Analysis and prediction of gene splice sites in four Aspergillus genomes

Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at http://www.cbs.dtu.dk/services/NetAspGene.     

Distribution of sterigmatocystin in filamentous fungi

During the last 50y, the carcinogenic mycotoxin sterigmatocystin (ST) has been reported in several phylogenetically and phenotypically different genera: Aschersonia, Aspergillus, Bipolaris, Botryotrichum, Chaetomium, Emericella, Eurotium, Farrowia, Fusarium, Humicola, Moelleriella, Monocillium and Podospora. We have reexamined all available strains of the original producers, in addition to ex type and further strains of each species reported to produce ST and the biosynthetically derived aflatoxins. We also screened strains of all available species in Penicillium and Aspergillus for ST and aflatoxin. Six new ST producing fungi were discovered: Aspergillus asperescens, Aspergillus aureolatus, Aspergillus eburneocremeus, Aspergillus protuberus, Aspergillus tardus, and Penicillium inflatum and one new aflatoxin producer: Aspergillus togoensis (=Stilbothamnium togoense). ST was confirmed in 23 Emericella, four Aspergillus, five Chaetomium, one Botryotrichum and one Humicola species grown on a selection of secondary metabolite inducing media, and using multiple detection methods: HPLC-UV/Vis DAD, - HRMS and - MS/MS. The immediate precursor for aflatoxin, O-methylsterigmatocystin was found in Chaetomium cellulolyticum, Chaetomium longicolleum, Chaetomium malaysiense and Chaetomium virescens, but aflatoxin was not detected from any Chaetomium species. In all 55 species, representing more than 11 clades throughout the Pezizomycotina, can be reliably claimed to be ST producers and 13 of these can also produce aflatoxins. It is not known yet whether the ST/aflatoxin pathway has been developed independently 11 times, or is the result of partial horizontal gene transfer.     

Fungi associated with stored unprocessed cowpea and groundnut varieties available in Borno State, Nigeria.

Five stored unprocessed cowpea (Vigna spp) and four groundnut (Arachis hypogeae) varieties available in Borno State were examined for the mould flora. The degree of infestation of the grains ranged from 31% to 100% and 68% to 86% for surface sterilized cowpea and groundnut respectively. The mould flora commonly encountered were species of the genera Aspergillus. Penicillium species, Scopulariopsis species and Trichoderma species were also found. The flora of the cowpea was dominated by Aspergillus niger while Aspergillus flavus was the dominant mould on groundnut.     

Conidium Germination Rate in Wild and Domesticated Yellow-Green Aspergilli

Conidia of domesticated yellow-green aspergilli from strains of Aspergillus oryzae (Ahlburg) Cohn and Aspergillus sojae Sakaguchi and Yamada ex Murakami, used in the preparation of koji inoculum, germinate approximately 3 h sooner than conidia produced by related wild species, Aspergillus flavus Link ex Fr. and Aspergillus parasiticus Speare. There was no consistent relationship between average conidium size and estimated 50% germination time. Germination trials were conducted on Czapek agar at 28°C. A hypothesis is offered that, in the propagation of koji inoculum, selection has favored those individuals capable of rapid conidium germination and germ tube extension, attributes that enable them to gain the available substrate during intraspecific competition.     

Purification and Some Properties of a Xylanase from Aspergillus sydowii MG49

Volume 62, no. 10, p. 3915, Author's Correction (Ghosh and Nanda). Errors were made in the original identification of the microorganism used in this study and in the reporting of the corrected species identification. The culture resubmitted to the American Type Culture Collection was identified by Dr. Frank Dugan as Aspergillus flavus, not Aspergillus citrinum, and is available as ATCC 96916. [This corrects the article on p. 3915b in vol. 62.].     

Improved method of screening for aflatoxin with a coconut agar medium.

Nine isolates of Aspergillus flavus and Aspergillus parasiticus were screened for aflatoxin production on a coconut extract agar medium. Aflatoxin-producing colonies were detected under long-wave UV light (365 nm) by blue fluorescence on the reverse side after 2 to 5 days of growth. Aflatoxin production was verified by chemical analysis. Several types of shredded coconut available in the United States were tested and found to be satisfactory. No additives were required. Various parameters affecting the test were investigated.     

Improved method of screening for aflatoxin with a coconut agar medium

Nine isolates of Aspergillus flavus and Aspergillus parasiticus were screened for aflatoxin production on a coconut extract agar medium. Aflatoxin-producing colonies were detected under long-wave UV light (365 nm) by blue fluorescence on the reverse side after 2 to 5 days of growth. Aflatoxin production was verified by chemical analysis. Several types of shredded coconut available in the United States were tested and found to be satisfactory. No additives were required. Various parameters affecting the test were investigated.     

