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.

Prevalence of WNT10A gene mutations in non-syndromic oligodontia.

OBJECTIVES: Non-syndromic oligodontia is an infrequent clinical condition whose etiology is not yet completely understood being a wide spectrum of gene mutations described in concomitance with this severe form of tooth agenesis. Recently, multiple observations have linked up to 50% of cases with isolated hypodontia to mutations in the WNT10A gene. Here, we hypothesized that mutations in the WNT10A gene could also be present in families affected by non-syndromic oligodontia. MATERIAL AND METHODS: All available patients with non-syndromic oligodontia (n = 20) treated at the Department of Orthodontics, University of Giessen, Germany between 1986 and 2013 as well as their family members were analyzed for mutations in the WNT10A gene. RESULTS: Mutation screening was positive in 50% of the 20 patients. The analysis revealed that the mutations 2:219755011(c.682T>TA)(p.F228I), 2:219754822(c.493G>GA)(p.G165R), 2:219754816(c.487C>CT)(p.R163W), and 2:219747090(c.321C>CA)(p.C107*), the novel missense mutation 2:219757676(c.937G/GT)(p.G313C), and the novel synonym variant 2:219754854(c.525C>CT)(p.H175H) were present. CONCLUSION: Multiple phenotypes are found in individuals presenting mutations in the WNT10A gene. Among them, the stop codon p.C107* as well as the biallelic p.F228I variants correlate with the most severe oligodontia phenotypes. In addition, we diagnosed the monoallelic mutations p.F228I, p.G165R, and p.G313C in healthy relatives with normal dentitions. CLINICAL RELEVANCE: A correct diagnosis of non-syndromic oligodontia is fundamental to discard a possible underlying pathology in which multiple tooth agenesis could be the most evidential clinical sign. Due to the wide spectrum of pathologies that are associated to mutations in the WNT10A gene, an extended genetic analysis of these individuals' relatives is also essential.

Ultrasound-guided radiofrequency ablation of symptomatic uterine fibroids: short-term evaluation of effect of treatment on quality of life and symptom severity.

OBJECTIVE: To evaluate the feasibility of ultrasound-guided radiofrequency ablation (USgRFA) for the treatment of women with symptomatic uterine fibroids in relation to volume of fibroid. METHODS: Forty-three women with symptomatic fibroids underwent USgRFA for treatment of uterine fibroids. Improvements in fibroid symptoms and quality of life were measured by the Uterine Fibroid Symptom and Quality of Life questionnaire scores at baseline and 3, 6 and 9 months after the intervention, and analyzed in relation to baseline fibroid volume. Volume reduction of fibroids was measured and the frequency of adverse events and re-interventions was recorded. RESULTS: Following USgRFA, mean Symptom Severity Scores (SSS) decreased from 60.7 ± 17.8 to 31.2 ± 19.5, corresponding to an improvement of 48.6%. The total Health-Related Quality of Life (HRQOL) score improved by 46.4% from 55.6 ± 20.9 to 81.4 ± 16.6. There was no correlation between fibroid volume at baseline and improvement in SSS and HRQOL scores. Fibroid volume was reduced in all patients, by a mean of 69.7 ± 19.4%. Two (4.7%) patients underwent hysterectomy. No adverse events occurred. CONCLUSION: USgRFA reduces fibroid symptom and size even in patients with larger fibroids. USgRFA is a promising new treatment for fibroids in gynecological settings and should be further investigated.

Proposal of a 2-tier histologic grading system for canine cutaneous mast cell tumors to more accurately predict biological behavior.

Currently, prognostic and therapeutic determinations for canine cutaneous mast cell tumors (MCTs) are primarily based on histologic grade. However, the use of different grading systems by veterinary pathologists and institutional modifications make the prognostic value of histologic grading highly questionable. To evaluate the consistency of microscopic grading among veterinary pathologists and the prognostic significance of the Patnaik grading system, 95 cutaneous MCTs from 95 dogs were graded in a blinded study by 28 veterinary pathologists from 16 institutions. Concordance among veterinary pathologists was 75% for the diagnosis of grade 3 MCTs and less than 64% for the diagnosis of grade 1 and 2 MCTs. To improve concordance among pathologists and to provide better prognostic significance, a 2-tier histologic grading system was devised. The diagnosis of high-grade MCTs is based on the presence of any one of the following criteria: at least 7 mitotic figures in 10 high-power fields (hpf); at least 3 multinucleated (3 or more nuclei) cells in 10 hpf; at least 3 bizarre nuclei in 10 hpf; karyomegaly (ie, nuclear diameters of at least 10% of neoplastic cells vary by at least two-fold). Fields with the highest mitotic activity or with the highest degree of anisokaryosis were selected to assess the different parameters. According to the novel grading system, high-grade MCTs were significantly associated with shorter time to metastasis or new tumor development, and with shorter survival time. The median survival time was less than 4 months for high-grade MCTs but more than 2 years for low-grade MCTs.

