Neural Transformers for Intraductal Papillary Mucosal Neoplasms (IPMN) Classification in MRI images

Early detection of precancerous cysts or neoplasms, i.e., Intraductal Papillary Mucosal Neoplasms (IPMN), in pancreas is a challenging and complex task, and it may lead to a more favourable outcome. Once detected, grading IPMNs accurately is also necessary, since low-risk IPMNs can be under surveillance program, while high-risk IPMNs have to be surgically resected before they turn into cancer. Current standards (Fukuoka and others) for IPMN classification show significant intra- and inter-operator variability, beside being error-prone, making a proper diagnosis unreliable. The established progress in artificial intelligence, through the deep learning paradigm, may provide a key tool for an effective support to medical decision for pancreatic cancer. In this work, we follow this trend, by proposing a novel AI-based IPMN classifier that leverages the recent success of transformer networks in generalizing across a wide variety of tasks, including vision ones. We specifically show that our transformer-based model exploits pre-training better than standard convolutional neural networks, thus supporting the sought architectural universalism of transformers in vision, including the medical image domain and it allows for a better interpretation of the obtained results.

Gonadal function in adult male patients with congenital adrenal hyperplasia

CONTEXT

Current knowledge on gonadal function in congenital adrenal hyperplasia (CAH) is mostly limited to single-center/country studies enrolling small patient numbers. Overall data indicate that gonadal function can be compromised in men with CAH.

OBJECTIVE

To determine gonadal function in men with CAH within the European 'dsd-LIFE' cohort.

DESIGN

Cross-sectional clinical outcome study, including retrospective data from medical records.

METHODS

Fourteen academic hospitals included 121 men with CAH aged 16-68 years. Main outcome measures were serum hormone concentrations, semen parameters and imaging data of the testes.

RESULTS

At the time of assessment, 14/69 patients had a serum testosterone concentration below the reference range; 7 of those were hypogonadotropic, 6 normogonadotropic and 1 hypergonadotropic. In contrast, among the patients with normal serum testosterone (55/69), 4 were hypogonadotropic, 44 normogonadotropic and 7 hypergonadotropic. The association of decreased testosterone with reduced gonadotropin concentrations (odds ratio (OR) = 12.8 (2.9-57.3)) was weaker than the association between serum androstenedione/testosterone ratio ≥1 and reduced gonadotropin concentrations (OR = 39.3 (2.1-732.4)). Evaluation of sperm quality revealed decreased sperm concentrations (15/39), motility (13/37) and abnormal morphology (4/28). Testicular adrenal rest tumor (TART)s were present in 39/80 patients, with a higher prevalence in patients with the most severe genotype (14/18) and in patients with increased current 17-hydroxyprogesterone 20/35) or androstenedione (12/18) serum concentrations. Forty-three children were fathered by 26/113 patients.

CONCLUSIONS

Men with CAH have a high risk of developing hypothalamic-pituitary-gonadal disturbances and spermatogenic abnormalities. Regular assessment of endocrine gonadal function and imaging for TART development are recommended, in addition to measures for fertility protection.

Adrenal Steroid Metabolites Accumulating in Congenital Adrenal Hyperplasia Lead to Transactivation of the Glucocorticoid Receptor

Patients with congenital adrenal hyperplasia (CAH) are often clinically less severely affected by cortisol deficiency than anticipated from their enzymatic defect. We hypothesize that adrenal steroid hormone precursors that accumulate in untreated or poorly controlled CAH have glucocorticoid activity and partially compensate for cortisol deficiency. We studied the in vitro effects of 17-hydroxyprogesterone (17OHP), progesterone (P), 21-deoxycortisol (21DF), and androstenedione (Δ4) on the human glucocorticoid receptor (hGR). Competitive binding assays were performed in HeLa cells. Nuclear translocation of the hGR was studied by transfection of COS-7 cells with a GFP-tagged hGR and fluorescence microscopy. Transactivation assays were performed in COS-7 cells and in HEK 293 cells after cotransfection with hGR and luciferase reporter vectors using a dual luciferase assay. 17OHP, P, and 21DF are able to bind to the hGR with binding affinities of 24-43% compared with cortisol. Δ4 has a low binding affinity. Incubation with 21DF led to complete nuclear translocation of the hGR, whereas treatment with 17OHP or P resulted in partial nuclear translocation. 21DF transactivated the hGR with an EC50 approximately 6 times the EC50 of cortisol. 17OHP and P transactivated the hGR with EC50s of more than 100 times the EC50 of cortisol. No hGR transactivation was detected after incubation with Δ4. 21DF, 17OHP, and P are able to bind, translocate, and transactivate the hGR in vitro and thus may have glucocorticoid activity. 21DF might have a clinically relevant agonistic effect on the hGR and could potentially partially compensate the cortisol deficiency in CAH patients.

