation and space led to a vote on some new policies to try to regulate numbers more fairly. The new measures will be announced by the FG policy committee in due course.
2. Metzenberg wins the Morgan Medal!
Bob Metzenberg was the 2005 recipient of the GSA's prestigious award the
Morgan Medal. The Morgan medal was presented to Bob by David Perkins, at the
Asilomar banquet.
3. Dunlap wins the new Metzenberg Award!
At the Asilomar meeting a new award was announced and presented in honour of
the outstanding career achievements of Bob Metzenberg. Nominees for this
award on this occasion were provided by the NPC, although in the future
nominations will be solicited from all the community. The next award will be
in 2007, and after that every 2-4 years at the discretion of the NPC.
Nomination files were screened by a panel of well-known researchers from
inside and outside the Neurospora community. The Metzenberg Award has been
accepted by the GSA as part of their official list of prestigious awards.
The award is to recognize Neurospora workers whose renown (like Bob's) has
spread beyond Neurospora. (Full details can be found
online).
This year the Metzenberg Award winner was Jay Dunlap, for his work on the genetics of the biological clock. The award itself was a copper charger with a border of swirling asci and engraved at the centre with the award title and Jay's name. The presentation was made at the conference banquet by Rowland Davis.
Jay Dunlap (holding the award) with Tony Griffiths (maker of the award) Photo by Matt Sachs.
4. Perkins Awardees.
Perkins Awards (with cash prizes) are given annually to a graduate student
and to a postdoc. This year the Perkins awards went to Michael Vitalini and
Hyojeong Kim. These were presented at the Neurospora Luncheon.
5. Announcing the new Neurospora Community Awards.
These awards will be in recognition of the fact that a significant part of
the success of Neurospora as a model research organism is due to the
collaborative nature of its research community. Certain individuals have
made exceptional contributions towards community, and these people will be
acknowledged by the awards.
At each Neurospora meeting, starting with the next one, two awards will be
made to individuals of any rank who have made sustained exceptional
contributions to the community. Nominations will be solicited before each
Neurospora meeting, and the two winners will be selected by the Neurospora
Policy Committee. Recipients will be presented with an appropriate trophy.
6. Fungal Genetics Policy Committee
At the Asilomar meeting, two Neurospora workers, John Taylor and Kathy
Borkovich, were voted onto this committee, whose main job is to oversee the
FG meetings.
Tony Griffiths (agriff@interchange.ubc.ca) takes over from Deb Bell-Pedersen as Chair of the NPC for one year.
8.
Exploiting the information obtained from the Neurospora genome sequence.
Cassettes for performing gene disruptions (based on homologous replacement)
of predicted genes of N. crassa are currently available for
distribution at Dartmouth and requests for specific knockout strains are now
being accepted (see http://www.fgsc.net/gpko.html for details). In the very
near future the cassette collection will cover all predicted genes of N.
crassa. The availability of mutants defective in nonhomologous
end-joining, in which homologous recombination rates are almost 100% (Ninomiya
et al., 2004) has significantly contributed to expediting the rate of
producing knockout strains. Strains are made available to the community as
they are produced with the intention of eventually completing a full-genome
knockout strain collection (well beyond the original goal of ~half the
genes). In parallel to the production of cassettes and strains,
community-friendly web-based resources for archiving and curating manual
gene annotation and phenotypic attributes of knockout strains are being
constructed. The success of integrating sequence information and phenotypic
data is very much based on input from community members. Specific details
will be provided once the relevant websites are launched.
9. Next Neurospora meeting
This will be at Asilomar March 30 - April 2, 2006. The programme committee
will be Nora and Oded, who welcome suggestions for symposia and speakers.
Another call for names will be sent out later.
The NIH program director for the P01 (Laurie Tompkins) will be attending the meeting, so this will be a great chance to show off the full Neurospora community at work. (If there are people you know who are peripheral to the Neurospora community, but might be interested in attending to check things out, the NPC can provide letters of invitation.)
10. Three new important websites
a) Neurospora has finally taken its rightful place on the main NIH web page
"Model Organisms for Biomedical Research". Go to http://www.nih.gov/science/models/
and click on 'Neurospora'.
b) GermOnline
This project on sexual reproduction of Neurospora crassa is an innovative
paradigm for a community-based cross-species knowledge base. It is freely
accessible via the internet through a global network of servers in Asia,
Europe and the USA. They invite the community to make contributions on N.
crassa genes relevant for meiosis, spore formation and spore germination.
GermOnline integrates curated entries on genes and microarray data relevant
for the mitotic and meiotic cell cycle, gametogenesis and fertility across
11 model organisms and H. sapiens. After a brief registration step, authors
access an intuitive online form similar to those used by journals for
uploading a manuscript. Contributions are based upon at least one
peer-reviewed paper. An entry consists of a title and a description,
GeneOntology terms, images and/or figures (jpeg less than 2MB; there is no
copyright issue), optional information about experimentally verified
homologues/orthologues of a given gene and the original PubMed reference(s).