Recommended guidelines for submission, trimming, margin evaluation, and reporting of tumor biopsy specimens in veterinary surgical pathology.

Neoplastic diseases are typically diagnosed by biopsy and histopathological evaluation. The pathology report is key in determining prognosis, therapeutic decisions, and overall case management and therefore requires diagnostic accuracy, completeness, and clarity. Successful management relies on collaboration between clinical veterinarians, oncologists, and pathologists. To date there has been no standardized approach or guideline for the submission, trimming, margin evaluation, or reporting of neoplastic biopsy specimens in veterinary medicine. To address this issue, a committee consisting of veterinary pathologists and oncologists was established under the auspices of the American College of Veterinary Pathologists Oncology Committee. These consensus guidelines were subsequently reviewed and endorsed by a large international group of veterinary pathologists. These recommended guidelines are not mandated but rather exist to help clinicians and veterinary pathologists optimally handle neoplastic biopsy samples. Many of these guidelines represent the collective experience of the committee members and consensus group when assessing neoplastic lesions from veterinary patients but have not met the rigors of definitive scientific study and investigation. These questions of technique, analysis, and evaluation should be put through formal scrutiny in rigorous clinical studies in the near future so that more definitive guidelines can be derived.

Recommended guidelines for the conduct and evaluation of prognostic studies in veterinary oncology.

There is an increasing need for more accurate prognostic and predictive markers in veterinary oncology because of an increasing number of treatment options, the increased financial costs associated with treatment, and the emotional stress experienced by owners in association with the disease and its treatment. Numerous studies have evaluated potential prognostic and predictive markers for veterinary neoplastic diseases, but there are no established guidelines or standards for the conduct and reporting of prognostic studies in veterinary medicine. This lack of standardization has made the evaluation and comparison of studies difficult. Most important, translating these results to clinical applications is problematic. To address this issue, the American College of Veterinary Pathologists' Oncology Committee organized an initiative to establish guidelines for the conduct and reporting of prognostic studies in veterinary oncology. The goal of this initiative is to increase the quality and standardization of veterinary prognostic studies to facilitate independent evaluation, validation, comparison, and implementation of study results. This article represents a consensus statement on the conduct and reporting of prognostic studies in veterinary oncology from veterinary pathologists and oncologists from around the world. These guidelines should be considered a recommendation based on the current state of knowledge in the field, and they will need to be continually reevaluated and revised as the field of veterinary oncology continues to progress. As mentioned, these guidelines were developed through an initiative of the American College of Veterinary Pathologists' Oncology Committee, and they have been reviewed and endorsed by the World Small Animal Veterinary Association.

Breast ultrasound in office gynecology--ten years of experience.

PURPOSE: Mammography in screening or on indication is regarded as the gold standard for breast examination to detect breast cancer. The present study was performed to evaluate breast ultrasound examination (BU) as a supplement to physical breast examination in a gynecological office setting. MATERIALS AND METHODS: BU was performed concomitantly with all physical breast examinations in a gynecological clinic. The results of all BUs during a 10-year period using the patients' personal numbers were crossed with the Danish Cancer Registry and the Danish Pathology Data Bank. All new breast malignancies registered from the date of BU and 12 months later were included. RESULTS: A total of 3030 BUs of both breasts was performed in 1428 women. Twenty-eight new breast malignancies were registered in 27 patients. Physical examination did not reveal any tumors not detected by ultrasound. Sixteen of the 28 malignancies were non-palpable (57 %). BU detected 25 of these malignancies, thus yielding a sensitivity of 89 %. Mammography performed within 12 months of the diagnosis was negative in 11 patients resulting in a rate of 44 % of malignancies with a negative mammography result. The tumors measured an average of 11 mm (range 4 - 30 mm) using the largest diameter. CONCLUSION: BU offers substantial help for the detection of breast cancer. The sensitivity is high, and in a gynecological setting where ultrasound is used for almost every consultation, it is natural to use the scanner for the breast examination. Larger studies with evaluation of interobserver variability for tumor detection by ultrasound are needed.

Vascular lesions in pigs experimentally infected with porcine circovirus type 2 serogroup B.