Pododermatitis in Captive and Free-Ranging Greater Flamingos (Phoenicopterus roseus)

Pododermatitis is frequent in captive flamingos worldwide, but little is known about the associated histopathologic lesions. Involvement of a papillomavirus or herpesvirus has been suspected. Histopathologic evaluation and viral assessment of biopsies from 19 live and 10 dead captive greater flamingos were performed. Selected samples were further examined by transmission electron microscopy and immunohistochemistry. Feet from 10 dead free-ranging greater flamingos were also evaluated. The histologic appearance of lesions of flamingos of increasing age was interpreted as the progression of pododermatitis. Mild histologic lesions were seen in a 3-week-old flamingo chick with no macroscopic lesions, and these were characterized by Micrococcus-like bacteria in the stratum corneum associated with exocytosis of heterophils. The inflammation associated with these bacteria may lead to further histologic changes: irregular columnar proliferations, papillary squirting, and dyskeratosis. In more chronic lesions, hydropic degeneration of keratinocytes, epidermal hyperplasia, and dyskeratosis were seen at the epidermis, as well as proliferation of new blood vessels and increased intercellular matrix in the dermis. Papillomavirus DNA was not identified in any of the samples, while herpesvirus DNA was seen only in a few cases; therefore, these viruses were not thought to be the cause of the lesions. Poor skin health through suboptimal husbandry may weaken the epidermal barrier and predispose the skin to invasion of Micrococcus-like bacteria. Histologic lesions were identified in very young flamingos with no macroscopic lesions; this is likely to be an early stage lesion that may progress to macroscopic lesions.

[Indications and limitations of fresh frozen sections in the pulmonary apparatus]

Recommendations for the diagnosis of lung tumors almost limit the use of fresh frozen sections to the evaluation of resection margins. In pathology pretherapeutic methods for assessment of clinically suspected lung cancer are favored over intraoperative frozen section diagnosis. For the interdisciplinary management of uncertain lung findings diagnostic methods, such as cytopathology and examination of biopsy material are available. The use of rapid on-site evaluation (ROSE) in cytopathology is limited due to the lack of necessary personnel. Diagnosis of unclear pulmonary lesions or distinction of metastases from primary lung tumors by intraoperative frozen sections is therefore limited to exceptional cases that were not resolved by preoperative biopsies. Such rare cases require a common consensus strategy between thoracic surgeons and pathologists in a preoperative tumor board.

Topography of maturational changes in EEG burst spectral power of the preterm infant with a normal follow-up at 2 years of age

OBJECTIVE

To quantify the electroencephalography (EEG) burst frequency spectrum of preterm infants by automated analysis and to describe the topography of maturational change in spectral parameters.

METHODS

Eighteen preterm infants <32weeks gestation and normal neurological follow-up at 2years underwent weekly 4-h EEG recordings (10-20 system). The recordings (n=77) represent a large variability in postmenstrual age (PMA, 28-36weeks). We applied an automated burst detection algorithm and performed spectral analysis. The frequency spectrum was divided into δ1 (0.5-1Hz), δ2 (1-4Hz), θ (4-8Hz), α (8-13Hz) and β (13-30Hz) bands. Spectral parameters were evaluated as a function of PMA by regression analysis. Results were interpolated and topographically visualised.

RESULTS

The majority of spectral parameters show significant change with PMA. Highest correlation is found for δ and θ band. Absolute band powers decrease with increasing PMA, while relative α and β powers increase. Maturational change is largest in frontal and temporal region.

CONCLUSIONS

Topographic distribution of maturational changes in spectral parameters corresponds with studies showing ongoing gyration and postnatal white matter maturation in frontal and temporal lobes.

