David D. Perkins

All Publications

• A fratricidal fungal prion PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Perkins, D. D. 2003; 100 (11): 6292-6294

  View details for DOI 10.1073/pnas.1332353100

  View details for Web of Science ID 000183190700002

  View details for PubMedID 12754381

• Neurospora from natural populations: a global study FUNGAL GENETICS AND BIOLOGY Turner, B. C., Perkins, D. D., Fairfield, A. 2001; 32 (2): 67-92

  Abstract

  This is a summary report on samples of conidiating Neurospora species collected over three decades, in many regions around the world, primarily from burned vegetation. The genus is ubiquitous in humid tropical and subtropical regions, but populations differ from region to region with regard to which species are present. The entire collection, >4600 cultures from 735 sites, is listed by geographical origin and species. Over 600 cultures from 78 sites have been added since the most recent report. Stocks have been deposited at the Fungal Genetics Stock Center. New cultures were crossed to testers for species identification; evident mixed cultures were separated into pure strains, which were identified individually. New techniques and special testers were used to analyze cultures previously listed without species identification. The discussion summarizes what has been learned about species and natural populations, describes laboratory investigations that have employed wild strains, and makes suggestions for future work.

  View details for DOI 10.1006/fgbi.2001.1247

  View details for Web of Science ID 000168362800001

  View details for PubMedID 11352529

• Neurospora at the millennium FUNGAL GENETICS AND BIOLOGY Perkins, D. D., Davis, R. H. 2000; 31 (3): 153-167

  View details for DOI 10.1006/fgbi.2000.1248

  View details for Web of Science ID 000167271900003

  View details for PubMedID 11273678

• Evidence for safety of Neurospora species for academic and commercial uses APPLIED AND ENVIRONMENTAL MICROBIOLOGY Perkins, D. D., Davis, R. H. 2000; 66 (12): 5107-5109

  View details for Web of Science ID 000167112400001

  View details for PubMedID 11097875

  View details for PubMedCentralID PMC92429

• Programmed ascospore death in the homothallic ascomycete Coniochaeta tetraspora FUNGAL GENETICS AND BIOLOGY Raju, N. B., Perkins, D. D. 2000; 30 (3): 213-221

  Abstract

  Immature asci of Coniochaeta tetraspora originally contain eight uninucleate ascospores. Two ascospore pairs in each ascus survive and mature, and two die and degenerate. Arrangement of the two ascospore types in individual linear asci is what would be expected if death is controlled by a chromosomal gene segregating at the second meiotic division in about 50% of asci. Cultures originating from single homokaryotic ascospores or from single uninucleate conidia are self-fertile, again producing eight-spored asci in which four spores disintegrate, generation after generation. These observations indicate that differentiation of two nuclear types occurs de novo in each sexual generation, that it involves alteration of a specific chromosome locus, and that the change occurs early in the sexual phase. One, and only one, of the two haploid nuclei entering each functional zygote must carry the altered element, which is segregated into two of the four meiotic products and is eliminated when ascospores that contain it disintegrate. Fusion of nuclei cannot be random-a recognition mechanism must exist. More study will be needed to determine whether the change that is responsible for ascospore death is genetic or epigenetic, whether it occurs just before the formation of each ascus or originates only once in the ascogonium prior to proliferation of ascogenous hyphae, and whether it reflects developmentally triggered alteration at a locus other than mating type or the activation of a silent mating-type gene that has pleiotropic effects. Similar considerations apply to species such as Sclerotinia trifoliorum and Chromocrea spinulosa, in which all ascospores survive but half the spores in each ascus are small and self-sterile. Unlike C. tetraspora, another four-spored species, Coniochaetidium savoryi, is pseudohomothallic, with ascus development resembling that of Podospora anserina.