Vasculitis is a hallmark lesion of the severe form of systemic porcine circovirus-associated disease (PCVAD). In 2 experimental studies with porcine circovirus type 2 serogroup b (PCV2b), 2 pigs developed fatal PCVAD with acute vasculitis, and 5 related pigs developed chronic lymphohistiocytic and plasmacytic peri- and endarteritis. Five of these pigs (1 with acute vasculitis and 4 with chronic vasculitis) had also been inoculated with bovine viral diarrhea virus type 1 (BVDV1) or BVDV1-like virus. Vascular lesions were similar, independent of whether pigs had been inoculated singly with PCV2b or dually with PCV2b and BVDV1 or BVDV1-like virus. The acute vasculitis was accompanied by marked pulmonary and mesenteric edema and pleural effusion. In situ hybridization demonstrated abundant intracytoplasmic porcine circovirus type 2 (PCV2) nucleic acid in endothelial, smooth muscle-like, and inflammatory cells within and around affected arteries. The pigs with lymphohistiocytic and plasmacytic vasculitis had lesions of systemic PCVAD, including multisystemic lymphoplasmacytic and histiocytic or granulomatous inflammation. PCV2 nucleic acid was detected in renal tubule epithelial cells, mononuclear inflammatory cells, and rare endothelial cells in noninflamed vessels in multiple tissues of these animals. The 2 pigs with acute vasculitis had no PCV2-specific antibodies (or a low titer of), whereas the pigs with lymphohistiocytic and plasmacytic vasculitis developed high antibody titers against this virus. These observations suggest that (1) acute vasculitis observed in the current studies is directly caused by PCV2b, (2) chronic vasculitis may in part be mediated by the subsequent immune response, and (3) host factors and viral strain may both contribute to vasculitis in animals infected with PCV2b.

Limited humoral immunoglobulin E memory influences serum immunoglobulin E levels in blood.

The switch of B cells expressing membrane-bound Igs, which serve as antigen receptors, to antibody-secreting plasmablasts and finally to non-dividing, long-lived plasma cells (PCs) lacking an antigen receptor, marks the terminal differentiation of a B cell. Antibody-secreting PCs represent the key cell type for the maintenance of a proactive humoral immunological memory. Although some populations of long-lived PCs persist in the spleen, most of them return to their 'place of birth' and travel to the bone marrow or invade inflamed tissues, where they survive up to several months in survival niches as resident, immobile cells. Existing data strongly support the notion that isotype-specific receptor signalling influences the migration behaviour of plasmablasts to the bone marrow. The recent observation in the murine system that the immigration of plasmablasts and the final differentiation to long-lived PCs in the bone marrow is dependent on the expressed B-cell isotype and the related expression of chemokine receptors leads to the conclusion that during a T-helper type 2 (Th2)-mediated immune response in wild type mice, IgE plasmablasts do not have the same chance to contribute to long-lived PC memory as IgG1 plasmablasts. The overall limited humoral IgE memory additionally restricts the quantity of IgE Igs in the serum.

Mswi bottom ash for upgrading of biogas and landfill gas.

A new upgrading process for biogas and landfill gas (LFG) has been designed recently by the authors' institute. The process uses the alkalinity of the fine fraction of bottom ash from municipal solid waste incineration (MSWI) for sorbing CO2 and H2S. Results from process development and optimisation are presented in this paper. It is expected that nearly pure CH4 can be produced for substitution of fossil fuels. Simultaneously, the leachability of MSWI bottom ash is clearly reduced.

SCN outputs and the hypothalamic balance of life.

The circadian clock in the suprachiasmatic nucleus (SCN) is composed of thousands of oscillator neurons, each dependent on the cell-autonomous action of a defined set of circadian clock genes. Still, the major question remains how these individual oscillators are organized into a biological clock producing a coherent output able to time all the different daily changes in behavior and physiology. In the present review, the authors discuss the anatomical connections and neurotransmitters used by the SCN to control the daily rhythms in hormone release. The efferent SCN projections mainly target neurons in the medial hypothalamus surrounding the SCN. The activity of these preautonomic and neuroendocrine target neurons is controlled by differentially timed waves of, among others, vasopressin, GABA, and glutamate release from SCN terminals. Together, the data on the SCN control of neuroendocrine rhythms provide clear evidence not only that the SCN consists of phenotypically (i.e., according to neurotransmitter content) different subpopulations of neurons but also that subpopulations should be distinguished (within phenotypically similar groups of neurons) based on the acrophase of their (electrical) activity. Moreover, the specialization of the SCN may go as far as a single body structure, that is, the SCN seems to contain neurons that specifically target the liver, pineal, and adrenal.

Quantitative prediction of nuclear-spin-diffusion-limited coherence times of molecular quantum bits based on copper(ii).