SIGNIFICANCE

Computer analysis of EEG may allow objective and reproducible analysis for long-term prognosis and/or stratification of clinical treatment.

[De novo sarcoidosis after kidney transplantation]

HISTORY AND CLINICAL FINDINGS

A 39-year-old man complained of unspecific chest pains four years after kidney transplantation.

INVESTIGATIONS

Laboratory tests revealed a slow increase of retentions values; the value of soluble IL-2 receptor was slightly elevated. Computed tomography of the chest confirmed mediastinal and bilateral hilar masses. The broncho-alveolar lavage (BAL) showed a marked increase of the CD4/CD8 T-lymphocyte ratio and the aspiration cytology of these lymphadenopathies revealed the cytopathological characteristics of sarcoidosis.

TREATMENT AND CLINICAL COURSE

An asymptomatic stage I sarcoidosis was diagnosed, and the immunosuppressive treatment with cyclosporine, mycophenolatmofetil and prednisone was retained. The patient has remained asymptomatic for now six months.

CONCLUSION

When bilateral hilar / mediastinal lymphadenopathies occur after organ transplantation with immunosuppression de novo sarcoidosis should be taken into account.

[Infectious bovine rhinotracheitis (IBR) in the canton of Jura: an epidemiological outbreak investigation]

Following an abortion in a beef herd in the summer of 2009, three outbreaks of infectious bovine rhinotracheitis (IBR) were diagnosed in the cantons of Jura and Neuchatel. An epidemiological outbreak investigation was conducted with the aims to identify the source of introduction of the bovine herpes virus 1 (BoHV-1) into the affected herds and to prevent further spread of the disease. The attack rates in the three outbreak farms were 0.89, 0.28 and 0, respectively. BoHV-1 could be isolated from nasal swabs of two animals originating from one of the affected farms. Comparative restriction enzyme analysis revealed slight differences between the isolates of the two animals, but a high similarity to previous BoHV-1 isolates from the canton of Jura, as well as to a French BoHV-1 isolate. This IBR outbreak has shown the importance of reporting and analyzing abortions. The current disease outbreaks recall the main risk factors for the spread of IBR in Switzerland: purchase and movement of bovines and semen of often unknown IBR status.

[Avian influenza: wildbird monitoring in Switzerland between 2003-2006]

During various surveillance programs more than 3500 cloacal swabs and organ samples from songbirds, waterbirds and poultry have been tested for avian influenza using real time RT-PCR. Switzerland carried out the first wildbird monitoring between autumn 2003 and spring 2005. 1053 samples, mostly from songbirds, were tested. LPAI-strains were found in two cases. A second intensified surveillance program started in October 2005 along with the first ban on free range poultry farming. Until the end of April 2006 2455 cloacal swabs from dead wildbirds have been analysed. By the end of february H5N1 was for the first time detected in Switzerland and by the end of march 32 waterbirds have been found positive for H5N1. 146 poultry flocks with a special permission for free range management proved to be AI negative.

1 M Gd-chelate (gadobutrol) for multislice first-pass magnetic resonance myocardial perfusion imaging

The aim of the study was to evaluate a 1 M gadolinium-chelate (gadobutrol) for first-pass MR myocardial perfusion examinations in patients with suspected coronary artery disease (CAD). In phantom studies, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) values of gadobutrol were compared with gadopentetate (Gd-DTPA). 25 consecutive patients with clinically suspected CAD were examined with dynamic rest/stress MR perfusion examinations using 0.05 mmol kg(-1) gadobutrol. Semi-quantitative evaluation of the myocardial perfusion was performed by calculating the myocardial perfusion reserve index (MPRI). Hypoperfused regions were correlated with data from X-ray coronary angiography. In phantom studies, SNR/CNR of gadobutrol-doped blood samples were consistently higher for all applied flip angles at concentrations < or =1.0 mmol L(-1) compared with Gd-DTPA. Assessment of 81 stress perfusion series with gadobutrol in 25 patients yielded a sensitivity of 82% and specificity of 91% for significant CAD. Combining the information from all perfusion series of one patient yielded a sensitivity of 89% and specificity of 94% on a per-vessel basis. Gadobutrol exhibited favourable signal properties in phantom studies. Rest/stress myocardial perfusion examinations using 1 M gadobutrol yielded high sensitivity and specificity in detection of malperfused areas (82% and 91%, respectively). This is comparable with recently published perfusion data using 0.5 M Gd-DTPA.

