The utility of aged seeds in DNA banks

2006 ◽  
Vol 16 (3) ◽  
pp. 169-178 ◽  
Author(s):  
Christina Walters ◽  
Ann A. Reilley ◽  
Patrick A. Reeves ◽  
Jennifer Baszczak ◽  
Christopher M. Richards
Keyword(s):  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Dna Degradation ◽  
Seed Banks ◽  
Nuclear Ribosomal Dna ◽  
High Molecular Weight Dna ◽  
Viable Seeds ◽  
The Stability ◽  
Seed Dna

The long-term utility of DNA banks is predicated on the stability of DNA during storage. The quality and yield of DNA extracted from seeds from four garden species, which varied in age from 1 to 135 years old, was used to examine the early stages of DNA degradation. Seeds that were 70 years old yielded high molecular weight DNA, which permitted amplification of a 650 bp segment of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and a 487 bp segment of the plastid-encoded large subunit of rubisco (rbcL). DNA extracted from seeds estimated to be about 135 years old was degraded, but still permitted amplification when routine extraction procedures were used. The rbcL sequences obtained from c. 135-year-old cucurbit seed DNA were consistent with species identifications based on seed morphological features; however, ITS sequences from the same samples were determined to be of fungal origin. A comparison of our results with studies of DNA stability in leaf specimens suggested that DNA degraded within both tissues, but perhaps more slowly within seeds. Evidence that high-quality DNA can be extracted from old, non-viable seeds expands the utility of seed banks in preserving genetic resources.

A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽  
2017 ◽  
Vol 312 (1) ◽  
pp. 111
Author(s):  
HUAN-DI ZHENG ◽  
WEN-YING ZHUANG
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Central China ◽  
Nuclear Ribosomal Dna ◽  
Light Blue ◽  
Ectal Excipulum ◽  
A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

Acrocordiella omanensis sp. nov. (Requienellaceae, Xylariales) from the Sultanate of Oman

Phytotaxa ◽  
2018 ◽  
Vol 338 (3) ◽  
pp. 294
Author(s):  
SAJEEWA S. N. MAHARACHCHIKUMBURA ◽  
KEVIN D. HYDE ◽  
REKHANI H. PERERA ◽  
ABDULLAH M. AL-SADI
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Sultanate Of Oman ◽  
Green Mountain ◽  
Al Jabal Al Akhdar ◽  
Internal Transcribed Spacer Sequences

Acrocordiella omanensis sp. nov. is described and illustrated from specimens on dead stem of Juniper sp. collected in Al Jabal al-Akhdar (Green Mountain), Sultanate of Oman. It strongly resembles Acrocordiella occulta, the type of the genus, in its similar asci and ascospore anatomy. It differs from A. occulta in having bell-shaped to cap-like clypeus around the ostiole and larger asci and ascospores. The combined large subunit nuclear ribosomal DNA and internal transcribed spacer sequences support the conclusions based on the morphological data.

Phylogenetic analyses of Nematoctonus and Hohenbuehelia (Pleurotaceae)

2007 ◽  
Vol 85 (8) ◽  
pp. 762-773 ◽  
Author(s):  
Alexandra T.E. Koziak ◽  
Kei Chin Cheng ◽  
R. Greg Thorn
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna ◽  
Monophyletic Clade ◽  
Parasitoid Species ◽  
Internal Transcribed Spacer Region ◽  
Species Limits ◽  
Additional Gene