Identification of the pathogenic Aspergillus species by nested PCR using a mixture of specific primers to DNA topoisomerase II gene

For PCR-based identification of Aspergillus species, a common primer of the DNA topoisomerase II genes of Candida, Aspergillus and Penicillium, and species-specific primers of the genomic sequences of DNA topoisomerase II of A. fumigatus, A. niger, A. flavus (A. oryzae), A. nidulans and A. terreus were tested for their specificities in PCR amplifications. The method consisted of amplification of the genomic DNA topoisomerase II gene by a common primer set, followed by a second PCR with a primer mix consisting of 5 species-specific primer pairs for each Aspergillus species. By using the common primer pair, a DNA fragment of approximately 1,200 bp was amplified from the Aspergillus and Penicillium genomic DNAs. Using each species-specific primer pair, unique sizes of PCR products were amplified, all of which corresponded to a species of Aspergillus even in the presence of DNAs of several fungal species. The sensitivity of A. fumigatus to the nested PCR was found to be 100 fg of DNA in the reaction mixture. In the nested PCR obtained by using the primer mix (PsIV), the specific DNA fragment of A. fumigatus was amplified from clinical specimens. These results suggest that this nested PCR method is rapid, simple and available as a tool for identification of pathogenic Aspergillus to a species level.     

A Review Molecular Typing Methods for <Emphasis Type="Italic">Aspergillus flavus</Emphasis> Isolates

Aspergillus flavus is the second most important Aspergillus species causing human infections. The importance of this fungus increases in regions with a dry and hot climate. Small phylogenetic studies in Aspergillus flavus indicate that the morphological species contains several genetically isolated species. Different genotyping methods have been developed and employed in order to better understand the genetic and epidemiological relationships between environmental and clinical isolates. Understanding pathogen distribution and relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. Typing techniques can also give us a deeper understanding of the colonization pattern in patients. Most of these studies focused on Aspergillus fumigatus because it is medically the most isolated species. To date, there has not been any publication exclusively reviewing the molecular typing techniques for Aspergillus flavus in the literature. This article reviews all these different available methods for this organism.     

Purification and physico-chemical characterisation of genetically modified phytases expressed in Aspergillus awamori

Two heterologous phytases from Aspergillus awamori and Aspergillus fumigatus obtained from submerged cultures of genetically modified fungal strains in addition to two commercially available phytase preparations (Allzyme and Natuphos phytases) were purified to homogeneity using a combination of ultrafiltration, gel filtration and ion exchange. The purified preparations were used in subsequent characterisation studies, in which Western Immunoblot analysis, pH and temperature optima, thermal stability and substrate specificity were assessed. A. fumigatus phyA phytase expressed in A. awamori exhibited activity over a broad pH range together with an increased temperature optimum, and slightly enhanced thermal stability compared to the other phytases tested, and is thus a promising candidate for animal feed applications. This particular phytase retains activity over a wide range of pH values characteristic of the digestive tract and could conceivably be more suited to the increasingly higher feed processing temperatures being utilised today, than the corresponding phytases from Aspergillus niger.     

Expression of the Cu,Zn superoxide dismutase of Aspergillus fumigatus as determined by immunochemistry and immunoelectron microscopy

Abstract A polyclonal antibody against purified Cu,Zn superoxide dismutase (SOD) from the pathogen Aspergillus fumigatus was raised in a sheep. This antibody recognised purified A. fumigatus SOD, together with a single band of 19 kDa in A. fumigatus cytoplasmic antigen, by immunodevelopment of Western blots. The polyclonal serum did not recognise either the manganese or iron containing forms of the enzyme; however, it was reactive against putative Cu,Zn SODs in other members of the genus Aspergillus . Immunofluorescent staining of A. fumigatus cultures demonstrated expression of the Cu,Zn SOD in conidia and hyphae, with the cell wall staining particularly intensely. Conidiophores were stained in an uniformly intense pattern. Immunoelectron microscopy confirmed that the SOD was present within the hyphal cell wall, although there was also labelling in the cytoplasm. SOD may protect Aspergillus against oxidants produced by immune effector cells and these observations demonstrate that the enzyme is available to perform its antioxidant function within the cell wall.     

Doxycycline-regulated gene expression in the opportunistic fungal pathogen Aspergillus fumigatus

Background  

Although Aspergillus fumigatus is an important human fungal pathogen there are few expression systems available to study the contribution of specific genes to the growth and virulence of this opportunistic mould. Regulatable promoter systems based upon prokaryotic regulatory elements in the E. coli tetracycline-resistance operon have been successfully used to manipulate gene expression in several organisms, including mice, flies, plants, and yeast. However, the system has not yet been adapted for Aspergillus spp.     