Bioflocculent algal-bacterial biomass improves low-cost wastewater treatment

An innovative technology for the biological treatment of wastewater in regions with sufficient solar radiation based on the simultaneous growth and degradation processes of algal and bacterial biomass is presented. The aim of the work is the improvement of pond technology through the formation of stable algae-bacteria aggregates, which a) permit a simple separation of the algal biomass by gravity sedimentation, b) enable a high removal efficiency for organic carbon and nutrients, and c) are independent in terms of oxygen provision through algal photosynthesis. Algae-bacteria aggregates could be developed with a suitable algal species (Chlorella vulgaris, Strain Hamburg) as a 'model organism' in a wastewater environment. The morphology of algal-bacterial flocs is similar to activated sludge flocs. They are stable and settle quickly. Floc size ranged between 400 and 800 microm. Results of our experiments with an artificially irradiated lab-scale system, operated in continuous flow mode, revealed that even at a relatively short hydraulic detention time of two days, a high elimination capacity of 9.96 g N m(-2) d(-1) and 0.87g Pm(-2) d(-1) can be achieved. Recent investigations confirmed that floc formation of unicellular algae and wastewater bacteria also could be developed and maintained in a pilot-scale system with a water depth of 0.5 m.

[Porcine malignant catarrhal fever: diagnostic findings and first detection of the pathogenic agent in diseased swine in Switzerland]

For the first time Ovine Herpesvirus 2 (OvHV-2) was identified in Swiss pigs as the causative agent of Porcine Malignant Catarrhal Fever (MCF). Diseased animals from two farms were observed to show weakness, anorexia, fever up to 41 degrees C, and neurological symptoms, i.e. ataxia, convulsions and hyperesthesia, erosion on the snout and in the oral and nasal mucosa, as well as multiple skin lesions. Histopathological findings included severe non-purulent inflammation with mononuclear cell infiltration in several organs. Most dominant were meningo-encephalitis, disseminated nephritis as well as purulent catarrhalic bronchopneumonia. The findings were quite reminiscent of the lesions due to MCF in cattle and give therefore substantial proof to use Porcine Malignant Catarrhal Fever as the term for the disease. Identification of the causative agent was done with a quantitative PCR specific for OvHV-2. Different tissues from diseased animals were positive. Furthermore, one animal which had been ill for more than five days tested positive for antibodies against an epitope conserved among MCF viruses. Serum samples from diseased animals reacted negative towards Classical Swine Fever- and Pseudorabies virus antigen. A weakly positive reaction against porcine enterovirus type I argued against the involvement of enteroviruses in the observed disease. Moreover, by means of different conventional PCRs, we detected the newly discovered porcine lymphotropic herpesviruses for the first time in Switzerland and could at the same time exclude their involvement in Porcine Malignant Catarrhal Fever.

Transduction of Vero cells and bovine monocytes with a herpes simplex virus-1 based amplicon carrying the gene for the bovine herpesvirus-1 Circ protein

Herpes simplex virus-1 (HSV-1) based amplicon vectors are promising gene delivery vehicles because they have a large transgene capacity and can efficiently transduce many different cell types, including non-dividing cells, of various animal species. The Circ protein of bovine herpesvirus-1 (BHV-1) is a myristylated virion component of unknown function. Preliminary experiments with a circ gene deletion mutant indicated that Circ may influence the host's immune response by downregulating MHC-II expression in bovine monocytes. To get more insight into the function of Circ, amplicon vectors were constructed with various open reading frames (ORFs) under the control of the HSV-1 IE4/5 promoter: (i) the Circ ORF alone, (ii) a fusion ORF encoding an N-terminal Circ fused to the enhanced green fluorescent protein (eGFP), (iii) the eGFP ORF alone, and (iv) the Circ ORF in the inverted orientation. Upon helpervirus-free packaging into HSV-1 amplicon particles and transduction of Vero cells, both Circ alone and the Circ-eGFP fusion protein produced a punctate pattern within the cytoplasm, suggesting membrane association of the myristylated protein. In contrast, eGFP alone was evenly distributed over the cytoplasm of transduced cells. Upon infection of bovine buffy-coat cells, it was observed that cells of the monocyte lineage but not lymphocytes were transduced. Transgene expression reached a peak around 20h after transduction and lasted for at least 90h. Transduced monocytes underwent specific morphological changes, which may be attributed to Circ synthesis.