We have investigated the electron spin dynamics in a series of copper(ii) ß-diketonate complexes both in frozen solutions and doped solids. Double digit microsecond coherence times were found at low temperatures. We report quantitative simulations of the coherence decays solely based on the crystal structure of the doped solids.

A network of (autonomic) clock outputs.

The circadian clock in the suprachiasmatic nuclei (SCN) is composed of thousands of oscillator neurons, each of which is dependent on the cell-autonomous action of a defined set of circadian clock genes. A major question is still how these individual oscillators are organized into a biological clock producing a coherent output that is able to time all the different daily changes in behavior and physiology. We investigated which anatomical connections and neurotransmitters are used by the biological clock to control the daily release pattern of a number of hormones. The picture that emerged shows projections contacting target neurons in the medial hypothalamus surrounding the SCN. The activity of these pre-autonomic and neuro-endocrine target neurons is controlled by differentially timed waves of, among others, vasopressin, GABA, and glutamate release from SCN terminals. Together our data indicate that, with regard to the timing of their main release period within the light-dark (LD) cycle, at least 4 subpopulations of SCN neurons should be discerned. The different subgroups do not necessarily follow the phenotypic differences among SCN neurons. Thus, different subgroups can be found within neuron populations containing the same neurotransmitter. Remarkably, a similar distinction of 4 differentially timed subpopulations of SCN neurons was recently also discovered in experiments determining the temporal patterns of rhythmicity in individual SCN neurons by way of the electrophysiology or clock gene expression. Moreover, the specialization of the SCN may go as far as a single body structure; i.e., the SCN seems to contain neurons that specifically target the liver, pineal, and adrenal.

A network of (autonomic) clock outputs.

The circadian clock in the suprachiasmatic nuclei (SCN) is composed of thousands of oscillator neurons, each dependent on the cell-autonomous action of a defined set of circadian clock genes. A major question is still how these individual oscillators are organized into a biological clock that produces a coherent output capable of timing all the different daily changes in behavior and physiology. We investigated which anatomical connections and neurotransmitters are used by the biological clock to control the daily release pattern of a number of hormones. The picture that emerged shows projections contacting target neurons in the medial hypothalamus surrounding the SCN. The activity of these pre-autonomic and neuro-endocrine target neurons is controlled by differentially timed waves of vasopressin, GABA, and glutamate release from SCN terminals, among other factors. Together our data indicate that, with regard to the timing of their main release period within the LD cycle, at least four subpopulations of SCN neurons should be discernible. The different subgroups do not necessarily follow the phenotypic differences among SCN neurons. Thus, different subgroups can be found within neuron populations containing the same neurotransmitter. Remarkably, a similar distinction of four differentially timed subpopulations of SCN neurons was recently also discovered in experiments determining the temporal patterns of rhythmicity in individual SCN neurons by way of the electrophysiology or clock gene expression. Moreover, the specialization of the SCN may go as far as a single body structure, i.e., the SCN seems to contain neurons that specifically target the liver, pineal gland, and adrenal gland.

[Procedures of temporary wall closure in abdominal trauma and sepsis]. / Verfahren zum temporären Bauchdeckenverschluss bei Trauma und Sepsis.

Temporary abdominal closure methods differ mainly between vacuum-assisted and conventional approaches. Each method has its indications. Vacuum-assisted methods seem to be superior especially for trauma indications--in terms of lethality, the possibility of secondary closure during primary hospital stay, and frequency of enterocutaneous fistulas. Skin-only closure might be used as a short-term application (e.g. when damage control closure is needed), and the Bogota bag silo gives space to protruding bowels in pending or manifest abdominal compartment syndrome. Temporary fascial mesh closure enables repetitive laparotomies through the mesh, thus sparing the fascia. For that reason it is to be preferred, especially for its good practicability in clinical situations and on mission abroad.

[Penetrating injuries to the pelvis]. / Penetrierende Beckenverletzung.

As criminality and weapon use increase, general and military surgeons are increasingly confronted with penetrating pelvic injuries both at home and on peacekeeping missions. Penetrating injuries to the iliac vascular axis are associated with considerable mortality, and thus the majority of these emergency patients arrive in a state of deep hypovolemic shock. Concomitant bowel injuries are present in one of five cases, resulting in contamination of the damaged area. Surgical options are simple lateral repair, ligation of the veins, temporary shunt insertion, and prosthetic graft interposition in the injured artery. In extremis ligation of the common or external iliac artery may be the only option to save the patient's life. Surgeons must be aware that damage control surgery and related methods may be needed early on to enable patient survival.

