The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

<p>Abstract</p> <p>Background</p> <p>Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common α/β-hydrolase fold and a catalytic triad, which is also found in other α/β-hydrolases.</p> <p>Results</p> <p>The PHA Depolymerase Engineering Database (DED, <url>http://www.ded.uni-stuttgart.de</url>) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity. For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated.</p> <p>Conclusion</p> <p>The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes <it>in silico</it>, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.</p

The Protein Storage Vacuole: A Unique Compound Organelle

doi: 10.1083/jcb.200107012Storage proteins are deposited into protein storage vacuoles (PSVs) during plant seed development and maturation and stably accumulate to high levels; subsequently, during germination the storage proteins are rapidly degraded to provide nutrients for use by the embryo. Here, we show that a PSV has within it a membrane-bound compartment containing crystals of phytic acid and proteins that are characteristic of a lytic vacuole. This compound organization, a vacuole within a vacuole whereby storage functions are separated from lytic functions, has not been described previously for organelles within the secretory pathway of eukaryotic cells. The partitioning of storage and lytic functions within the same vacuole may reflect the need to keep the functions separate during seed development and maturation and yet provide a ready source of digestive enzymes to initiate degradative processes early in germination.This work was supported by grants from the National Science Foundation (MCB-9974429), Department of Energy (DE-FG03-97ER20277), and Human Frontier Science Program (RG0018/2000) to J.C. Rogers, and from the Department of Energy (DE-FG02-91ER20055) to P.A. Rea. Y.M. Drozdowicz is an NSF/DOE/USDA Plant Training Grant fellow. L. Jiang is supported by a Direct Grant (project code 2030238) and a Special Grant for Conducting Research Abroad in the Summer of 2001 from the Chinese University of Hong Kong, and a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (project CUHK4156/ 01M)

CT radiomics to predict Deauville score 4 positive and negative Hodgkin lymphoma manifestations

18F-FDG-PET/CT is standard to assess response in Hodgkin lymphoma by quantifying metabolic activity with the Deauville score. PET/CT, however, is time-consuming, cost-extensive, linked to high radiation and has a low availability. As an alternative, we investigated radiomics from non-contrast-enhanced computed tomography (NECT) scans. 75 PET/CT examinations of 43 patients on two different scanners were included. Target lesions were classified as Deauville score 4 positive (DS4+) or negative (DS4-) based on their SUVpeak and then segmented in NECT images. From these segmentations, 107 features were extracted with PyRadiomics. All further statistical analyses were then performed scanner-wise: differences between DS4+ and DS4- manifestations were assessed with the Mann-Whitney-U-test and single feature performances with the ROC-analysis. To further verify the reliability of the results, the number of features was reduced using different techniques. The feature median showed a high sensitivity for DS4+ manifestations on both scanners (scanner A: 0.91, scanner B: 0.85). It furthermore was the only feature that remained in both datasets after applying different feature reduction techniques. The feature median from NECT concordantly has a high sensitivity for DS4+ Hodgkin manifestations on two different scanners and thus could provide a surrogate for increased metabolic activity in PET/CT

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

QuantiFERON®-TB gold in-tube performance for diagnosing active tuberculosis in children and adults in a high burden setting.

To determine whether QuantiFERON®-TB Gold In-Tube (QFT) can contribute to the diagnosis of active tuberculosis (TB) in children in a high-burden setting and to assess the performance of QFT and tuberculin skin test (TST) in a prospective cohort of TB suspect children compared to adults with confirmed TB in Tanzania. Sensitivity and specificity of QFT and TST for diagnosing active TB as well as indeterminate QFT rates and IFN-γ levels were assessed in 211 TB suspect children in a Tanzanian district hospital and contrasted in 90 adults with confirmed pulmonary TB. Sensitivity of QFT and TST in children with confirmed TB was 19% (5/27) and 6% (2/31) respectively. In adults sensitivity of QFT and TST was 84% (73/87) and 85% (63/74). The QFT indeterminate rate in children and adults was 27% and 3%. Median levels of IFN-γ were lower in children than adults, particularly children <2 years and HIV infected. An indeterminate result was associated with age <2 years but not malnutrition or HIV status. Overall childhood mortality was 19% and associated with an indeterminate QFT result at baseline. QFT and TST showed poor performance and a surprisingly low sensitivity in children. In contrast the performance in Tanzanian adults was good and comparable to performance in high-income countries. Indeterminate results in children were associated with young age and increased mortality. Neither test can be recommended for diagnosing active TB in children with immature or impaired immunity in a high-burden setting

Predictors of early scaffold thrombosis: results from the multicenter prospective German-Austrian ABSORB RegIstRy