Biomass, productivity and density of the seagrass Thalassia testudinum at three sites in Cahuita National Park, Costa Rica

The basic ecology of seagrass beds was investigated by comparing biomass, productivity and density of Thalassia testudinum (turtle grass) at three sites: Puerto Vargas, Punta Cahuita and Rio Perezoso, in Cahuita National Park, Limón, Costa Rica, over a two month period (March-April 1999). Above ground biomass, density, and productivity were highest in the Puerto Vargas site while Punta Cahuita had the least non-green above ground biomass was significantly lower in total biomass than Puerto Vargas. Punta Cahuita was distinguished by the largest grain size, a very hard substrate, and shallower water. Rio Perezoso, on the other hand, had extremely fine sediment and lower salinity, while Puerto Vargas was intermediate both in sediment size and environmental conditions. It appears, therefore, that higher biomass and productivity result from a combination of moderate environmental characteristics and an intermediate sediment size.

Latency and reactivation of bovine herpesvirus 1 (BHV-1) in goats and of caprine herpesvirus 1 (CapHV-1) in calves

Bovine Herpesvirus 1 (BHV-1) and Caprine Herpesvirus 1 (CapHV-1) are related members of the herpesvirus family. Since their natural hosts are often kept in close contact with each other, concern was raised that a reservoir might be established in the heterologous host in addition to the homologous host. To investigate this possibility, cross-infection experiments with BHV-1 in goats and CapHV-1 in calves were performed. BHV-1 infected goats developed mild disease signs during acute infection, whereas CapHV-1 infection in calves took a subclinical course. However, virus excretion and antibody production were indicative of successful cross-infection of both BHV-1 and CapHV-1. Reactivation of BHV-1 was achieved in 5 out of 8 goats as demonstrated by recurrent virus excretion and rising antibody titers. In constrast CapHV-1 in calves could not be reactivated experimentally. Nevertheless, PCR revealed that both viruses established latency in the trigeminal ganglia of the heterologous host. Based on these results we conclude that goats should indeed be regarded as a potential BHV-1 reservoir, which must be considered during IBR eradication programs.

Glycoprotein C of bovine herpesvirus 5 (BHV-5) confers a distinct heparin-binding phenotype to BHV-1

Bovine herpesvirus type 1 (BHV-1) causes respiratory and genital diseases in cattle, whereas the closely related BHV-5 can induce severe meningoencephalitis in calves. To characterize BHV-5 glycoprotein C (gC5) within the backbone of BHV-1, three consecutive recombinant viruses were constructed: A deletion mutant (rBHV-1delta gC blue) with gC replaced by the lacZ gene, an exchange mutant (rBHV-1gC5) with the lacZ of BHV-1delta gC blue exchanged by gC5, and a rescue mutant (rescue BHV-1) from rBHV-1gC5 with an additional XbaI site in gC1. The recombinant and wildtype viruses were characterized on MDBK cells. Although no significant differences were observed in growth behaviour and entry kinetics, rBHV-1gC5 showed a distinct phenotype in a heparin blocking assay. The gC5 was able to transfer the heparin binding phenotype of BHV-5 to BHV-1. This indicates that gC1 and gC5 differ in their receptor binding qualities, which might modulate the ability of the viruses to spread within the central nervous system.

Restriction endonuclease analysis of the genome of two Italian caprine herpesvirus 1 strains

Two caprine herpesvirus (CpHV.1) strains isolated in two goat flocks in southern Italy were compared with E/CH and McK/US reference CpHV.1 strains by restriction endonuclease analysis. BamHI, KpnI, NotI and PstI restriction enzymes were used. With these enzymes McK/US strain was clearly differentiated from the others. KpnI and NotI digestion resulted in unique patterns for all four strains. Restriction enzyme analysis might be a useful method to distinguish CpHV.1 isolated from animals and provide a basis for further epidemiological studies of the CpHV.1 infection.

