Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.

A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.

Rocuronium potency and recovery characteristics during steady-state desflurane, sevoflurane, isoflurane or propofol anaesthesia.

We have studied the potency and recovery characteristics of rocuronium during 1.25 MAC of isoflurane, desflurane, sevoflurane or propofol anaesthesia in 84 patients using electromyography. Potency was determined by a cumulative bolus technique. The mean ED50 of rocuronium was 169 (SD 41), 126 (32), 121 (28) and 136 (25) micrograms kg-1 during propofol, isoflurane, sevoflurane and desflurane anaesthesia, respectively (ns), and ED90 values were 358 (62), 288 (29), 289 (28) and 250 (28) micrograms kg-1, respectively. The reduction in ED90 was statistically significant for all three inhalation anaesthetics (P < 0.05) compared with propofol. After 120 min, the cumulative infusion rate of rocuronium to obtain twitch depression of 90-95% was 9.0 (1.9), 6.3 (1.6), 6.1 (2.0) and 6.1 (1.1) micrograms kg-1 min-1 during propofol, isoflurane, sevoflurane and desflurane anaesthesia, respectively (P < 0.01). Recovery index was 22 (13), 27 (10), 28 (13) and 26 (14) min under propofol, isoflurane, sevoflurane and desflurane anaesthesia, respectively (ns). There were no significant differences between the three potent inhalation anaesthetics in relation to potency, infusion requirements or recovery characteristics of rocuronium.

Assessment of autonomic dysreflexia in patients with spinal cord injury.

OBJECTIVES AND METHODS: To assess the impairment of supraspinal control over spinal sympathetic centres and the occurrence of autonomic dysreflexia in patients with spinal cord injury. Autonomic dysreflexia is caused by the disconnection of spinal sympathetic centres from supraspinal control and is characterised by paroxysmal hypertensive episodes caused by non-specific stimuli below the level of the lesion. Therefore, patients with spinal cord injury were examined clinically and by different techniques to assess the occurrence of autonomic dysreflexia and to relate disturbances of the sympathetic nervous system to episodes of autonomic dysreflexia. RESULTS: None of the paraplegic patients, but 59% (13/22) of tetraplegic patients (91% of the complete, 27% of the incomplete patients) presented signs of autonomic dysreflexia during urodynamic examination. Only 62% of the tetraplegic patients complained about symptoms of autonomic dysreflexia. Pathological sympathetic skin responses (SSRs) of the hands were related to signs of autonomic dysreflexia in 93% of cases. No patient with preserved SSR potentials of the hands and feet showed signs of autonomic dysreflexia, either clinically or during urodynamic examination. Ambulatory blood pressure measurements (ABPMs) indicated a loss of circadian blood pressure rhythm (sympathetic control) but preserved heart rate rhythm (parasympathetic regulation) only in patients with complete tetraplegia. Pathological ABPM recordings were seen in 70% of patients with symptoms of autonomic dysreflexia. CONCLUSIONS: The urodynamic examination was more sensitive in indicating signs of autonomic dysreflexia in patients with spinal cord injury, whereas SSR allowed the assessment of the degree of disconnection of the sympathetic spinal centres from supraspinal control. Using ABPM recordings the occurrence of episodes of autonomic dysreflexia over 24 hours and the effectiveness of therapeutical treatment can be assessed.

[Social integration of patients of a long-term institution]. / Uber die soziale Integration von Patienten einer Langzeiteinrichtung.

With a mean duration of hospitalisation of 28 years the patients of a long-term hospital had on the average only 2.6 visits from outside in one year. Above all the frequency of visits depended on the age, the duration of illness, the distance of the hospital to the homes of the patients and on communication inhibiting symptoms. In a three years follow-up the social integration of patients could be improved by specific rehabilitative treatment. Contacts to persons from outside the hospital and activities inside increased significantly. Improvement was not possible for patients whose homes were very far away and who had communication inhibiting symptoms at the outset of the follow-up.

Loss of circadian blood pressure variability in complete tetraplegia.