The genetic analysis of mitosis in Aspergillus nidulans

We describe here recent work on the molecular genetics of mitosis in the filamentous fungus Aspergillus nidulans. Aspergillus is one of three simple eukaryotes with powerful genetic systems that have been used to analyze mitosis. The modern molecular biological techniques available with this organism have made it possible to use mutations to identify genes and proteins that play an important role in mitosis. Three Aspergillus genes that affect mitosis are described. One gene, nimA, is specifically expressed late in the cell cycle and codes for a putative protein kinase that induces mitosis, even in cells blocked in S-phase. The second gene, bimG, codes for a putative phosphatase that interacts functionally with the nimA kinase. The third gene, bimE, codes for a protein that suppresses mitosis during interphase, apparently by keeping nimA turned off. None of these genes appear to be similar to any of the genes affecting mitosis that have been characterized in other eukaryotes, but rather appear to be elements of a system that prevents mitosis from occurring during interphase.     

Lytic Enzymes for Gram-negative Bacteria Produced by Bacillus subtilis YT-25

The available energy, gross protein value, phosphorus availability and palatability of 16 samples of single cell protein were evaluated in 20 bioassays using total 2,136 depleted chicks.

Four protein samples were products from Aspergillus tamarii grown on waste water of a fish processing factory, three were from Aspergillus oryzae grown on either acetic acid medium or cooked soybean waste, three were from Candida sp. grown on citrus molasses extracted from peel wastes of citrus processing plants, four were from Candida utitis grown on wood molasses produced from various wood wastes, and two were from Pseudomonas sp. and Alteromonas thlasomethanolica grown on methanol.

Five of 16 samples had excellent nutritive value, comparable to single cell proteins available commercially in Europe. All samples were palatable to the chicks, and no sign of acute toxicity was observed.     

Availability of phosphorus in a calcareous soil treated with rock phosphate or superphosphate as affected by phosphate-dissolving fungi

A study was undertaken to isolate some fungi exhibiting phosphate-dissolution ability, and to test whether these fungi are capable of increasing the amount of available P in a calcareous soil treated with rock phosphate (RP) or with triple superphosphate (TSP) and its subsequent uptake by sorghum (Sorghum bicolor L. Moench).Penicillium sp. and twoAspergillus foetidus (Naka) isolates significantly increased the availability of P in soil treated with RP or TSP during the growing season.Penicillium sp. isolate was more effective in increasing available P in the soil treated with RP or TSP than were Aspergillus isolates. However, the dry matter and P uptake responses to inoculation with these fungi were better in the soil treated with RP than in soil treated with TSP. In the TSP treated soil, the fungi achieved their maximum P releasing capacity two weeks earlier than in soil treated with RP. Positive and significant correlation coefficients among available P, P uptake and dry matter production at different periods of the growing season were observed following inoculation. However, none of these variables were found to be significantly correlated with the fungal populations.     

Glyceride synthesis by four kinds of microbial lipase

Apart from their usual mechanism of action, lipases from Aspergillus niger and Rhizopus delemar also catalyzed the synthesis of glycerides from oleic acid and glycerol. Lipases from Geotrichum candidum and Penicillium cyclopium were inactivated by oleic acid, but were stable in the presence of casein, albumin or buffer of appropriate pH. Lipases from Aspergillus niger and Rhizopus delemar synthesized glycerides from, not only fatty acid, but dibasic acids and aromatic acids, making ester bonds only at position 1 and 3 of glycerol. In contrast, lipases from Geotricum candidum and Penicillium cyclopium synthesized glycerides only from long chain fatty acids, and made ester bonds at all three available positions of the glycerol molecule.     

Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?

Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through rapid DNA-based tests. The question of whether we can reliably detect and identify species of Aspergillus and Penicillium turns mainly upon the completeness of our alpha taxonomy, our species concepts, and how well the available DNA data coincide with the taxonomic diversity in the family Trichocomaceae. No single gene is yet known that is invariant within species and variable between species as would be optimal for the barcode approach. Data are published that would make an MLST approach to isolate identification possible in the most well-studied clades of Aspergillus and Penicillium.     

盐碱地柠条根围土中黑曲霉的分离鉴定及解磷能力测定

在盐碱滩地的改良过程中,柠条具有提升土壤供氮、供磷、供钾的潜力.以盐碱滩地上建植的柠条灌木林为研究对象,以柠条根围土壤为培养基质,采用无机磷培养基筛选,用平板溶菌圈法分离获得1株具有溶磷能力的真菌.将测得的ITS基因序列在NCBI上进行同源性检索,结果表明,所测序列与黑曲霉(Aspergillus niger)同源性为100％.综合形态特征和ITS基因序列同源性两方面分析,该菌株鉴定为黑曲霉(Aspergillus niger).168h连续监测无机磷培养液pH值、速效磷含量、菌丝重量和菌体吸磷量,研究该菌株的解磷能力.研究结果表明:随着培养时间的延长,培养液pH值从7.0下降到2.0左右,溶液中速效磷含量逐渐增加到4.7 mg,菌体自身吸磷量由5.4 mg下降到0.5mg,在36-48h后各项指标达到稳定状态.可见,黑曲霉菌体可以有效利用难溶性磷源,并将其转化成可被植物吸收利用的有效磷.     

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes. AVAILABILITY: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate