Improving quantitative susceptibility mapping for the identification of traumatic brain injury neurodegeneration at the individual level

BACKGROUND

Emerging evidence suggests that traumatic brain injury (TBI) is a major risk factor for developing neurodegenerative disease later in life. Quantitative susceptibility mapping (QSM) has been used by an increasing number of studies in investigations of pathophysiological changes in TBI. However, generating artefact-free quantitative susceptibility maps in brains with large focal lesions, as in the case of moderate-to-severe TBI (ms-TBI), is particularly challenging. To address this issue, we utilized a novel two-pass masking technique and reconstruction procedure (two-pass QSM) to generate quantitative susceptibility maps (QSMxT; Stewart et al., 2022, Magn Reson Med.) in combination with the recently developed virtual brain grafting (VBG) procedure for brain repair (Radwan et al., 2021, NeuroImage) to improve automated delineation of brain areas. We used QSMxT and VBG to generate personalised QSM profiles of individual patients with reference to a sample of healthy controls.

METHODS

Chronic ms-TBI patients (N = 8) and healthy controls (N = 12) underwent (multi-echo) GRE, and anatomical MRI (MPRAGE) on a 3T Siemens PRISMA scanner. We reconstructed the magnetic susceptibility maps using two-pass QSM from QSMxT. We then extracted values of magnetic susceptibility in grey matter (GM) regions (following brain repair via VBG) across the whole brain and determined if they deviate from a reference healthy control group [Z-score < -3.43 or > 3.43, relative to the control mean], with the aim of obtaining personalised QSM profiles.

RESULTS

Using two-pass QSM, we achieved susceptibility maps with a substantial increase in quality and reduction in artefacts irrespective of the presence of large focal lesions, compared to single-pass QSM. In addition, VBG minimised the loss of GM regions and exclusion of patients due to failures in the region delineation step. Our findings revealed deviations in magnetic susceptibility measures from the HC group that differed across individual TBI patients. These changes included both increases and decreases in magnetic susceptibility values in multiple GM regions across the brain.

CONCLUSIONS

We illustrate how to obtain magnetic susceptibility values at the individual level and to build personalised QSM profiles in ms-TBI patients. Our approach opens the door for QSM investigations in more severely injured patients. Such profiles are also critical to overcome the inherent heterogeneity of clinical populations, such as ms-TBI, and to characterize the underlying mechanisms of neurodegeneration at the individual level more precisely. Moreover, this new personalised QSM profiling could in the future assist clinicians in assessing recovery and formulating a neuroscience-guided integrative rehabilitation program tailored to individual TBI patients.

Examination of Cerebellar Grey-Matter Volume in Children with Neurodevelopmental Disorders: a Coordinated Analysis Using the ACAPULCO Algorithm

Alterations in cerebellar morphology relative to controls have been identified in children with autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), and developmental coordination disorder (DCD). However, it is not clear if common cerebellar regions are affected in each neurodevelopmental disorder and whether cerebellar morphological changes reflect a generic developmental vulnerability, or disorder-specific characteristic. The present study concatenated anatomical MRI scans from five existing cohorts, resulting in data from 252 children between the age of 7 and 12 years (ASD = 58, ADHD = 86, DCD = 22, Controls = 86). The ACAPULCO processing pipeline for cerebellar segmentation was conducted on T1-weighted images. A voxel-wise approach with general linear model was used to compare grey-matter volume of the 27 cerebellar lobules between each clinical group and controls. Our findings revealed that the ADHD group showed lower grey-matter volume in the left Crus I - part of the executive/non-motor portion of the cerebellum, relative to controls (p = 0.02). This no longer remained significant after controlling for medication status. There were no regions of significant differences in volume of the cerebellar lobules in ASD or DCD compared to controls. Future work will conduct harmonisation of behavioural data (cognitive and motor outcomes) across cohorts, enabling more advanced analyses to identify symptom cluster across neurodevelopmental disorders.

Individualised profiling of white matter organisation in moderate-to-severe traumatic brain injury patients

BACKGROUND AND PURPOSE

Approximately 65% of moderate-to-severe traumatic brain injury (m-sTBI) patients present with poor long-term behavioural outcomes, which can significantly impair activities of daily living. Numerous diffusion-weighted MRI studies have linked these poor outcomes to decreased white matter integrity of several commissural tracts, association fibres and projection fibres in the brain. However, most studies have focused on group-based analyses, which are unable to deal with the substantial between-patient heterogeneity in m-sTBI. As a result, there is increasing interest and need in conducting individualised neuroimaging analyses.

MATERIALS AND METHODS

Here, we generated a detailed subject-specific characterisation of microstructural organisation of white matter tracts in 5 chronic patients with m-sTBI (29 - 49y, 2 females), presented as a proof-of-concept. We developed an imaging analysis framework using fixel-based analysis and TractLearn to determine whether the values of fibre density of white matter tracts at the individual patient level deviate from the healthy control group (n = 12, 8F, M_age = 35.7y, age range 25 - 64y).

RESULTS

Our individualised analysis revealed unique white matter profiles, confirming the heterogenous nature of m-sTBI and the need of individualised profiles to properly characterise the extent of injury. Future studies incorporating clinical data, as well as utilising larger reference samples and examining the test-retest reliability of the fixel-wise metrics are warranted.

CONCLUSIONS

Individualised profiles may assist clinicians in tracking recovery and planning personalised training programs for chronic m-sTBI patients, which is necessary to achieve optimal behavioural outcomes and improved quality of life.

[Renaissance of mouse favus : Retrospective analysis of Trichophyton quinckeanum infections at Jena University Hospital in the period 2015-2020]

The number of Trichophyton quinckeanum infections has increased significantly in recent years. In 2020 in particular, the number of cases increased fivefold compared to 2015. Infections multiplied, especially in the second half of the year, which correlated with the upsurge in field mouse populations. Typical vectors are mice and rats as well as dogs and cats, which hunt the rodents. The animals are usually asymptomatic. In humans, on the other hand, the course is usually more inflammatory corresponding to other zoophilic mycoses. Typical clinical manifestations of the infections are tinea corporis and tinea capitis. Treatment of T. quinckeanum infections is similar to other dermatophyte infections, depending on the severity, location and age of the patient as well as the immune status, previous illnesses and medication. The duration of local therapy should be at least 4 weeks and continued for up to 14 days after the normalization of the skin presentation. Systemic treatment should take place with terbinafine 250 mg once a day orally (in adults). Alternatives are itraconazole, fluconazole and griseofulvin. Only the preparation griseofulvin, which is no longer available in Germany, is approved for children. Alternatively, terbinafine, itraconazole or fluconazole can also be used in children as an "off-label" treatment in an individual healing attempt.

Individual differences in attentional lapses are associated with fiber-specific white matter microstructure in healthy adults

Attentional lapses interfere with goal-directed behaviors, which may result in harmless (e.g., not hearing instructions) or severe (e.g., fatal car accident) consequences. Task-related functional MRI (fMRI) studies have shown a link between attentional lapses and activity in the frontoparietal network. Activity in this network is likely to be mediated by the organization of the white matter fiber pathways that connect the regions implicated in the network, such as the superior longitudinal fasciculus I (SLF-I). In the present study, we investigate the relationship between susceptibility to attentional lapses and relevant white matter pathways in 36 healthy adults (23 females, M_age  = 31.56 years). Participants underwent a diffusion MRI (dMRI) scan and completed the global-local task to measure attentional lapses, similar to previous fMRI studies. Applying the fixel-based analysis framework for fiber-specific analysis of dMRI data, we investigated the association between attentional lapses and variability in microstructural fiber density (FD) and macrostructural (morphological) fiber-bundle cross section (FC) in the SLF-I. Our results revealed a significant negative association between higher total number of attentional lapses and lower FD in the left SLF-I. This finding indicates that the variation in the microstructure of a key frontoparietal white matter tract is associated with attentional lapses and may provide a trait-like biomarker in the general population. However, SLF-I microstructure alone does not explain propensity for attentional lapses, as other factors such as sleep deprivation or underlying psychological conditions (e.g., sleep disorders) may also lead to higher susceptibility in both healthy people and those with neurological disorders.

Navigating the link between processing speed and network communication in the human brain

Processing speed on cognitive tasks relies upon efficient communication between widespread regions of the brain. Recently, novel methods of quantifying network communication like 'navigation efficiency' have emerged, which aim to be more biologically plausible compared to traditional shortest path length-based measures. However, it is still unclear whether there is a direct link between these communication measures and processing speed. We tested this relationship in forty-five healthy adults (27 females), where processing speed was defined as decision-making time and measured using drift rate from the hierarchical drift diffusion model. Communication measures were calculated from a graph theoretical analysis of the whole-brain structural connectome and of a task-relevant fronto-parietal structural subnetwork, using the large-scale Desikan-Killiany atlas. We found that faster processing speed on trials that require greater cognitive control are correlated with higher navigation efficiency (of both the whole-brain and the task-relevant subnetwork). In contrast, faster processing speed on trials that require more automatic processing are correlated with shorter path length within the task-relevant subnetwork. Our findings reveal that differences in the way communication is modelled between shortest path length and navigation may be sensitive to processing of automatic and controlled responses, respectively. Further, our findings suggest that there is a relationship between the speed of cognitive processing and the structural constraints of the human brain network.

95 Jahre Universitäts-Hautklinik Jena: Geschichte und Gegenwart

Anlässlich des 95-jährigen Jubiläums der Universitäts-Hautklinik Jena beleuchtet dieser Beitrag die historische Entwicklung des Hauses in den verschiedenen politischen Systemen des letzten Jahrhunderts sowie die aktuelle Situation der Klinik als Teil des Universitätsklinikums Jena. Verschiedene Klinikleitungen in der Vergangenheit prägten die Ausrichtung des Hauses in Bezug auf Therapie und Forschung und setzten Schwerpunkte auf Themen wie Phototherapie, Autoimmunerkrankungen, Dermatoonkologie, Andrologie und Biomaterialforschung. Die Universitäts-Hautklinik vereint neben hochqualitativer Patientenversorgung und Lehre umfangreiche Forschungsaktivitäten.

Mating analyses of Trichophyton benhamiae offspring reveals linkage of genetic markers used in taxonomy

Mating experiments were conducted with four clinical Trichophyton benhamiae isolates, genetically similar to the Trichophyton benhamiae CBS 112371, featuring the plus mating type and with two minus type strains. One minus type strain belonged to the white subgroup, and the other minus type strain, DSM 6916, showed genetic kinship to the yellow subgroup. Only two plus type strains were able to form mature, pigmented gymnothecia with DSM 6916. These two plus type strains demonstrated dark pigmentation and powdery mycelium on Takashio agar, whereas the other three strains exhibited a low degree of pigmentation on the same medium. All five plus strains were able to mate with the minus type strain of their own white subgroup. Cultures from single ascospore isolates showed highly variable morphology and pigmentation. Three genetic markers (ITS, mating type, EF1 alpha) were analyzed in polymerase chain reaction (PCR) experiments with optimized primers and PCR conditions to discriminate between subgroups. Furthermore, RAPD-PCR was used to generate a DSM 6916-specific DNA-fragment which served as an additional genetic marker. Assessing the isolates with recombinant genotypes, it was found that three genetic markers behave like linked genes. The recombination of plus mating type went together with ITS, EF1 alpha and RAPD marker of the DSM 6916 parental strain and was most frequently isolated, whereas plus types recombinants in this case were completely missing. This shows a high imbalance in mating type distribution of recombinants.

[Dermatophytosis caused by rare anthropophilic and zoophilic agents]

The basis for effective treatment of any dermatomycosis is the correct and timely identification of the pathogen, which allows the targeted choice of the most suitable antimycotic and is important for the prevention of repeated infections. In recent years, infections with dermatophytes seem to have increased. In fact, from 2007 to 2018, there was an increase in the number of samples processed in the Mycology Laboratory of the Department of Dermatology at the University Hospital Jena. The most common isolated dermatophytes between 2007 and 2018 were Trichophyton (T.) rubrum, T. interdigitale, Microsporum (M.) canis and T. benhamiae. However, dermatophytoses may also be caused by rare anthropophilic agents such as Epidermophyton floccosum, zoophiles such as T. verrucosum, T. quinckeanum or Nannizzia (N.) persicolor as well as by geophiles such as N. gypsea. Therefore, these dermatophytes should at least be known, so that in case of unusual observations investigations can be performed accordingly. Changes in the pathogen spectrum of dermatophytoses have taken place over time and it is expected that the occurrence of dermatophytes will be subject of continuous fluctuations, which may mean that the incidence of some of these "rare" dermatophytes, as described here in five clinical examples, may be changing.

Contrasting Predictions of Low- and High-Threshold Models for the Detection of Changing Visual Features

Change blindness is the failure of observers to notice otherwise obvious changes to a visual scene when those changes are masked in some way (eg by blotches or a blanking of the screen). Typically, change blindness is taken as evidence that our representation of the visual world is capacity limited. The locus of this capacity limit is thought to be visual short-term memory (vSTM). The capacity of vSTM is usually estimated with a high-threshold model which assumes that each element in the stimulus array is either fully encoded or not encoded at all, and, furthermore, that false alarms can arise only by guessing, not by noise. Low-threshold models, by contrast, suggest that false alarms can arise by noise at the level of detection/discrimination and/or decision. In this study, we use a well-controlled stimulus display in which a single element changes over a blanking of the screen and contrast predictions from a popular high-threshold model of vSTM with the predictions of a low-threshold model (specifically, the sample-size model) of visual search and vSTM. The data were better predicted by the low-threshold model.

Thresholds for the detection of changing visual features

Change blindness refers to the difficulty observers have in detecting otherwise obvious changes to visual stimuli, when these changes are masked in some way. Typically, change blindness is studied by using complex visual scenes and complex changes to these scenes. In the current study, we used a more controlled visual environment, presenting observers with a series of oriented, sinusoidal patterns (Gabors), one of which underwent a change during a blanking of the screen. Changes were made to different features (size, colour, spatial frequency, and speed) with the target-distractor discriminability varying. The detectability of these changes was quantified by calculating psychometric functions and thresholds for each individual observer. Thresholds for the detection of changing features were higher than those for non-changing features, but thresholds for both tasks show consistency across observers. Psychometric-function slopes show consistency across observers and change type only for non-changing targets. For changing targets, psychometric-function slopes show no obvious pattern across observers or change types. We suggest this reflects vSTM treating different features as abstract, interchangeable tokens, as alternative explanations (such as additional noise in vSTM) can be ruled out.

Flexible resource allocation for the detection of changing visual features

Failure to detect change under circumstances where visual input is interrupted or attention is distracted is indicative of the capacity limits of visual short-term memory. The current study attempts to probe the nature of these limits. In experiment 1, the appearance of single Gabor patches was altered across colour, size, or speed, and set size was manipulated by means of a visual cue. In experiment 2, performance for detecting single and multiple changes to Gabor patches was compared under the constraint that the inherent detectability of each individual change was the same. Experiment 1 yielded a particular set size (4) and a particular level of change magnitude at which performance was equivalent across change type. On the basis of these parameter values, experiment 2 revealed that the detectability of two features changing within one object was the same as the detectability of a single feature changing across two objects, and that this level of detectability could be predicted by a simple model of probability summation. Together, these results suggest that performance is determined by the magnitude of featural changes independently of the way they are distributed across objects. We suggest they are adequately explained by a flexible-resource-allocation model rather than a slot-allocation model.

Adaptation to combinations of form, colour, and movement

Observers typically report illusory colour on achromatic gratings after being adapted to orthogonally oriented gratings presented in complementary colours, where the colour apparent on each grating is complementary to the one that had been presented with that grating during adaptation (McCollough, 1965 Science 149 1115-1116). We used this procedure, but presented homogenous fields at test instead of achromatic gratings. When adaptation stimuli moved in directions locally orthogonal to their orientation, we found that, for up to 7-8 min after adaptation, a flower-like illusory pattern was evident on both homogenous fields; after this time illusory radial lines and concentric circles were evident and were colour-contingent (eg for adaptation with green concentric circles and magenta radial lines, concentric circles were apparent on a magenta test field and radial lines were apparent on a green test field). When stimuli were stationary during induction, colour-contingent illusory forms were also apparent at test. The results demonstrate that an aftereffect, reciprocal to the McCollough effect, can be produced under appropriate induction conditions, and that this effect is not due to retinal afterimages.

Green fluorescent protein as a reporter for gene expression in the mucoralean fungus Absidia glauca

Mucoralean fungi (Zygomycota) are used for many industrial processes and also as important model organisms for investigating basic biological problems. Their genetic analysis is severely hampered by low transformation frequencies, by their strong tendency towards autonomous replication of plasmids instead of stable integration, and by the lack of reliable genetic reporter systems. We constructed plasmids for transforming the model zygomycete Absidia glauca that carry the versatile reporter gene coding for green fluorescent protein (GFP). gfp expression is controlled either by the homologous actin promoter or the promoter for the elongation factor of translation, EF1alpha. These plasmids also confer neomycin resistance and carry one of two genetic elements (rag1, seg1) that improve mitotic stability of the plasmid. The gfp constructs were replicated extrachromosomally and could be recovered from retransformed Escherichia coli cells. gfp expression was monitored by epifluorescence microscopy. The gfp reporter gene plasmids presented here for the model zygomycete A. glauca constitute the first reliable system that allows the monitoring of gene expression in this important group of fungi.