Hohenbuehelia (Agaricales, Pleurotaceae) and Nematoctonus (Hyphomycetes) are the names for the sexual and asexual stages of a genus of nematode-destroying fungi (Basidiomycota). We obtained partial sequences of nuclear ribosomal DNA, including the internal transcribed spacer region and the 5′ end of the large subunit, of 37 isolates of Hohenbuehelia and Nematoctonus representing 13 of the 16 described species in Nematoctonus. Phylogenetic analyses support Hohenbuehelia–Nematoctonus as a monophyletic clade of the Pleurotaceae, within which the species were placed in five main subclades. Exclusively predatory species ( Nematoctonus brevisporus Thorn & G.L. Barron, Nematoctonus campylosporus Drechsler, Nematoctonus robustus F.R. Jones, and Nematoctonus sp. UAMH 5317) appear to be basal. In these species, adhesive knobs to capture prey are produced on their hyphae but not on their conidia. A single mycelial individual may feed on many nematodes. From these have arisen both exclusively parasitoid species ( Nematoctonus cylindrosporus Thorn & G.L. Barron, Nematoctonus leiosporus Drechsler, Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, Nematoctonus tylosporus Drechsler), and species that we call intermediate predators ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus concurrens Drechsler, Nematoctonus geogenius Thorn & GL. Barron, Nematoctonus hamatus Thorn & G.L. Barron, and Nematoctonus subreniformis Thorn & G.L. Barron). Exclusively parasitoid species have conidia that germinate to form sticky knobs that attach to passing nematodes but lack adhesive knobs on the hyphae. Each mycelial individual feeds on only one nematode. Intermediate predators have adhesive knobs both on hyphae and on germinated conidia and can act in both predatory and parasitoid modes. Most morphospecies are resolved as monophyletic, but sequences of additional gene regions are required to clarify species limits within the N. angustatus – N. geogenius group.

Morphological characteristics and phylogenetic analyses revealed a new Calocybe (Lyophyllaceae, Basidiomycota) species from northeast China

Phytotaxa ◽  
2021 ◽  
Vol 490 (2) ◽  
pp. 203-210
Author(s):  
JIZE XU ◽  
XIAODONG YU ◽  
CHUNLAN ZHANG ◽  
YU LI
Keyword(s):  
New Species ◽  
Internal Transcribed Spacer ◽  
Northeast China ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Molecular Phylogenetic ◽  
A New Species

A new species, Calocybe decurrens, is illustrated and described in detail based on morphological characteristics and phylogenetic analyses. Calocybe decurrens is mainly characterized by its decurrent gills and by its stipe that discolors upon maturation. Molecular phylogenetic analyses were based on the internal transcribed spacer (ITS1-5.8S-ITS2) and the large subunit of the nuclear ribosomal DNA (nrLSU) sequences. The results indicated that its affiliation is in genus Calocybe, where it occupies an isolated position. A full description, color images, illustrations and a phylogenetic tree to show the placement of the new species are provided.

Molecular phylogeny of two coelomycetous fungal genera with stellate conidia,ProsthemiumandAsterosporium, on Fagales trees

Botany ◽  
2010 ◽  
Vol 88 (12) ◽  
pp. 1057-1071 ◽  
Author(s):  
Kazuaki Tanaka ◽  
Vadim A. Mel’nik ◽  
Maasa Kamiyama ◽  
Kazuyuki Hirayama ◽  
Takashi Shirouzu
Keyword(s):  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Diagnostic Value ◽  
Small Subunit ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Phylogenetic Relatedness ◽  
Close Relationship ◽  
Phylogenetic Affinities ◽  
A New Species

Prosthemium (teleomorph Pleomassaria ) and Asterosporium (teleomorph unknown) are coelomycetous genera with stellate conidia on Fagales trees. Their morphological resemblance suggests their close relationship, but phylogenetic relatedness remains unknown. They have been distinguished on the basis of either conidiomatal morphology (pycnidia in Prosthemium and acervuli in Asterosporium) or their differing conidial septation (euseptate in Prosthemium and distoseptate in Asterosporium). To reveal their phylogenetic affinities and clarify reliable distinguishing phenotypical characters, five species of Prosthemium and two species of Asterosporium were investigated using sequences of the small subunit, large subunit, and internal transcribed spacer region of nuclear ribosomal DNA and β-tubulin gene from 43 isolates of these species. The analyses revealed the following: (i) Asterosporium typified by Asterosporium asterospermum on Fagus is a member of the Sordariomycetes and is distinct from Prosthemium belonging to the Dothideomycetes; (ii) Asterosporium betulinum on Betula species should be excluded from Asterosporium and transferred to Prosthemium as Prosthemium neobetulinum nom. nov.; (iii) conidial septation does not seem to have a diagnostic value, whereas conidiomatal morphology is useful in distinguishing both genera; (iv) the number and length of conidial arms are useful criteria in distinguishing Prosthemium species. A new species, Prosthemium intermedium sp. nov., found on both Betula ermanii and Betula maximowicziana , is described and illustrated.