Novel entry pathway of bovine herpesvirus 1 and 5

Herpesviruses enter cells by a yet poorly understood mechanism. We visualized the crucial steps of the entry pathway of bovine herpesvirus 1 (BHV-1) and BHV-5 by transmission and scanning electron microscopy, employing cryotechniques that include time monitoring, ultrarapid freezing, and freeze substitution of cultured cells inoculated with virus. A key step in the entry pathway of both BHV-1 and BHV-5 is a unique fusion of the outer phospholipid layer of the viral envelope with the inner layer of the plasma membrane and vice versa resulting in "crossing" of the fused membranes and in partial insertion of the viral envelope into the plasma membrane. The fusion area is proposed to function as an axis for driving the virus particle into an invagination that is concomitantly formed close to the fusion site. The virus particle enters the cytoplasm through the opened tip of the invagination, and the viral envelope defuses from the plasma membrane. There is strong evidence that the intact virus particle is then transported to the nuclear region.

Radiation-induced impairment of urinary bladder function. Assessment of micturition volumes

PURPOSE

The present investigation was initiated in order to study the feasibility of repeat micturition volume measurements for the determination of acute variations in urinary bladder function in radiotherapy patients.

PATIENTS AND METHODS

Thirty-seven consecutive patients with malignancies of the prostate (11), rectum (9), corpus uteri (11), or cervix uteri (6) were included in this pilot study. All patients were treated according to standard irradiation protocols. All patients were asked to present with maximum bladder filling for each radiation treatment. After irradiation, patients were weighed before and after micturition, and the weight difference was assumed to reflect the micturition volume.

RESULTS

No systematical variations in bladder capacity could be assessed during treatment for uterine tumors. In rectum carcinoma patients, a decrease in micturition volume by about 20% was observed between weeks 2 and 5 which, however, was not statistically significant; subsequently, normal to supra-normal values were measured. In patients treated for prostate cancer, volumes were reduced from week 2; in weeks 5 to 6, minimum values of approximately 70% of the control volumes were seen, which represent a significant reduction (p < 0.05).

CONCLUSIONS

Functional changes represent the majority of side effects of radiation therapy in the urinary bladder. The assessment of urinary bladder function by pre- and post-micturition weighing is a feasible and sensitive method to objectively determine radiation-induced changes. This method may be applied for the documentation of acute radiotherapy side effects.

Pathogenesis of ruminant herpesvirus infections

Ruminants are hosts for members of both Alpha- and Gamma-herpesvirinae. A wide range of disease syndromes is associated with infections by these agents. The associated diseases reflect the biological nature of the causative viruses. Clinically, the symptoms may be mild and localized or include severe generalized disease, leading eventually to death. Much knowledge has been gained concerning the pathogenesis of some alpha-herpesviruses. Initially, these viruses replicate in epithelial cells at the portal of entry. The symptoms of the acute diseases are often associated with the destruction of those epithelial cells. However, as in the case of bovine herpesvirus 1 (BHV-1), the virus may spread in the infected host by viremia, gaining access to a broader range of tissues and organs, and causing a broader variety of diseases. Furthermore, many herpesviruses are capable of entering neuronal cells. There, they may replicate, which may lead to neuronal diseases, for example, encephalitis. In addition, the herpesviruses may establish latency in neuronal or lymphoid cells. During latency, apparently no viral antigens are synthesized but the genomes of the latent viruses are present in the nuclei of long living cells, such as, e.g., neurones of the ganglia corresponding to the sites of peripheral replication. Upon reactivation, the viruses re-establish the lytic cycle of replication. Shielded from the effectors of the immune system, they migrate back to the peripheral tissues where they are excreted and may be transmitted. Although a strong immune response is provoked during primary viral replication, these mechanisms help the herpesviruses to escape from immune surveillance during latency and to a lesser degree during reactivation. It has been observed that certain herpesviruses may behave differently upon infection of different hosts. Relatively little progress has been made concerning the understanding of the pathogenesis of ruminant herpesviruses but much has been learned about viral molecular biology. Many viral proteins have been identified and characterized and the technology to create recombinant viruses has been established. With these tools in our hands, it is now possible to address the really interesting questions concerning pathogenesis. We postulate that herpesviruses contain at least two sets of genes, a first set involved in gene expression and viral replication, and a second set responsible for functions, which may affect pathogenesis, latency, and virus/host interactions. Using recombinant virus technology, it will be possible in the future to design targeted deletions and gene transfers in ruminant herpesviruses in order to study the viral and host factors involved in pathogenesis on the molecular level.