4-Dihydromethyltrisporate dehydrogenase from Mucor mucedo, an enzyme of the sexual hormone pathway: purification, and cloning of the corresponding gene

We have purified the NADP-dependent 4-dihydromethyltrisporate dehydrogenase from the zygomycete Mucor mucedo. The enzyme is involved in the biosynthesis of trisporic acid, the sexual hormone of zygomycetes, which induces the first steps of zygophore development. Protein was obtained from the (-) mating type of M. mucedo after induction with trisporic acid, and purified by gel filtration and affinity chromatography steps. On SDS-PAGE a band with an apparent molecular mass of 33 kDa was ascribed to the enzyme. After transferring onto PVDF membranes the protein was digested with endoprotease Lys-C, and several peptides were sequenced. Oligonucleotides derived from protein sequence data were used for PCR amplification of genomic M. mucedo DNA. The PCR fragment was used as probe for isolation of the corresponding cDNA and complete genomic DNA clones. Comparison of protein and DNA sequence data showed that the cloned fragment corresponded to the purified protein. Search for similarity with protein sequences of the Swiss-Prot database revealed a relationship to enzymes belonging to the aldo/keto reductase superfamily. Southern-blot analysis of genomic DNA with the labelled cloned fragment detected a single-copy gene in both mating types of M. mucedo. PCR with genomic DNA from other zygomycetes gave rise to several fragments. Hybridization analysis with the cloned M. mucedo fragment showed that a fragment of similar length cross-hybridized in Blakeslea trispora (Choanephoraceae) as well as in Parasitella parasitica and Absidia glauca (Mucoraceae). The promoter region of the gene contains DNA elements with similarity to a cAMP-regulated gene of Dictyostelium discoideum.

Relationships between sexual processes and parasitic interactions in the host–pathogen systemAbsidia glauca–Parasitella parasitica

Parasitella parasitica is a facultative parasite of many Mucorales including Absidia glauca. The infection process includes the formation of a plasmatic continuum between host and parasite, which allows the invasion of the host by nuclei of the parasite. This process gives rise to interspecies recombinants. Auxotrophic A. glauca mutants are complemented by the transfer of genes from the parasite to the host. At the molecular level, we could show that plasmid-coded genes are also transferred. The successful formation of infection structures is mating-type dependent. Parasitella parasitica exclusively infects hosts belonging to the complementary mating type. The formation of infection structures is correlated with the ability to synthesise the sex pheromone trisporic acid, which is produced in mixed cultures by compatible combinations between host and parasite. Normally, trisporic acid is formed by a cooperative biosynthesis involving both mating types. Trisporic acid seems to be involved also in mediating the recognition between P. parasitica and A. glauca. To test the hypothesis of direct hormonal correlations between sex and parasitism, we have isolated one of the key enzymes for trisporic acid synthesis, dihydromethyltrisporic acid dehydrogenase, sequenced the N-termini of some proteolytic cleavage products, and have started to isolate the corresponding gene. Key words: mycoparasitism, zygomycetes, trisporic acid, Absidia glauca, Parasitella parasitica, Mucor.

Analysis of the gene for the elongation factor 1 alpha from the zygomycete Absidia glauca. Use of the promoter region for constructions of transformation vectors

The complete genomic DNA sequence was determined for one of the gene for the elongation factor 1 alpha (TEF), isolated from the zygomycete Absidia glauca. Sequence comparison with TEF genes from other fungi show the highest similarity to TEF-genes of the closely related zygomycete Mucor racemosus (Sundstrom et al. 1987). Southern-blot analysis of genomic DNA from A. glauca with the TEF gene reveals six chromosomal copies in the genome. In transformation experiments of A. glauca, vector constructions were used which allow targeting of one of the TEF loci. Several transformants of A. glauca were analyzed at the DNA level. In most cases, rearranged forms of autonomously replicated plasmids could be found in these isolates. However, some transformants show a different restriction pattern of the TEF loci if compared with the parental strains. From Southern-blot data it could be concluded that in one case the rearrangement lies downstream of one TEF locus. In a second case genetic parts following the 3'-end of the TEF gene are moved towards the 5'-end of the gene.