Multiple entries from different labs working on the same gene are possible
and encouraged. GermOnline also serves as an online database service for
your microarray data that are displayed as a graph and in numerical form to
support your paper.The project is funded by a long-term grant from the Swiss
Institute of Bioinformatics (http://www.isb-sib.ch) and it has so far been
greatly appreciated by people in the field. GermOnline is recognized as a
reliable source of information by Uniprot, GRID, ISI Current Web Content and
a growing number of species-specific databases. Moreover, many of these
important sources of information including SGD, GeneDB, AGD, RGD and TAIR
link back to GermOnline, increasing its visibility and impact. We are now in
the process of soliciting researchers at a large scale. Please access
http://www.germonline.org and retrieve information on many hundred genes as
well as more than 10 array expression studies.
c) Textspresso
This is a new information retrieval and extraction system for Neurospora
literature. Go to http://www.textpresso.org/nspora/
More Asilomar photos by Matt Sachs will soon be posted on the Neurospora Home Page.
Tony Griffiths NPC Chair
3/04/05
The E-NEWS is issued by the Neurospora Policy Committee (NPC). Names and
addresses are listed at the end of this message. Items that you wish to
include in future issues can be sent to Deborah Bell-Pedersen at dpedersen@mail.bio.tamu.edu.
************************************
1. A very big and heart-felt congratulations to:
Charles Yanofsky for receiving the National Medal of Science Award.
The National Medal of Science was established in 1959 as a Presidential
Award to be given to individuals "deserving of special recognition by reason
of their outstanding contributions to knowledge in the physical, biological,
mathematical, or engineering sciences." Since its establishment, the
National Medal of Science has been awarded to 409 distinguished scientists
and engineers whose careers spanned decades of research and development.
See http://www.nsf.gov/news/news_summ.jsp?cntn_id=102953&org=olpa&from=news
and http://news-service.stanford.edu/news/2005/february16/medalSR-021605.html
Robert Metzenberg for receiving the Genetics Society's 2005 Thomas Hunt
Morgan Medal in recognition of his lifetime contribution to genetics. See
the Feb issue of Genetics at http://www.genetics.org/current.shtml
************************************
2. A new version of Alan Radford's Neurospora crassa Gene List is now
available at http://www.bioinf.leeds.ac.uk/~gen6ar/newgenelist/genes/gene_list.htm
It has a number of new features:
1. It is now platform independent as the original ActiveX has been replaced
by Perl/cgi.
2. A search utility for the gene database has been added as well as the
original browse utility.
3. It has an independent search utility and a browse utility for the
bibliography.
4. It links all sequence codes to the Broad Institute, Genbank, and where
available to Swissprot.
5. It links references in individual gene entries to the bibliography
entries.
6. It links from individual bibliography entries to Pubmed if an abstract or
full article is available.
7. It has a form for submission of new genes for entry in the Gene List.
8. It has a form for submission of new relevant references.
9. Mainstream metabolic genes are linked to diagrams of the pathways.
10. EC numbers are linked to Expasy Enzyme.
11. Morphological mutants have links to images where available.
Its future usefulness depends on the entire Neurospora community providing
data promptly.
I would appreciate feedback on this new version and the value of the new
features and the links.
Finally, although I have put an automatic redirect on the old url for the
time being, if you were using the original Gene List, please update your
bookmark.
Alan Radford, School of Biology, The University of Leeds, a.radford@leeds.ac.uk
************************************
3. John R S Fincham, 1926-2005
John was born in 1926, attended Hertford Grammar School, and went on to
Cambridge University as an undergraduate. He graduated in Botany in 1946,
and stayed on to obtain his Ph D in 1950 for work on amination-deficient
mutants of Neurospora crassa.
In 1950, John married Ann Emerson, the daughter of pioneer fungal
geneticists Stirling and Mary Emerson. They had one son and three daughters.
Appointed first as Lecturer in Botany at Leicester University from 1950-1954
and Reader from 1954-60, then Associate Professor of Genetics at
Massachusetts Institute of Technology from 1960-61, John moved on to become
Head of the Genetics Division of the John Innes Institute from 1961-66.
John was appointed as Professor and Head of the new Department of Genetics
in Leeds post in 1966. He was elected a Fellow of the Royal Society in 1969.
After a decade in Leeds and a sabbatical year at Caltech, John moved to
pastures new, first as Buchanan Professor of Genetics at Edinburgh from
1976-84, and then as Balfour Professor of Genetics at Cambridge from
1984-91. John then "retired" and moved back to Edinburgh, but continued
actively working and publishing until 2000.