Computational studies of the early intermediates of the bacteriorhodopsin photocycle

Starting from a refined model of bacteriorhodopsin's ground state, alternative models of the K and L intermediates with retinal in either 13-cis or 13-14-dicis configuration have been generated by molecular dynamics simulations. All models have been submitted to electrostatic calculations in order to determine the pK1/2 values of particular residues of interest in the active site. Our pK1/2 calculations for the refined ground state can reestablish our former results, this time without adjusting the intrinsic pK of the Schiff base. For the K intermediate the electrostatic calculations show no significant change in the pK1/2 values compared to the ground state for most of the titrating groups in the active site. For the L intermediate where retinal possesses a 13-cis configuration, we found that electrostatic factors decrease the pK1/2 value of the Schiff base by 4-5 pK-units compared to the ground state. The calculations suggest that changes of the electrostatic environment via a pure 13-cis model are sufficient to produce a pK reduction of the Schiff base that will promote subsequent proton transfer steps.

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

Molecular dynamics simulations have proven to be a valuable tool to investigate the dynamic behavior of stable macromolecules at finite temperatures. However, considerable conformational transitions take place during a simulation only accidentally or at exceptionally high temperatures far from the range of experimental conditions. Targeted molecular dynamics (TMD) is a method to induce a conformational change to a known target structure at ordinary temperature by applying a time-dependent, purely geometrical constraint. The transition is enforced independently of the height of energy barriers, while the dynamics of the molecule is only minimally influenced by the constraint. Simulations of decaalanine and insulin show the ability of the method to explore the configurational space for pathways accessible at a given temperature. The transitions studied at insulin comprise unfolding of an alpha-helical portion and, in the reverse direction, refolding from an extended conformation. A possible application of TMD is the search for energy barriers and stable intermediates from rather local changes up to protein denaturation.

Modeling of G-protein coupled receptors with bacteriorhodopsin as a template. A novel approach based on interaction energy differences

The structure of bacteriorhodopsin was used as a template to generate a model for G-protein coupled receptors. However, these receptors and the template are not related by sequence homology. Therefore a pragmatic and reproducible approach was developed to achieve an energetically favourable accommodation of receptor sequences to the backbone structure of bacteriorhodopsin. Improved interaction energy differences are used in a two step procedure analogous to a hypothetical folding mechanism for integral membrane proteins. The resulting model is in good agreement with existing data from structure-function studies.

Identification and zinc dependence of the bovine herpesvirus 1 transactivator protein BICP0

Bovine herpesvirus 1 (BHV-1) specifies and unspliced early 2.6-kb RNA (ER2.6) which is 3' coterminal with exon 2 of the 2.9-kb immediate-early (IE) RNA. The two transcripts have a common open reading frame (676 codons). The predicted protein, designated BHV-1 infected cell protein 0 (BICP0), contains a zinc finger domain with homology to ICP0 of herpes simplex virus type 1 and protein 61 of varicella-zoster virus, and depending on the promoter, it acts as a strong activator or as a repressor in transient expression assays. In situ immunoadsorbent assays using antisera against synthetic oligopeptides demonstrated that BICP0 accumulates in nuclei of BHV-1-infected cells, as expected for an IE gene product involved in gene regulation. Western blots (immunoblots) revealed a BHV-1-specific 97-kDa protein which was detectable during the IE phase and also at later periods of infection, indicating that the kinetics of BICP0 synthesis is consistent with the switch from IER2.9 to ER2.6. To confirm that ER2.6 encoded the 97-kDa BICP0 protein, a DNA fragment containing BICP0-coding sequences was inserted into the Autographa californica baculovirus genome. A recombinant protein, identified by its reactivity with antipeptide sera, exhibited the same electrophoretic mobility as BICP0 specified by BHV-1. We microinjected Xenopus oocytes with a BICP0 effector plasmid and a promoter-chloramphenicol acetyltransferase plasmid. BICP0-induced stimulation of this promoter was strongly reduced when intracellular zinc was chelated by thionein, indicating that the effect of BICP0 is zinc dependent.