Variability in genome organization of the zygomycete Parasitella parasitica

In addition to conventional methods for the identification of fungi, molecular techniques at the DNA level are increasingly being employed. In order to check the validity of such experimental approaches, we have analyzed the well-defined species Parasitella parasitica, which belongs to the family Mucoraceae (Mucorales, Zygometes). The seven strains of this species, which are available from international strain collections, were analyzed by several molecular methods: restriction fragment length polymorphism analysis (RFLP), the random primer-dependent polymerase chain reaction (RAPD-PCR), and electrophoretic karyotyping. Unexpectedly, these strains are highly diverse at the molecular level. By these techniques they can be divided consistently into two different groups. Nevertheless, all seven strains belong to a single species. They show no morphological differences and sexual spores (zygospores) were found in all possible combinations either within or between the two groups. Southern-blot analysis of genomic DNA of all P. parasitica strains with RAPD-PCR-derived labelled probes shows the existence of repetitive elements characteristic for only one group of P. parasitica. In addition, chromosome sizes, which were separated by rotating-field electrophoresis, were highly divergent, and ranged from 3 to 6.5 Mb in one group and between 2 and 4.5 Mb in the other. The RAPD-PCR patterns also discriminate both groups of P. parasitica. However, they are very similar if strains of a single group are compared. Therefore, we propose that the determination of fungal species by molecular techniques should be vetted at least by morphological and physiological parameters and, whenever possible, by mating experiments.

Sequence comparison of a segment of the gene for 3-hydroxy-3-methylglutaryl-coenzyme A reductase in zygomycetes

In this paper we compare the sequences of a segment of the 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase gene, isolated from eleven different strains belonging to four species of the fungal order Mucorales, Parasitella parasitica, Absidia glauca, Mucor mucedo (Mucoraceae) and Blakeslea trispora (Choanephoraceae). The segment was obtained by polynucleotide-chain-reaction amplification with primers derived from conservative regions of the gene. For the species M. mucedo and P. parasitica we have obtained evidence for two different types of HMG-CoA reductase genes by hybridization of genomic DNA with the amplified fragment and by cloning and sequencing of two different fragments. The different genes from one species show a sequence similarity of around 80% at the protein sequence level, whereas sequences of the same type from different species show similarity ranging between 91-96%. The highest similarity was found between the genes of type 1 from B. trispora and M. mucedo, although these species belong to different families. Southern-blot analysis of A. glauca DNA and B. trispora DNA revealed a second copy of the genes.

Transfer of genetic information from the mycoparasite Parasitella parasitica to its host Absidia glauca

The infection of the model organism Absidia glauca by P. parasitica is accompanied by the fusion of both mycelia. By two lines of evidence we were able to show that this process is associated with the transfer of genes. First, auxotrophically labelled A. glauca mutants are efficiently complemented as a consequence of transfer of the parasite's genetic material. Second, for a plasmid-coded dominant marker (neomycin resistance), which is expressed in either organism, we proved the presence of plasmid DNA in recombinant recipients by molecular analysis at the DNA level. We propose the term para-recombinants for describing recombinant inter-generic chimaerae, which are generated as a consequence of mycoparasitism.

The SEG1 element: a new DNA region promoting stable mitotic segregation of plasmids in the zygomycete Absidia glauca

A series of new vectors for the model zygomycete Absidia glauca was constructed on the basis of the structural neomycin resistance (Neor) gene controlled by the promoter of the gene for elongation factor 1 (TEF). In order to select for transformed colonies with a stable Neor phenotype, spores from primary transformants were pooled and grown for two sporulation cycles under non-selective conditions. Southern blot analysis of DNA from single spore isolates originating from independent transformant pools allowed the identification of two autonomously replicating plasmids. Retransformation of Escherichia coli and restriction analysis of the two plasmids provided evidence for spontaneous in vivo insertion of a new DNA element (SEG1) from the A. glauca genome. The inserted regions in both plasmids are essentially identical and do not represent repetitive DNA. Compared with other autonomously replicating vectors, these SEG1-containing plasmids are mitotically extremely stable and are passed on to the vegetative spore progeny of a retransformed A. glauca strain. We assume that SEG1 contains structural elements involved in partitioning and stable segregation of plasmids. For the construction of stable transformants of A. glauca, the SEG1 element may be regarded as a major breakthrough, because stabilization of transformed genetic traits by integration is difficult to achieve in all mucoraceous fungi and all known replicating plasmids are mitotically unstable.