During his career, John served as Editor of Heredity from 1971-78 and
President of The Genetical Society from 1978-81.
John¹s abiding interest was fungal genetics, specifically relating to
Neurospora crassa. In this, his publications reflect his pioneering work on
genetic and molecular analysis of the am gene, genetic analysis of acu genes
and the TCA cycle, chemical mutagenesis, reversion and the nature of
mutants, intragenic complementation, fine structure mapping of am, protein
sequencing of the am gene product, colinearity of gene and gene product,
nonsense mutants and non-allelic suppressors. Apart from fungal genetics,
John was also involved in research on highly mutable anthocyanin pigment
genes and transposons in plants was another interest he pursued for a
significant part of his research career. In addition to his research papers,
he wrote the classic monograph "Fungal Genetics" which ran to four editions,
a monograph on complementation and an authoritative review on fungal
transformation
If anyone can take the credit for leading fungal genetics from the classical
to the molecular era, it is John Fincham.
Alan Radford
************************************
4. The abstracts for the 23rd FUNGAL GENETICS CONFERENCE are now online at
http://www.fgsc.net/asil2005/asil2005posterabs.htm
************************************
5. The Neurospora business lunch will be held during the FUNGAL GENETICS
CONFERENCE on Friday in the small lunch room. If you have any business that
you would like to discuss during the meeting, please let someone from the
NPC know.
************************************
6. Don¹t forget to visit the Neurospora home page at
http://www.fgsc.net/Neurospora/ Please direct any feedback or suggestions to
Tony Griffiths at: agriff@interchange.ubc.ca.
************************************
7. Also, please visit the Perkins lab website, where Raju has compiled a
photo resource of wild type and mutant Neurospora http://www.stanford.edu/group/neurospora/Photos.html
************************************
8. Recent publications Nov 2004 - Feb 2005
He Q, Shu H, Cheng P, Chen S, Wang L, Liu Y.
Light-independent phosphorylation of white collar-1 regulates its function
in the Neurospora circadian negative feedback loop.
J Biol Chem. 2005 Feb 24; [Epub ahead of print]
PMID: 15731099 [PubMed - as supplied by publisher]
Maas MF, van Mourik A, Hoekstra RF, Debets AJ.
Polymorphism for pKALILO based senescence in Hawaiian populations of
Neurospora intermedia and Neurospora tetrasperma.
Fungal Genet Biol. 2005 Mar;42(3):224-32. Epub 2005 Jan 05.
PMID: 15707843 [PubMed - in process]
Alcantara-Sanchez F, Reynaga-Pena CG, Salcedo-Hernandez R, Ruiz-Herrera J.
Possible role of ionic gradients in the apical growth of Neurospora crassa.
Antonie Van Leeuwenhoek. 2004 Nov;86(4):301-11.
PMID: 15702382 [PubMed - in process]
Krystofova S, Borkovich KA.
The Heterotrimeric G-Protein Subunits GNG-1 and GNB-1 Form a G{beta}{gamma}
Dimer Required for Normal Female Fertility, Asexual Development, and G{alpha}
Protein Levels in Neurospora crassa.
Eukaryot Cell. 2005 Feb;4(2):365-78.
PMID: 15701799 [PubMed - in process]
Schmitt S, Ahting U, Eichacker L, Granvogl B, Go NE, Nargang FE, Neupert W,
Nussberger S.
Role of TOM5 in maintaining the structural stability of the TOM complex of
mitochondria.
J Biol Chem. 2005 Feb 8; [Epub ahead of print]
PMID: 15701639 [PubMed - as supplied by publisher]
D'Souza AD, Sultana S, Maheshwari R.
Characterization and prevalence of a circular mitochondrial plasmid in
senescence-prone isolates of Neurospora intermedia.
Curr Genet. 2005 Feb 8; [Epub ahead of print]
PMID: 15700140 [PubMed - as supplied by publisher]
Paukstelis PJ, Coon R, Madabusi L, Nowakowski J, Monzingo A, Robertus J,
Lambowitz AM.
A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by
acquiring a new RNA binding surface.
Mol Cell. 2005 Feb 4;17(3):417-28.
PMID: 15694342 [PubMed - in process]
\
de Paula RM, Wilson WA, Terenzi HF, Roach PJ, Bertolini MC.
GNN is a self-glucosylating protein involved in the initiation step of
glycogen biosynthesis in Neurospora crassa.
Arch Biochem Biophys. 2005 Mar 1;435(1):112-24.
PMID: 15680913 [PubMed - in process]
Pregueiro AM, Price-Lloyd N, Bell-Pedersen D, Heintzen C, Loros JJ, Dunlap
JC.
Assignment of an essential role for the Neurospora frequency gene in
circadian entrainment to temperature cycles.
Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2210-5. Epub 2005 Jan 26.
PMID: 15677317 [PubMed - in process]
D'Souza AD, Bertrand H, Maheshwari R.
Intramolecular recombination and deletions in mitochondrial DNA of
senescent, a nuclear-gene mutant of Neurospora crassa exhibiting "death"
phenotype.
Fungal Genet Biol. 2005 Feb;42(2):178-90. Epub 2004 Dec 29.
PMID: 15670715 [PubMed - in process]
Scheffer J, Ziv C, Yarden O, Tudzynski P.
The COT1 homologue CPCOT1 regulates polar growth and branching and is
essential for pathogenicity in Claviceps purpurea.
Fungal Genet Biol. 2005 Feb;42(2):107-18. Epub 2004 Nov 25.
PMID: 15670709 [PubMed - in process]
Youssar L, Schmidhauser TJ, Avalos J.
The Neurospora crassa gene responsible for the cut and ovc phenotypes
encodes a protein of the haloacid dehalogenase family.
Mol Microbiol. 2005 Feb;55(3):828-38.
PMID: 15661007 [PubMed - in process]
Park C, Bennion B, Francois IE, Ferket KK, Cammue BP, Thevissen K, Levery
SB. Characterization of neutral glycolipids of the model filamentous fungus,
neurospora crassa: altered expression in plant defensin-resistant mutants.
J Lipid Res. 2005 Jan 16; [Epub ahead of print]
PMID: 15654124 [PubMed - as supplied by publisher]
Francois P.
A model for the Neurospora circadian clock.
Biophys J. 2005 Jan 14; [Epub ahead of print]
PMID: 15653726 [PubMed - as supplied by publisher]
Li YY, Zhao YZ.
[A Simple Method to Correct Genetic Distance Between Linked Genes and a
Correction of Calculating Data in Tetrad Analysis in Neurospora crassa.] Yi
Chuan. 2003 May;25(3):330-2. Chinese.
PMID: 15639882 [PubMed - in process]
Laurila MR, Salgado PS, Makeyev EV, Nettelship J, Stuart DI, Grimes JM,
Bamford DH.
Gene silencing pathway RNA-dependent RNA polymerase of Neurospora crassa:
yeast expression and crystallization of selenomethionated QDE-1 protein.
J Struct Biol. 2005 Jan;149(1):111-5.
PMID: 15629662 [PubMed - in process]
Cheng P, He Q, He Q, Wang L, Liu Y.
Regulation of the Neurospora circadian clock by an RNA helicase.
Genes Dev. 2005 Jan 15;19(2):234-41. Epub 2004 Dec 29.
PMID: 15625191 [PubMed - in process]
Kumar KS, Dayananda S, Subramanyam C.
Copper alone, but not oxidative stress, induces copper-metallothionein gene
in Neurospora crassa.
FEMS Microbiol Lett. 2005 Jan 1;242(1):45-50.
PMID: 15621418 [PubMed - in process]
Pratt RJ, Lee DW, Aramayo R.
DNA methylation affects meiotic trans-sensing, not meiotic silencing, in
Neurospora.
Genetics. 2004 Dec;168(4):1925-35.
PMID: 15611165 [PubMed - in process]
Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, Zhang X, Selker EU,
Shinkai Y, Cheng X. Related Articles, Links
In vitro and in vivo analyses of a phe/tyr switch controlling product
specificity of histone lysine methyltransferases.
J Biol Chem. 2005 Feb 18;280(7):5563-70. Epub 2004 Dec 06.
PMID: 15590646 [PubMed - in process]
Rajyalaxmi RS, Sowjanya TN, Kiranmayi P, Mohan MP.
Mechanism of nickel resistance in a cobalt-resistant wall-less mutant of
Neurospora crassa (fz; sg; os-1).
Indian J Exp Biol. 2004 Nov;42(11):1117-22.
PMID: 15587120 [PubMed - indexed for MEDLINE]
Francis K, Russell B, Gadda G.
Involvement of a flavosemiquinone in the enzymatic oxidation of nitroalkanes
catalyzed by 2-nitropropane dioxygenase.
J Biol Chem. 2005 Feb 18;280(7):5195-204. Epub 2004 Dec 06.
PMID: 15582992 [PubMed - in process]
Dettman JR, Taylor JW.
Mutation and evolution of microsatellite Loci in neurospora.
Genetics. 2004 Nov;168(3):1231-48.
PMID: 15579682 [PubMed - in process]
Karaoglu H, Lee CM, Meyer W.
Survey of Simple Sequence Repeats in Completed Fungal Genomes.
Mol Biol Evol. 2005 Mar;22(3):639-649. Epub 2004 Nov 24.
PMID: 15563717 [PubMed - as supplied by publisher]
Freitas FZ, Bertolini MC.
Genomic organization of the Neurospora crassa gsn gene: possible involvement
of the STRE and HSE elements in the modulation of transcription during heat
shock.
Mol Genet Genomics. 2004 Dec;272(5):550-61. Epub 2004 Nov 19.
PMID: 15558319 [PubMed - in process]
Faou P, Tropschug M.
Neurospora crassa CyPBP37: a cytosolic stress protein that is able to
replace yeast Thi4p function in the synthesis of vitamin B1.
J Mol Biol. 2004 Dec 3;344(4):1147-57.
PMID: 15544818 [PubMed - indexed for MEDLINE]
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB.Conservation
and evolution of cis-regulatory systems in ascomycete fungi.
PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 09.
PMID: 15534694 [PubMed - in process]
Xie X, Wilkinson HH, Correa A, Lewis ZA, Bell-Pedersen D, Ebbole DJ.
Transcriptional response to glucose starvation and functional analysis of a
glucose transporter of Neurospora crassa.
Fungal Genet Biol. 2004 Dec;41(12):1104-19.
PMID: 15531214 [PubMed - in process]
Xiang Q, Glass NL.
The control of mating type heterokaryon incompatibility by vib-1, a locus
involved in het-c heterokaryon incompatibility in Neurospora crassa.
Fungal Genet Biol. 2004 Dec;41(12):1063-76.
PMID: 15531211 [PubMed - in process]
Hu G, Leger RJ. Related Articles, Links
A phylogenomic approach to reconstructing the diversification of serine
proteases in fungi.
J Evol Biol. 2004 Nov;17(6):1204-14.
PMID: 15525405 [PubMed - indexed for MEDLINE]
Gooch VD, Freeman L, Lakin-Thomas PL.
Time-lapse analysis of the circadian rhythms of conidiation and growth rate
in neurospora.
J Biol Rhythms. 2004 Dec;19(6):493-503.
PMID: 15523111 [PubMed - in process]
Radford A.
Metabolic highways of Neurospora crassa revisited.
Adv Genet. 2004;52:165-207.
PMID: 15522735 [PubMed - in process]
Cobine PA, McKay RT, Zangger K, Dameron CT, Armitage IM.
Solution structure of Cu6 metallothionein from the fungus Neurospora crassa.
Eur J Biochem. 2004 Nov;271(21):4213-21.
PMID: 15511227 [PubMed - indexed for MEDLINE]
Lakin-Thomas PL, Brody S.
Circadian rhythms in microorganisms: new complexities.
Annu Rev Microbiol. 2004;58:489-519. Review.
PMID: 15487946 [PubMed - indexed for MEDLINE]
Fuchs F, Westermann B.
Role of Unc104/KIF1-related motor proteins in mitochondrial transport in
Neurospora crassa.
Mol Biol Cell. 2005 Jan;16(1):153-61. Epub 2004 Oct 13.
PMID: 15483054 [PubMed - in process]
Descheneau AT, Cleary IA, Nargang FE.
Genetic Evidence for a Regulatory Pathway Controlling Alternative Oxidase
Production in Neurospora crassa.
Genetics. 2005 Jan;169(1):123-35. Epub 2004 Sep 30.
PMID: 15466423 [PubMed - in process]
Goldoni M, Azzalin G, Macino G, Cogoni C.
Efficient gene silencing by expression of double stranded RNA in Neurospora
crassa.
Fungal Genet Biol. 2004 Nov;41(11):1016-24.
PMID: 15465390 [PubMed - indexed for MEDLINE]
Lew RR, Levina NN, Walker SK, Garrill A.
Turgor regulation in hyphal organisms.
Fungal Genet Biol. 2004 Nov;41(11):1007-15.
PMID: 15465389 [PubMed - indexed for MEDLINE]
Yu JH, Hamari Z, Han KH, Seo JA, Reyes-Dominguez Y, Scazzocchio C.
Double-joint PCR: a PCR-based molecular tool for gene manipulations in
filamentous fungi.
Fungal Genet Biol. 2004 Nov;41(11):973-81.
PMID: 15465386 [PubMed - indexed for MEDLINE]
************************************
Cheers,
The NPC
Deb Bell-Pedersen dpedersen@mail.bio.tamu.edu Tony Griffiths agriff@unixg.ubc.ca
Nora Plesofsky nora@biosci.cbs.umn.edu Oded Yarden Oded.Yarden@huji.ac.il
August, 2004
The E-NEWS is issued by the Neurospora Policy Committee (NPC).
Names and addresses are listed at the end of this message.
Items that you wish to include in future issues can be sent to Deb
Bell-Pedersen at dpedersen@mail.bio.tamu.edu.
1. Funding opportunities - NPC query.
The National Institute of General Medical Sciences (NIGMS) has issued a
program announcement (PA) entitled, Tools for Genetic and Genomic Studies in
Emerging Model Organisms. The purpose of this initiative is to stimulate
resource and technology development for studying novel and promising model
organism systems. Application receipt dates are October 1, February 1, and
June 1. Further details, including eligibility and special requirements, can
be found at http://grants.nih.gov/grants/guide/pa-files/PA-04-135.html.
A couple of groups have made preliminary contact with the NIH and it is
clear that they are interested in Neurospora.
These are not big grants that would support many labs (i.e. comparable to
the Program Project Grant), but NIH would likely favor projects that are
broadly supported by the community.
The Neurospora policy committee would like to help coordinate efforts
(putting people together who have similar interests). It is important that
we have at least one, but
probably not numerous, proposal going in at different times (Oct. 1, Feb 1,
etc).
If you are interested in putting together a proposal and would like the help
of the NPC in coordinating this, please let the NPC know your intentions.
2. The Neurospora 2004 meeting
There was a great turnout for the bienneial Neurospora Conference, held in
Asilomar California, March 25-28. In terms of both the level of science
and the personal interactions it was a real success. Abstracts of both the
talks and the posters can be viewed at FGSC website. Two new members of
the Neurospora Policy Committee were elected, Nora Plesofsky and Oded
Yarden. They will serve for four years and will organize the program for
Neurospora
2006. Gloria Turner and Barry Bowman rotate off the committee, with the
gratitude of the Neurospora Community.
Matt Sachs kindly put together a photo gallery of the meeting which can be
viewed on the FGSC web site.
3. Beadle and Tatum Award.
Yi Liu from UT Southwestern was the recipeint of the Beadle and Tatum Award
for outstanding research. Yi's research on circadian clocks is an excellent
example of the power of combining biochemical, molecular, genetic and
physiological approaches to address a fundamental biological question. Yi
has used Neurospora
to make many important contributions to understanding the mechanism of the
cellular oscillator, beginning with his postdoctoral work in the labs of Jay
Dunlap and
Jennifer Loros at Dartmouth where he demonstrated that temperature directly
affects key components of the clock. In recent years Yi has continued his
focus on
identifying the mechanisms by which organisms keep time and has added
several new components to the basic feedback loop. The award was presented
by David Perkins,
Stanford University, at the Neurospora meeting in Asilomar. Congratulations
to Yi for his outstanding contributions to understanding central questions
in cell and molecular biology.
4. Perkins Award.
Graduate student Carolyn Rasmussen was this years recipient of the Perkins
Award. This award was established in honor of our colleague, Dr. David
Perkins, to support outstanding
students attending the Neurospora and Fungal Genetics Conferences. Carolyn
is a graduate student in Louise Glass's lab and her work has focused on
characterizing the hyphal
fusion process in filamentous fungi using Neurospora crassa as a model. She
is an author on several papers, and her enthusiasm for science was clearly
evident in her presentation
at the meeting. We would like to congratulate Carolyn for her outstanding
achievements and her continued success.
5. Neurospora crassa Program Project Grant
A Program Project Grant was funded by the NIH (NIGMS) entitled "Functional
Analysis of a Model Filamentous Fungus. The overall goal of the four
projects is to conduct functional
genomics, annotation, and expression analyses of Neurospora crassa. The
first project (PI-Jay Dunlap, Co-PI, Kathy Borkovich) will be to carry out
systematic gene disruption using
targeted gene replacements, preliminary phenotype analysis of the
disruptants (Investigator, Richard Weiss), and distribution of the strains
to the community by the FGSC.
Project 2 (PI Bruce Birren, Co-PI James Galagan, Investigator Matthew Sachs)
will produce a framework for electronically capturing community feedback and
data about the existing annotation,
and building a data base to display phenotype and expression information
from the other projects in the grant. Project 3 (Louise Glass PI, Michael
Eisen, Co-PI) will involve the production of
microarrays using oligonucleotides representing all of the genes. The slides
will be used to provide a baseline analysis of gene expression under a
variety of growth conditions, and then will
analyze the global effects of the loss of novel genes in strains created by
the knockout project. The data will be made available to the community
through a WICGR web site created
in project 2. In project 4 (PI Mary Anne Nelson, Investigators Jennifer
Loros and Bruce Birren) cDNA libraries will be generated and sequenced from
Oak Ridge and Mauriceville strains to
aid in the annotation of project 2 and to allow for the assembly of a SNP
map.
6. Neurospora Home Page.
Thanks to the heroic efforts of Tony Griffiths and the FGSC, the finishing
touches are being put on the new Neurospora Home Page.
You can view a draft of the site at http://www.fgsc.net/Neurospora/
Please direct any feedback or suggestions to Tony at agriff@interchange.ubc.ca.
7. Neurospora Methods Book.
The Neurospora Methods Book is progressing. Many of you have already
submitted your methods and these will soon be going out for review. Once
they are reviewed, they will be posted on
the new Neurospora Home Page. For those of you who have volunteered to
contribute a method, I would like to take this opportunity to encourage you
to get them submitted to
dpedersen@mail.bio.tamu.edu.
8. Fungal Genetics Stock Center http://www.fgsc.net/
The FGSC moved from KUMC to the University of Missouri, Kansas City in June,
2004.
Dr. Mike Plamann is the new FGSC director. Dr. Kevin McCluskey (curator of
the FGSC and a Research Associate Professor) and Sheera Garcia
moved with the FGSC from the University of Kansas to the University of
Missouri.
The FGSC has been an invaluable asset to our community. The core function of
the FGSC is the collection and distribution of mutant and wild type strains.
The best way you can support the
FGSC is to use it. Send in your strains and make use of the many strains
available.
From publications we see that many interesting and important mutant strains
are being generated. It is essential that the FGSC continue to be the
central repository for these strains.
9. Upcoming Meetings
The First International Fungal Proteomics Symposium
October 20-24, 2004
Hotel Vintage Plaza, Portland, Oregon
co-hosted by the U.S. Department of Energy's Pacific Northwest National
Laboratory and Oregon Health & Science University
sponsored by
Pacific Northwest National Laboratory
10. Recent publications (Apr 2004 - Aug 2004).
If an article was omitted by mistake, please send the reference to dpedersen@mail.bio.tamu.edu
and it will be included in the next e-news.
Agustin Chicas, Carlo Cogoni, and Giuseppe Macino
RNAi-dependent and RNAi-independent mechanisms contribute to the silencing
of RIPed sequences in Neurospora crassa
Nucleic Acids Res., Aug 2004; 32: 4237 - 4243.
Emma C. Forrest, Carlo Cogoni, and Giuseppe Macino
The RNA-dependent RNA polymerase, QDE-1, is a rate-limiting factor in
post-transcriptional gene silencing in Neurospora crassa
Nucleic Acids Res., Apr 2004; 32: 2123 - 2128.
P. Jane Yeadon, F. J. Bowring, and D. E. A. Catcheside
Alleles of the Hotspot cog Are Codominant in Effect on Recombination in the
his-3 Region of Neurospora
Genetics, Jul 2004; 167: 1143 - 1153.
R Ambra, B Grimaldi, S Zamboni, P Filetici, G Macino, and P Ballario
Photomorphogenesis in the hypogeous fungus Tuber borchii: isolation and
characterization of Tbwc-1, the homologue of the blue-light photoreceptor of
Neurospora crassa.
Fungal Genet Biol, Jul 2004; 41(7): 688-97.
Michael W. Vitalini, Louis W. Morgan, Irene J. March, and Deborah
Bell-Pedersen
A Genetic Selection for Circadian Output Pathway Mutations in Neurospora
crassa
Genetics, May 2004; 167: 119 - 129.
Lori Bailey-Shrode and Daniel J. Ebbole
The fluffy Gene of Neurospora crassa Is Necessary and Sufficient to Induce
Conidiophore Development
Genetics, Apr 2004; 166: 1741 - 1749.
Ashwin Bhat, Ranjan Tamuli, and Durgadas P. Kasbekar
Genetic Transformation of Neurospora tetrasperma , Demonstration of
Repeat-Induced Point Mutation (RIP) in Self-Crosses and a Screen for
Recessive RIP-Defective Mutants
Genetics, Jul 2004; 167: 1155 - 1164.
Dong W. Lee, Kye-Yong Seong, Robert J. Pratt, Kevin Baker, and Rodolfo
Aramayo
Properties of Unpaired DNA Required For Efficient Silencing in Neurospora
crassa
Genetics, May 2004; 167: 131 - 150.
Amita Pandey, M. Gabriela Roca, Nick D. Read, and N. Louise Glass
Role of a Mitogen-Activated Protein Kinase Pathway during Conidial
Germination and Hyphal Fusion in Neurospora crassa
Eukaryot. Cell, Apr 2004; 3: 348 - 358.
Yuuko Ninomiya, Keiichiro Suzuki, Chizu Ishii, and Hirokazu Inoue
From The Cover: Highly efficient gene replacements in Neurospora strains
deficient for nonhomologous end-joining
PNAS, Aug 2004; 101: 12248 - 12253.
XIN CHEN, GEORG MOHR, and ALAN M. LAMBOWITZ
The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps
stabilize interdomain tertiary interactions in group I introns
RNA, Apr 2004; 10: 634 - 644.
PJ Yeadon, FJ Bowring, and DE Catcheside
Sequence heterology and gene conversion at his-3 of Neurospora crassa.
Curr Genet, May 2004; 45(5): 289-301.
Soledad Funes, Frank E. Nargang, Walter Neupert, and Johannes M. Herrmann
The Oxa2 Protein of Neurospora crassa Plays a Critical Role in the
Biogenesis of Cytochrome Oxidase and Defines a Ubiquitous Subbranch of the
Oxa1/YidC/Alb3 Protein Family
Mol. Biol. Cell, Apr 2004; 15: 1853 - 1861.
M Riquelme and S Bartnicki-Garcia
Key differences between lateral and apical branching in hyphae of Neurospora
crassa.
Fungal Genet Biol, Sep 2004; 41(9): 842-51.
EL Bain, AJ Millar, and MS Turner
The wild-type circadian period of Neurospora is encoded in the residual
network of the null frq mutants.
J Theor Biol, Aug 2004; 229(3): 413-20.
Emma Jean Bowman, Laurie A. Graham, Tom H. Stevens, and Barry J. Bowman
The Bafilomycin/Concanamycin Binding Site in Subunit c of the V-ATPases from
Neurospora crassa and Saccharomyces cerevisiae
J. Biol. Chem., Aug 2004; 279: 33131 - 33138.
NB Raju and AG Burk
Abnormal ascospore morphology in the bud mutant of Neurospora tetrasperma.
Fungal Genet Biol, Jun 2004; 41(6): 582-9.
AL Rosa, HD Folco, and MR Mautino
In vivo levels of S-adenosylmethionine modulate C:G to T:A mutations
associated with repeat-induced point mutation in Neurospora crassa.
Mutat Res, Apr 2004; 548(1-2): 85-95.
RR Lew and NN Levina
Oxygen flux magnitude and location along growing hyphae of Neurospora
crassa.
FEMS Microbiol Lett, Apr 2004; 233(1): 125-30.
Zelter, M Bencina, BJ Bowman, O Yarden, and ND Read
A comparative genomic analysis of the calcium signaling machinery in
Neurospora crassa, Magnaporthe grisea, and Saccharomyces cerevisiae.
Fungal Genet Biol, Sep 2004; 41(9):827-41.
Yuji Furutani, Arandi G. Bezerra Jr , Stephen Waschuk, Masayo Sumii, Leonid
S. Brown, and Hideki Kandori
FTIR Spectroscopy of the K Photointermediate of Neurospora Rhodopsin:
Structural Changes of the Retinal, Protein, and Water Molecules after
Photoisomerization.
Biochemistry, Aug 2004; 43(30): 9636-9646.
MK Christensen, G Falkeid, JJ Loros, JC Dunlap, C Lillo, and P Ruoff
A Nitrate-Induced frq-Less Oscillator in Neurospora crassa.
J Biol Rhythms, Aug 2004; 19(4): 280-6.
F Kempken and F Windhofer
Alternative splicing of transcripts of the transposon Restless is maintained
in the foreign host Neurospora crassa and can be modified by introducing
mutations at the 5' and 3' splice sites.
Curr Genet, Jul 2004; 46(1): 59-65.
H Kim and KA Borkovich
A pheromone receptor gene, pre-1, is essential for mating type-specific
directional growth and fusion of trichogynes and female fertility in
Neurospora crassa.
Mol Microbiol, Jun 2004; 52(6): 1781-98.\
Y Tan, M Merrow, and T Roenneberg
Photoperiodism in Neurospora crassa.
J Biol Rhythms, Apr 2004; 19(2): 135-43.
Michael Freitag, Dong W. Lee, Gregory O. Kothe, Robert J. Pratt, Rodolfo
Aramayo, and Eric U. Selker
DNA Methylation Is Independent of RNA Interference in Neurospora
Science, Jun 2004; 304: 1939.
****************************************************
The Neurospora Policy Committee
Tony Griffiths
Department of Botany
University of British Columbia
6270 University Blvd.
Vancouver, B. C. V6T 1Z4 Canada
Phone 604-822-5629
Email agriff@unixg.ubc.ca
Oded Yarden
Dept. of Plant Pathology and Microbiology
Faculty of Agricultural, Food and Environmental Quality Sciences
The Hebrew University of Jerusalem
Rehovot 76100
Israel
Email Oded.Yarden@huji.ac.il
Phone 972-8-9489298
Deborah Bell-Pedersen
Department of Biology
Texas A&M University
3258 TAMU
College Station , TX 77843
Phone 979-845-2891
Email dpedersen@mail.bio.tamu.edu
Nora Plesofsky
Dept. of Plant Biology
University of Minnesota
220 BioSciences Center, 1445 Gortner Ave
St. Paul, MN 55108
Phone 612-624-5375
Email nora@biosci.cbs.umn.edu