In vivo evidence for a controlled offset of melatonin synthesis at dawn by the suprachiasmatic nucleus in the rat.

The daily rhythm of melatonin synthesis in the rat pineal gland is controlled by the central biological clock, located in the suprachiasmatic nucleus (SCN), via a multi-synaptic pathway involving, successively, neurones of the paraventricular nucleus of the hypothalamus (PVN), sympathetic preganglionic neurones of the intermediolateral cell column of the spinal cord, and norepinephrine containing sympathetic neurones of the superior cervical ganglion. Recently, we showed that, in the rat, the SCN uses a combination of daytime inhibitory and nighttime stimulatory signals toward the PVN-pineal pathway in order to control the daily rhythm of melatonin synthesis, GABA being responsible for the daytime inhibitory message and glutamate for the nighttime stimulation. The present study was initiated to further check this concept, and to investigate the involvement of the inhibitory SCN output in the early morning circadian decline of melatonin release, with the hypothesis that, at dawn, the increased release of GABA onto pre-autonomic PVN neurones results in a diminished norepinephrine stimulation of the pineal, and ultimately an arrest of melatonin release. First, we established that prolonged norepinephrine stimulation of the pineal gland was indeed sufficient to prevent the early morning decline of melatonin release. Blockade of GABA-ergic signaling in the PVN at dawn could not prevent the early morning decline of melatonin completely. Therefore, these results show that an increased GABAergic inhibition of the PVN neurones that control the sympathetic innervation of the pineal gland, at dawn, is not sufficient to explain the early morning decline of melatonin release.

[German education for treatment of penetrating gut traumata in army service]. / Penetrierendes Bauchtrauma aus der Sicht der Bundeswehr.

On military missions abroad, surgical care for penetrating abdominal injuries differentiates from that given at home. The different conditions in the field usually include a single general surgeon with no further specialists or hospitals to rely upon. Thus a mismatch between treatment capacity and needs can be experienced in mass casualty situations. Therefore the focus is on damage control surgery, getting patients fit for evacuation, and transport home under intensive care if needed. Knowledge of ballistics and explosive devices are adjunct fields of interest, as they improve the understanding and treatment of military injuries. Although these aspects add up to additional training requirements to be met by our surgeons, we are convinced that the new German education standards will allow successful training of future military surgeons.

[Pancreatic resection in the elderly : Is the risk justified?]. / Pankreasresektionen im Alter : Ist das Risiko vertretbar?

BACKGROUND: Due to demographic changes and improved diagnostic and therapeutic options surgery in the elderly is an essential field of discussion in medicine. Working groups are becoming increasingly more concerned with the question whether old age is a risk factor for complex surgical procedures. OBJECTIVE: This study was carried out to help assess and evaluate the risk of pancreatic resection in the elderly. MATERIAL AND METHODS: In a retrospective analysis of a prospectively maintained database of pancreatic resections, data from a 4-year period were evaluated and analyzed. A division into two age groups was defined according to the literature with the age of 75 years being the dividing line. RESULTS: During the 4 years of the study 209 pancreatic resections were performed in 146 patients under the age of 75 years and 63 patients over the age of 75 years. A pancreatic head resection was performed in 133 patients, distal pancreatectomy in 57, pancreatectomy in 16 and segmental resection in 3 patients. The overall mortality rate was 2.4 %, only patients over the age of 75 years were affected and was not directly related to surgery in any of the cases. The risk of patients dying perioperatively was significantly increased over the age of 75 years as was the comorbidity rate. Regarding surgically related complications there were no differences between the two groups. CONCLUSION: Pancreatic resection in elderly patients > 75 years is justified because of the very low surgical morbidity and mortality which can now be achieved in experienced centers if comorbidities of patients are taken into account in the decision-making process. The age per se does not constitute a contraindication.

Alkali myosin light chains in man are encoded by a multigene family that includes the adult skeletal muscle, the embryonic or atrial, and nonsarcomeric isoforms.

A set of cDNA clones coding for alkali myosin light chains (AMLC) was isolated from fetal human skeletal muscle. Nucleotide sequence analysis and RNA expression patterns of individual clones revealed related sequences corresponding to (i) fast fiber type MLC1 and MLC3; (ii) the embryonic MLC that is also expressed in fetal ventricle and adult atrium (MLCemb); and (iii) a nonsarcomeric MLC isoform that is found in all nonmuscle cell types and smooth muscle. The AMLC gene family in man comprises unique copies for MLC1, MLC3 and MLCemb, and multiple copies for the nonsarcomeric MLC genes. The gene coding for MLC1 and MLC3 is located on human chromosome 2.