Blood pressure (BP) and heart rate (HR) were monitored over 24 h utilising an ambulatory blood pressure monitoring (ABPM) system in 33 subjects with spinal cord injury: 11 patients with complete tetraplegia, 13 patients with incomplete tetraplegia and nine patients with complete paraplegia. Measurements were analysed for overall levels of BP and HR, presence of a physiological day/night cycle and events of autonomic dysreflexia. Paraplegic patients exhibited normal BP and HR levels with a physiological circadian rhythm. In complete tetraplegic patients the circadian rhythm was abolished for BP but preserved for HR, while in patients with incomplete tetraplegia circadian rhythm was preserved for both BP and HR. Complete tetraplegic patients with autonomic dysreflexia revealed a typical pattern in ABPM with multiple hypertensive episodes and concomitant bradycardia. Under adequate treatment these episodes could be reduced or abolished, while the disturbed circadian BP rhythm persisted. These observations shed further light on mechanisms of central BP and HR control. In tetraplegic patients ABPM is an efficient method to assess treatment for autonomic dysreflexia.

Incidence and morphology of spontaneous thyroid tumours in different strains of rats.

The incidence and morphology of thyroid neoplasms in different strains and stocks of rats are reported. The frequency of thyroid tumours varied to a great extent between different strains of rats. Low incidences were observed in DA/Han (0.85 per cent) and BDII/Han rats (1.25 per cent), while somewhat higher incidences occurred in Han:WIST rats (7.3 per cent). The highest number of thyroid tumour-bearing rats was found in the Han:SPRD stock (55.5 per cent). Thyroid neoplasms were classified histologically as polymorphofollicular adenomas, papillary adenomas, cystadenomas, polymorphofollicular carcinomas, papillary carcinomas, C-cell adenomas and C-cell carcinomas (medullary carcinomas). C-cell neoplasms were predominant in Han:SPRD rats (93.0 per cent), while the majority of tumour-bearing Han:WIST rats (61.4 per cent) had follicular tumours.

Site-specific location of covalent DNA-polypeptide complexes in the chicken genome.

A nitrocellulose filter binding assay was applied to isolate and to analyze the fraction of chicken DNA fragments associated with residual nuclear polypeptides resistant to SDS/proteinase K treatment and phenol extraction. It is shown that the DNA-polypeptide complexes retained on nitrocellulose filters are located on a non-random sub-set of DNA sequences. (a) Southern analysis reveals that the fractions of DNA fragments from chicken erythrocytes and from hen oviduct cells associated with the resistant polypeptides have a lower sequence complexity than unfractionated DNA. Moreover, the retained DNA fractions from different cell types of the same species are highly homologous. (b) All DNA fragments of the transcriptionally active and inactive ovalbumin gene map in the DNA fraction passing the filters indicating that the tight DNA-polypeptide complexes are not remnants of transcription complexes. (c) By use of a genomic sub-set library prepared from DNA retained on filters, clones were isolated with sequences mapping specifically in the DNA fraction associated with the tight DNA-polypeptide complexes. The results are consistent with fixed covalent DNA-polypeptide complexes in the chicken genome whose location is essentially identical in different cell types of the same species and apparently determined by DNA signal-sequences.

Rhizopus oligosporus as a cause of mucormycosis in man.

After a fracture of the spinal column a 49-year-old male developed a mucormycosis due to Rhizopus oligosporus. This appears to be the first report of a disease caused by this thermotolerant Rhizopus species in a human being.

Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

Sub-set characteristics of DNA sequences involved in tight DNA/polypeptide complexes and their homology to nuclear matrix DNA.

Polypeptides co-isolating with DNA induce the binding of a fraction of native DNA fragments to nitrocellulose filters. Southern analysis reveals a high intensity of self-hybridization of the DNA sequences retained on nitrocellulose filters. Consistently, the DNA fraction passing the filters shows only weak hybridization when probed with DNA retained on filters. This indicates that the DNA/polypeptide complexes reside on a non-random sub-set of DNA sequences. Moreover, a high degree of homology was found between residual nuclear matrix DNA sequences and the DNA sequences retained on nitrocellulose filters. This indicates that the DNA sequences associated with tightly bound polypeptides originate from sites where the genome is salt-stably anchored in the nuclear matrix.

Non-neoplastic lesions of female virgin Han:NMRI mice, incidence and influence of food restriction throughout life span. I: Thyroid.

A life span study with 900 female virgin Han:NMRI mice (300 outbred controls, 300 of a fat subline and 300 of a lean subline) was carried out to determine the occurrence of spontaneous disease with ad libitum or restricted feeding. The major age-dependent non-neoplastic alteration of the thyroid was a cystic distension of the ultimobranchial bodies (up to 90% in the oldest age groups). Most of the severely cystic thyroids were found in animals of the fat sublines and development seemed to be slightly delayed by food restriction. The cyst walls were composed of ciliated and non-ciliated granular or highly attenuated cells. The cysts contained Alcian blue and periodic acid Schiff positive substances.