  View details for DOI 10.1006/fgbi.2000.1217

  View details for Web of Science ID 000165114700006

  View details for PubMedID 11035943

• Occurrence of repeat induced point mutation in long segmental duplications of Neurospora GENETICS Perkins, D. D., Margolin, B. S., Selker, E. U., HAEDO, S. D. 1997; 147 (1): 125-136

  Abstract

  Previous studies of repeat induced point mutation (RIP) have typically involved gene-size duplications resulting from insertion of transforming DNA at ectopic chromosomal positions. To ascertain whether genes in larger duplications are subject to RIP, progeny were examined from crosses heterozygous for long segmental duplications obtained using insertional or quasiterminal translocations. Of 17 distinct mutations from crossing 11 different duplications, 13 mapped within the segment that was duplicated in the parent, one was closely linked, and three were unlinked. Half of the mutations in duplicated segments were at previously unknown loci. The mutations were recessive and were expressed both in haploid and in duplication progeny from Duplication x Normal, suggesting that both copies of the wild-type gene had undergone RIP. Seven transition mutations characteristic of RIP were found in 395 base pairs (bp) examined in one ro-11 allele from these crosses and three were found in approximately 750 bp of another. A single chain-terminating C to T mutation was found in 800 bp of arg-6. RIP is thus responsible. These results are consistent with the idea that the impaired fertility that is characteristic of segmental duplications is due to inactivation by RIP of genes needed for progression through the sexual cycle.

  View details for Web of Science ID A1997XT62000011

  View details for PubMedID 9286673

• Chromosome rearrangements in Neurospora and other filamentous fungi ADVANCES IN GENETICS, VOL 36 Perkins, D. D. 1997; 36: 239-398

  Abstract

  Knowledge of fungal chromosome rearrangements comes primarily from N. crassa, but important information has also been obtained from A. nidulans and S. macrospora. Rearrangements have been identified in other Sordaria species and in Cochliobolus, Coprinus, Magnaporthe, Podospora, and Ustilago. In Neurospora, heterozygosity for most chromosome rearrangements is signaled by the appearance of unpigmented deficiency ascospores, with frequencies and ascus types that are characteristic of the type of rearrangement. Summary information is provided on each of 355 rearrangements analyzed in N. crassa. These include 262 reciprocal translocations, 31 insertional translocations, 27 quasiterminal translocations, 6 pericentric inversions, 1 intrachromosomal transposition, and numerous complex or cryptic rearrangements. Breakpoints are distributed more or less randomly among the seven chromosomes. Sixty of the rearrangements have readily detected mutant phenotypes, of which half are allelic with known genes. Constitutive mutations at certain positively regulated loci involve rearrangements having one breakpoint in an upstream regulatory region. Of 11 rearrangements that have one breakpoint in or near the NOR, most appear genetically to be terminal but are in fact physically reciprocal. Partial diploid strains can be obtained as recombinant progeny from crosses heterozygous for insertional or quasiterminal rearrangements. Duplications produced in this way precisely define segments that cover more than two thirds of the genome. Duplication-producing rearrangements have many uses, including precise genetic mapping by duplication coverage and alignment of physical and genetic maps. Typically, fertility is greatly reduced in crosses parented by a duplication strain. The finding that genes within the duplicated segment have undergone RIP mutation in some of the surviving progeny suggests that RIP may be responsible for the infertility. Meiotically generated recessive-lethal segmental deficiencies can be rescued in heterokaryons. New rearrangements are found in 10% or more of strains in which transforming DNA has been stably integrated. Electrophoretic separation of rearranged chromosomal DNAs has found useful applications. Synaptic adjustment occurs in inversion heterozygotes, leading progressively to nonhomologous association of synaptonemal complex lateral elements, transforming loop pairing into linear pairing. Transvection has been demonstrated in Neurospora. Beginnings have been made in constructing effective balancers. Experience has increased our understanding of several phenomena that may complicate analysis. With some rearrangements, nondisjunction of centromeres from reciprocal translocation quadrivalents results in 3:1 segregation and produces asci with four deficiency ascospores that occupy diagnostic positions in linear asci. Three-to-one segregation is most frequent when breakpoints are near centromeres. With some rearrangements, inviable deficiency ascospores become pigmented. Diagnosis must then depend on ascospore viability. In crosses between highly inbred strains, analysis may be handicapped by random ascospore abortion. This is minimized by using noninbred strains as testers.