Background: In randomized clinical trials, the risk of thrombotic events with the absorb bioresorbable vascular scaffold (BVS) was significantly higher than with metallic drug-eluting stents. We evaluated predictors of scaffold thrombosis in the large-scale, multicenter German-Austrian ABSORB RegIstRy.Methods and Results: 3178 patients with treatment of 4252 lesions using 5020 scaffolds were included. Follow-up rate at 6 months was 97.4%. Forty-five (1.42%) patients experienced definite/probable scaffold thrombosis during follow-up. Multiple regression analysis showed implantation of absorb BVS in bifurcation lesions [odds ratio (OR): 4.43;95% confidence interval (CI): 1.69-11.59;P=0.0024] or treatment in the years 2013/2014 (OR: 1.88;95% CI: 1.02-3.47;P=0.04) to be significant predictors of scaffold thrombosis. Excluding bifurcation lesions, the incidence of definite/probable scaffold thrombosis decreased from 1.8% (95% CI: 1.17-2.64%) in 2013/2014 to 0.89% (95% CI: 0.5-1.46%) in 2015/2016. In the latter period, absorb BVS were implanted more often in younger patients with less complex de novo lesions, and debulking devices and postdilatation were used more frequently. Between the two treatment periods, there was a significant reduction in myocardial infarction (2.73-1.24%, P<0.01;OR: 0.45;95% CI: 0.26-0.77), definite/probable scaffold thrombosis (1.79-0.88%, P<0.05;OR: 0.49;95% CI: 0.26-0.93), and target lesion failure and revascularization during follow-up.Conclusion: Improved procedural technique and more strict patient selection may explain a significant decrease in the absorb BVS thrombosis rates during the recruitment period of the large-scale German-Austrian ABSORB RegIstRy. In addition, treatment of bifurcation lesions was identified as an independent predictor of definite/probable scaffold thrombosis

Incidental finding of strut malapposition is a predictor of late and very late thrombosis in coronary bioresorbable scaffolds

Malapposition is a common finding in stent and scaffold thrombosis (ScT). Evidence from studies with prospective follow-up, however, is scarce. We hypothesized that incidental observations of strut malapposition might be predictive of late ScT during subsequent follow-up. One hundred ninety-seven patients were enrolled in a multicentre registry with prospective follow-up. Optical coherence tomography (OCT), performed in an elective setting, was available in all at 353 (0–376) days after bioresorbable scaffold (BRS) implantation. Forty-four patients showed evidence of malapposition that was deemed not worthy of intervention. Malapposition was not associated with any clinical or procedural parameter except for a higher implantation pressure (p = 0.0008). OCT revealed that malapposition was associated with larger vessel size, less eccentricity (all p < 0.01), and a tendency for more uncovered struts (p = 0.06). Late or very late ScT was recorded in seven of these patients 293 (38–579) days after OCT. OCT-diagnosed malapposition was a predictor of late and very late scaffold thrombosis (p < 0.001) that was independent of the timing of diagnosis. We provide evidence that an incidental finding of malapposition—regardless of the timing of diagnosis of the malapposition—during an elective exam is a predictor of late and very late ScT. Our data provide a rationale to consider prolonged dual antiplatelet therapy if strut malapposition is observed

Stem Cell Based Drug Delivery for Protection of Auditory Neurons in a Guinea Pig Model of Cochlear Implantation

Background: The success of a cochlear implant (CI), which is the standard therapy for patients suffering from severe to profound sensorineural hearing loss, depends on the number and excitability of spiral ganglion neurons (SGNs). Brain-derived neurotrophic factor (BDNF) has a protective effect on SGNs but should be applied chronically to guarantee their lifelong survival. Long-term administration of BDNF could be achieved using genetically modified mesenchymal stem cells (MSCs), but these cells should be protected – by ultra-high viscous (UHV-) alginate (‘alginate-MSCs’) – from the recipient immune system and from uncontrolled migration.Methods: Brain-derived neurotrophic factor-producing MSCs were encapsulated in UHV-alginate. Four experimental groups were investigated using guinea pigs as an animal model. Three of them were systemically deafened and (unilaterally) received one of the following: (I) a CI; (II) an alginate-MSC-coated CI; (III) an injection of alginate-embedded MSCs into the scala tympani followed by CI insertion and alginate polymerization. Group IV was normal hearing, with CI insertion in both ears and a unilateral injection of alginate-MSCs. Using acoustically evoked auditory brainstem response measurements, hearing thresholds were determined before implantation and before sacrificing the animals. Electrode impedance was measured weekly. Four weeks after implantation, the animals were sacrificed and the SGN density and degree of fibrosis were evaluated.Results: The MSCs survived being implanted for 4 weeks in vivo. Neither the alginate-MSC injection nor the coating affected electrode impedance or fibrosis. CI insertion with and without previous alginate injection in normal-hearing animals resulted in increased hearing thresholds within the high-frequency range. Low-frequency hearing loss was additionally observed in the alginate-injected and implanted cochleae, but not in those treated only with a CI. In deafened animals, the alginate-MSC coating of the CI significantly prevented SGN from degeneration, but the injection of alginate-MSCs did not.Conclusion: Brain-derived neurotrophic factor-producing MSCs encapsulated in UHV-alginate prevent SGNs from degeneration in the form of coating on the CI surface, but not in the form of an injection. No increase in fibrosis or impedance was detected. Further research and development aimed at verifying long-term mechanical and biological properties of coated electrodes in vitro and in vivo, in combination with chronic electrical stimulation, is needed before the current concept can be tested in clinical trials

Religious conversion among high security hospital patients: a qualitative analysis of patients’ accounts and experiences on changing faith

Research has shown the importance of religion in recovery from mental illness. Previous studies have investigated why individuals change faith during custody in prison, but there has been no research to date on religious conversion in forensic-psychiatric hospitals. The aim of this study was to understand the experience of religious conversion among patients detained in a UK secure hospital. Thirteen patients who had converted their religion were interviewed and the resultant data were analysed using thematic analysis. Three superordinate themes (‘reasons for changing faith’, ‘benefits of having a new faith’ and ‘difficulties with practising a faith’), incorporating eight subordinate themes, emerged. Understanding patients’ reasons for religious conversion is important for the treatment and support not merely of these individuals, but more broadly with patients in forensic psychiatric care