Amanita rufobrunnescens, a new species of Amanita section Amidella from South China

Phytotaxa ◽  
2016 ◽  
Vol 243 (2) ◽  
pp. 147 ◽  
Author(s):  
Wangqiu Deng ◽  
Taihui Li ◽  
MD. IQBAL HOSEN
Keyword(s):  
New Species ◽  
South China ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Guangdong Province ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic ◽  
A New Species

Amanita rufobrunnescens is described as a new species in the subgenus Lepidella section Amidella from Guangdong Province, China. It is characterized by whitish basidiomes that bruise reddish brown, brownish sub-membranous to fibrillose volval remnants on the pileus, a striate pileus margin, white lamellae with truncate lamellulae, grayish orange to light brown volva, amyloid basidiospores that are ellipsoid to elongate (9.5–)10–12(–13) × (5–)5.5–6.5(–7) µm, and 5–10 μm wide pileipellis hyphae with yellowish vacuolar pigments. There are no clamp connections. Molecular phylogenetic analyses based on the nuclear ribosomal large subunit of nuclear ribosomal DNA (LSU) and internal transcribed spacer (ITS) sequences reveal that A. rufobrunnescens is a distinct species.

Two new species of Phaeosaccardinula from Southwest China

Phytotaxa ◽  
2020 ◽  
Vol 458 (3) ◽  
pp. 207-214
Author(s):  
HUI YANG ◽  
HAI-XIA WU ◽  
CHAO DENG ◽  
ZHI-CHANG ZHANG ◽  
CHANG-HUA GU ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Yunnan Province ◽  
Southwest China ◽  
Large Subunit ◽  
Molecular Data ◽  
Fungal Species ◽  
Nuclear Ribosomal Dna ◽  
Two New Species

Two new fungal species, Phaeosaccardinula dalbergiae and Phaeosaccardinula yunnanensis collected from Yunnan Province, China are described based on morphology and molecular data. They are compared with related taxa of Phaeosaccardinula. Detailed description, illustrations and notes are provided for each species. Molecular analysis based on the phylogenetic tree of combined internal transcribed spacer and large subunit nuclear ribosomal DNA sequences show that the two species form distinct clusters within the genus Phaeosaccardinula.

A comparison of ITS and LSU nrDNA phylogenies of Fulgensia (Teloschistaceae, Lecanorales), a genus of lichenised ascomycetes

2000 ◽  
Vol 78 (12) ◽  
pp. 1580-1589 ◽  
Author(s):  
Thomas Kasalicky ◽  
Heidi Döring ◽  
Gerhard Rambold ◽  
Mats Wedin
Keyword(s):  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Data Set ◽  
Spliceosomal Introns ◽  
Nuclear Its ◽  
Combined Data

The phylogeny of the lichen genus Fulgensia Massal. & De Not. (Teloschistaceae, Lecanorales) is analysed using maximum parsimony and neighbor joining analyses of nuclear ITS and partial large subunit nuclear ribosomal DNA (nrDNA) sequences. Three matrices were analysed with maximum parsimony; an internal transcribed spacer nrDNA matrix, a large subunit nrDNA matrix, and a combined data set. The internal transcribed spacer region contributes 70% of the informative sites to the combined data set. The topology of the trees resulting from the analysis of the internal transcribed spacer region is identical to the tree topology resulting from the combined analysis, but it shows less resolution at basal parts of the tree. Two sites for putative spliceosomal introns in the large subunit nrDNA, at position 808 and 914 (relative to Saccharomyces cerevisiae) are reported. Fulgensia, as currently understood, is polyphyletic and some species have to be excluded. The molecular analyses identified groups of species within the genus that are also supported by anatomical and morphological characters. The results of the analyses are compared with existing classification concepts based on morphological and anatomical data.Key words: LSU, ITS, nrDNA, introns, Fulgensia, phylogeny.

The Stability of the WHO Reference Thromboplastin NIBS & C 67/40

1979 ◽  
Vol 42 (04) ◽  
pp. 1135-1140 ◽  
Author(s):  
G I C Ingram
Keyword(s):  
Human Brain ◽  
Collaborative Study ◽  
Calibration Constant ◽  
Long Term Stability ◽  
Freeze Dried ◽  
Show Evidence ◽  
Human Material ◽  
Reference Preparation ◽  
The Stability

SummaryThe International Reference Preparation of human brain thromboplastin coded 67/40 has been thought to show evidence of instability. The evidence is discussed and is not thought to be strong; but it is suggested that it would be wise to replace 67/40 with a new preparation of human brain, both for this reason and because 67/40 is in a form (like Thrombotest) in which few workers seem to use human brain. A �plain� preparation would be more appropriate; and a freeze-dried sample of BCT is recommended as the successor preparation. The opportunity should be taken also to replace the corresponding ox and rabbit preparations. In the collaborative study which would be required it would then be desirable to test in parallel the three old and the three new preparations. The relative sensitivities of the old preparations could be compared with those found in earlier studies to obtain further evidence on the stability of 67/40; if stability were confirmed, the new preparations should be calibrated against it, but if not, the new human material should receive a calibration constant of 1.0 and the new ox and rabbit materials calibrated against that.The types of evidence available for monitoring the long-term stability of a thromboplastin are discussed.

Application of the method of mathematical modeling for forecasting channel deformations at the underwater crossing of the main pipeline

2020 ◽  
Vol 10 (6) ◽  
pp. 599-609
Author(s):  
Valery А. Gruzdev ◽  
◽  
Georgy V. Mosolov ◽  
Ekaterina A. Sabayda ◽  
◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Mathematical Model ◽  
Roughness Coefficient ◽  
Computational Domain ◽  
Channel Deformations ◽  
Geological Surveys ◽  
Kuban River ◽  
The Stability ◽  
Protective Structures

In order to determine the possibility of using the method of mathematical modeling for making long-term forecasts of channel deformations of trunk line underwater crossing (TLUC) through water obstacles, a methodology for performing and analyzing the results of mathematical modeling of channel deformations in the TLUC zone across the Kuban River is considered. Within the framework of the work, the following tasks were solved: 1) the format and composition of the initial data necessary for mathematical modeling were determined; 2) the procedure for assigning the boundaries of the computational domain of the model was considered, the computational domain was broken down into the computational grid, the zoning of the computational domain was performed by the value of the roughness coefficient; 3) the analysis of the results of modeling the water flow was carried out without taking the bottom deformations into account, as well as modeling the bottom deformations, the specifics of the verification and calibration calculations were determined to build a reliable mathematical model; 4) considered the possibility of using the method of mathematical modeling to check the stability of the bottom in the area of TLUC in the presence of man-made dumping or protective structure. It has been established that modeling the flow hydraulics and structure of currents, making short-term forecasts of local high-altitude reshaping of the bottom, determining the tendencies of erosion and accumulation of sediments upstream and downstream of protective structures are applicable for predicting channel deformations in the zone of the TLUC. In all these cases, it is mandatory to have materials from engineering-hydro-meteorological and engineering-geological surveys in an amount sufficient to compile a reliable mathematical model.

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