Transformation of the mycoparasite Parasitella simplex to neomycin resistance

The facultatively parasitic zygomycete Parasitella simplex was transformed to neomycin resistance by a vector, which had been developed primarily for transformation of its host Absidia glauca. This plasmid, pAmNEF21, contained the bacterial resistance gene for neomycin (NPTII) under the control of the promoter region from the gene for elongation factor 1 (tef) isolated from A. glauca. Both flanking regions of the marker gene contain parts of the structural tef gene. DNA isolated from two Parasitella transformants was re-transformed in E. coli and the resulting plasmids, pAt21 and pAt35, were analyzed. The restriction map and Southern blot analysis show that both plasmids are rearranged. They had lost the structural tef information and were found to contain new DNA fragments, which were identical in both cases. Southern blot analysis of the transformants indicates that the rearranged plasmids are present in the fungal transformants and that the changes are not the result of re-transformation in E. coli. Plasmids were only recovered after growth under selective conditions. Southern blot analysis and re-transformation with undigested transformant DNA shows that the plasmids are replicated autonomously.

DNA sequence and functional analysis of an ARS-element from the zygomycete Absidia glauca

A DNA fragment of mitochondrial origin from the mucoraceous fungus Absidia glauca promoting autonomous plasmid replication in Saccharomyces cerevisiae was sequenced and functionally characterised. We could show that the original mitochondrial insert cloned in Yip5 contains two regions with ARS activity which mutually inhibit each other. All plasmid derivatives replicating in yeast are rapidly lost during growth under non-selective conditions. In addition to one ARS consensus sequence with only one base substitution, the mitochondrial insert contains 18 related sequences with two base pair exchanges. With one exception all consensus sequences are preceded by sequence motifs strongly resembling ARS boxes.

Neomycin resistance as a dominantly selectable marker for transformation of the zygomycete Absidia glauca

A plasmid (pAmN61) containing the NPT II structural gene (neomycin phosphotransferase) fused to the N-terminal region of a homologous actin gene was used for the transformation of Absidia glauca protoplasts. Neomycin resistant transformants could be selected for on complete medium containing 1.2 mg/ml neomycin sulfate. The physical presence of plasmid DNA in Absidia glauca was demonstrated by retransformation into Escherichia coli and by Southern blot analysis. No integration of plasmid DNA at either one of the two actin loci was observed; Southern blot experiments provide evidence that pAmN61 is autonomously replicated in Absidia glauca.

Structural organization of the genome of the zygomycete Absidia glauca: evidence for high repetitive DNA content

Total cell DNA of Absidia glauca has a GC-content of 44.6% +/- 0.5% as determined from optical melting profiles which is in good accordance with values from equilibrium centrifugation in bisbenzimide containing CsCl gradients (46.2% +/- 1.1%), whereas mitochondrial DNA has a GC-content of only 30%. The genome size of Absidia glauca is approximately 36,000 kb, 8.6 times that of Escherichia coli. Three kinetically different fractions could be identified in reassociation experiments: a foldback-DNA fraction, comprising approximately 10% of the total DNA, repetitive DNA (25%) and single copy DNA (65%). This relatively high amount of repetitive DNA could partly be ascribed to ribosomal DNA (13%) and a new interspersed repetitive element ("rAg1") which has been cloned in pBR325.

Cloned mitochondrial DNA from the zygomycete Absidia glauca promotes autonomous replication in Saccharomyces cerevisiae

We have cloned fragments from mitochondrial and chromosomal DNA of the zygomycete Absidia glauca in Saccharomyces cerevisiae using the ARS selection vector YIp5. Though it has not been possible to select ARS elements from chromosomal DNA, we succeeded in isolating two clones of mitochondrial origin that support autonomous replication in bakers' yeast. DNA from these plasmids has been shown to hybridize with mitochondrial DNA from both mating types. Generation times of the transformed yeast strain in selective medium are around 20 h. In liquid minimal medium only 6% of the cells contain the plasmid; in complete medium a mitotic stability of 50% has been determined.