  View details for Web of Science ID A1997BJ62A00006

  View details for PubMedID 9348657

• CYTOGENETICS OF AN INTRACHROMOSOMAL TRANSPOSITION IN NEUROSPORA CHROMOSOMA Perkins, D. D., Turner, B. C., Barry, E. G., POLLARD, V. C. 1995; 104 (4): 260-273

  Abstract

  Knowledge of intrachromosomal transpositions has until now been primarily cytological and has been limited to Drosophila and to humans, in both of which segmental shifts can be recognized by altered banding patterns. There has been little genetic information. In this study, we describe the genetic and cytogenetic properties of a transposition in Neurospora crassa. In Tp(IR-->IL)T54M94, a 20 map unit segment of linkage group I has been excised from its normal position and inserted near the centromere in the opposite arm, in inverted order. In crosses heterozygous for the transposition, about one-fifth of surviving progeny are duplications carrying the transposed segment in both positions. These result from crossing over in the interstitial region. There is no corresponding class of progeny duplicated for the interstitial segment. The duplication strains are barren in test crosses. A complementary deficiency class is represented by unpigmented, inviable ascospores. Extent of the duplication was determined by duplication-coverage tests. Orientation of the transposed segment was determined using Tp x Tp crosses heterozygous for markers inside and outside the transposed segment, and position of the insertion relative to the centromere was established using quasi-ordered half-tetrads from crosses x Spore killer. Quelling was observed in the primary transformants that were used to introduce a critical marker into the transposed segment by repeat-induced point mutation (RIP).

  View details for Web of Science ID A1995TJ92400004

  View details for PubMedID 8565702

• CHROMOSOME REARRANGEMENTS THAT INVOLVE THE NUCLEOLUS ORGANIZER REGION IN NEUROSPORA GENETICS Perkins, D. D., Raju, N. B., Barry, E. G., Butler, D. K. 1995; 141 (3): 909-923

  Abstract

  In approximately 3% of Neurospora crassa rearrangements, part of a chromosome arm becomes attached to the nucleolus organizer region (NOR) at one end of chromosome 2 (linkage group V). Investigations with one inversion and nine translocations of this type are reported here. They appear genetically to be nonreciprocal and terminal. When a rearrangement is heterozygous, about one-third of viable progeny are segmental aneuploids with the translocated segment present in two copies, one in normal position and one associated with the NOR. Duplications from many of the rearrangements are highly unstable, breaking down by loss of the NOR-attached segment to restore normal chromosome sequence. When most of the rearrangements are homozygous, attenuated strands can be seen extending through the unstained nucleolus at pachytene, joining the translocated distal segment to the remainder of chromosome 2. Although the rearrangements appear genetically to be nonreciprocal, molecular evidence shows that at least several of them are physically reciprocal, with a block of rDNA repeats translocated away from the NOR. Evidence that NOR-associated breakpoints are nonterminal is also provided by intercrosses between pairs of translocations that transfer different-length segments of the same donor-chromosome arm to the NOR.

  View details for Web of Science ID A1995TB62900011

  View details for PubMedID 8582636

  View details for PubMedCentralID PMC1206854

• 3-TO-ONE SEGREGATION FROM RECIPROCAL TRANSLOCATION QUADRIVALENTS IN NEUROSPORA AND ITS BEARING ON THE INTERPRETATION OF SPORE-ABORTION PATTERNS IN UNORDERED ASCI GENOME Perkins, D. D., Raju, N. B. 1995; 38 (4): 661-672

  Abstract

  In Neurospora, viable ascospores become black (B) when mature, whereas ascospores that are deficient for a chromosome segment are inviable and usually fail to blacken. The presence of a chromosome rearrangement can be recognized and the type of rearrangement can usually be inferred by visual inspection of asci. When a cross is heterozygous for a reciprocal translocation, asci with eight black ascospores (8B:0W) and asci with eight abortive unpigmented ("white" (W)) ascospores (0B:8W) are theoretically produced in equal numbers if homologous centromeres are equally likely to segregate from the quadrivalent in alternate or adjacent modes. In addition, 4B:4W asci are produced with a frequency characteristic of each reciprocal translocation. Information on ascospore-abortion patterns in Neurospora crassa has come predominantly from unordered ascospore octads ejected from the perithecium. Unordered asci of the 4B:4W type were initially presumed to originate by interstitial crossing over in a centromere-breakpoint interval and their frequency was used as a predictor of centromere locations. However, 4B:4W asci can result not only from interstitial crossing over but also from nondisjunction of centromeres at the first meiotic division, which leads to 3:1 segregation. Ordered linear 4B:4W asci retain the sequence information necessary for distinguishing one mode of origin from the other but unordered asci do not. Crossing over results in one abortive duplication-deficiency ascospore pair in each opposite half of a linear ascus, while 3:1 segregation places both abortive ascospore pairs together, either in the distal half or the basal half of the ascus. In the present study, perithecia were opened and intact linear asci were examined in crosses heterozygous for a varied sample of translocations. Three-to-one segregation rather than interstitial crossing over is apparently the main cause of 4B:4W asci when breakpoints are near centromeres, whereas crossing over is responsible for most or all 4B:4W asci when breakpoints are far-distal. Three-to-one segregation does not impair the usefulness of ejected unordered asci for detecting chromosome rearrangements. Ejected octads are superior to ordered linear asci for distinguishing one type of rearrangement from another, because ascus ejection from the perithecium does not occur until viable ascospores are fully pigmented, enabling true 0B:8W asci to be distinguished from those with eight immature ascospores.

  View details for Web of Science ID A1995RR17400005

  View details for PubMedID 7672602

• DIVERSE PROGRAMS OF ASCUS DEVELOPMENT IN PSEUDOHOMOTHALLIC SPECIES OF NEUROSPORA, GELASINOSPORA, AND PODOSPORA DEVELOPMENTAL GENETICS Raju, N. B., Perkins, D. D. 1994; 15 (1): 104-118

  Abstract

  Meiosis and ascospore development in the four-spored pseudohomothallic ascomycetes Neurospora tetrasperma, Gelasinospora tetrasperma, Podospora anserina, and P. tetraspora have been reexamined, highlighting differences that reflect independent origins of the four-spored condition in the different genera. In these species, as in the heterothallic eight-spored N. crassa, fusion of haploid nuclei is followed directly by meiosis and a postmeiotic mitosis. These divisions take place within a single unpartitioned giant cell, the ascus, which attains a length of > 0.1 mm before nuclei are enclosed by ascospore walls. Two basically different modes underlie the delivery of opposite mating type nuclei into each of the four ascospores in the different genera. In N. tetrasperma on the one hand, the mating type locus is closely centromere-linked. Mating types therefore segregate at the first meiotic division. The second-division spindles of N. tetrasperma overlap and are usually parallel to one another, in contrast to the their tandem arrangement in N. crassa. As a result, nonsister nuclei of opposite mating type are placed close together in each half-ascus and a pair is enclosed in each ascospore. In the Podospora and Gelasinospora species on the other hand, the second-division spindles are in tandem, with sister nuclei of opposite mating type associated as a pair in each half-ascus. It is established for P. anserina and inferred for P. tetraspora and G. tetrasperma that a single reciprocal crossing over almost always occurs in the mating type-centromere interval, ensuring that mating types segregate at the second meiotic division and that nuclei of opposite mating type are enclosed in each ascospore. Other differences are also seen that are less fundamental. Neurospora tetrasperma differs from the other species in the orientation of chromosomes and spindle pole body plaques at interphase II. Third-division spindles are oriented parallel to the ascus wall in Gelasinospora but across the ascus in Podospora and Neurospora. The two Podospora species differ from one another in nuclear behavior following mitosis in the young ascospores. In P. tetraspora, two of the four nuclei migrate into the tail cell, which degenerates, leaving one functional nucleus of each mating type. In P. anserina, by contrast, only one of the four nuclei moves into the tail cell, leaving the germinating ascospore with two functional nuclei of one mating type and one of the other. The pseudohomothallic condition with its heterokaryotic vegetative phase has significant consequences for both the individual organism and the breeding system. Genetic controls of development and recombination are complex.(ABSTRACT TRUNCATED AT 400 WORDS)

  View details for Web of Science ID A1994MZ20400010

  View details for PubMedID 8187347

• CHROMOSOME REARRANGEMENTS RECOVERED FOLLOWING TRANSFORMATION OF NEUROSPORA-CRASSA GENETICS Perkins, D. D., Kinsey, J. A., Asch, D. K., Frederick, G. D. 1993; 134 (3): 729-736

  Abstract

  New chromosome rearrangements were found in 10% or more of mitotically stable transformants. This was shown for transformations involving a variety of different markers, vectors and recipient strains. Breakpoints were randomly distributed among the seven linkage groups. Controls using untransformed protoplasts of the same strains contained almost no rearrangements. A study of molecularly characterized Am+ transformants showed that rearrangements are frequent when multiple ectopic integration events have occurred. In contrast, rearrangements are absent or infrequent when only the resident locus is restored to am+ by a homologous event. Sequences of the transforming vector were genetically linked to breakpoints in 6 of 10 translocations that were examined using Southern hybridization or colony blots.

  View details for Web of Science ID A1993LJ51300006

  View details for PubMedID 8349106

• THE BASIS OF DECREASED RECOMBINATION IN CERTAIN OUTCROSSES OF NEUROSPORA-CRASSA GENOME Perkins, D. D., Bojko, M. 1992; 35 (3): 503-509

  Abstract

  Crossing over in a multiply marked segment of linkage group I was conspicuously reduced in outcrosses between a marked laboratory strain and each of six unrelated wild-collected strains, compared with crosses between inbred laboratory strains. The marked chromosome segment was transferred intact from the inbred strain to one of the wild-collected strains by seven recurrent backcrosses, and conversely, the corresponding segment of the wild strain was transferred to the inbred background by backcrossing to the multiply marked laboratory strain. Recombination was then monitored in crosses from parents having the marked and unmarked chromosome segments from the same or from unrelated sources. Meiotic crossing-over in the marked segment remained low in crosses between parents that were dissimilar with respect to genetic background, but crossing over was restored to a high level when the genetic background of both parents was that of the inbred laboratory strain, regardless of the source of the marked segments. Reduced recombination in outcrosses was therefore not due to heterologies in the marked segment but must be attributed to modifiers that are unlinked or distant from the monitored region.

  View details for Web of Science ID A1992JA00800019

  View details for PubMedID 1385584

• NEUROSPORA - THE ORGANISM BEHIND THE MOLECULAR REVOLUTION GENETICS Perkins, D. D. 1992; 130 (4): 687-701

  View details for Web of Science ID A1992HL49000001

  View details for PubMedID 1582553

• EXPRESSION OF MEIOTIC DRIVE ELEMENTS SPORE KILLER-2 AND SPORE KILLER-3 IN ASCI OF NEUROSPORA-TETRASPERMA GENETICS Raju, N. B., Perkins, D. D. 1991; 129 (1): 25-37

  Abstract

  It was shown previously that when a chromosomal Spore killer factor is heterozygous in Neurospora species with eight-spored asci, the four sensitive ascospores in each ascus die and the four survivors are all killers. Sk-2K and Sk-3K are nonrecombining haplotypes that segregate with the centromere of linkage group III. No killing occurs when either one of these killers is homozygous, but each is sensitive to killing by the other in crosses of Sk-2K x Sk-3K. In the present study, Sk-2K and Sk-3K were transferred by recurrent backcrosses from the eight-spored species Neurospora crassa into Neurospora tetrasperma, a pseudohomothallic species which normally makes asci with four large spores, each heterokaryotic for mating type and for any other centromere-linked genes that are heterozygous in the cross. The action of Sk-2K and Sk-3K in N. tetrasperma is that predicted from their behavior in eight-spored species. A sensitive nucleus is protected from killing if it is enclosed in the same ascospore with a killer nucleus. Crosses of Sk-2K x Sk-2S, Sk-3K x Sk-3S, and Sk-sK x Sk-3K all produce four-spored asci that are wild type in appearance, with the ascospores heterokaryotic and viable. The Eight-spore gene E, which shows variable penetrance, was used to obtain N. tetrasperma asci in which two to eight spores are small and homokaryotic. When killer and sensitive alleles are segregating in the presence of E, only those ascospores that contain a killer allele survive. Half of the small ascospores are killed. In crosses of Sk-2K x Sk-3K (with E heterozygous), effectively all small ascospores are killed. The ability of N. tetrasperma to carry killer elements in cryptic condition suggests a possible role for Spore killers in the origin of pseudohomothallism, with adoption of the four-spored mode restoring ascospore viability of crosses in which killing would otherwise occur.

  View details for Web of Science ID A1991GD51200004

  View details for PubMedID 1834522