| 1. |
- Galosi, Serena, et al.
(author)
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De novo DHDDS variants cause a neurodevelopmental and neurodegenerative disorder with myoclonus
- 2022
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In: Brain : a journal of neurology. - : Oxford University Press (OUP). - 1460-2156. ; 145:1, s. 208-223
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Journal article (peer-reviewed)abstract
- Subcellular membrane systems are highly enriched in dolichol, whose role in organelle homeostasis and endosomal-lysosomal pathway remains largely unclear besides being involved in protein glycosylation. DHDDS encodes for the catalytic subunit (DHDDS) of the enzyme cis-prenyltransferase (cis-PTase), involved in dolichol biosynthesis and dolichol-dependent protein glycosylation in the endoplasmic reticulum. An autosomal recessive form of retinitis pigmentosa (retinitis pigmentosa 59) has been associated with a recurrent DHDDS variant. Moreover, two recurring de novo substitutions were detected in a few cases presenting with neurodevelopmental disorder, epilepsy, and movement disorder. We evaluated a large cohort of patients (n=25) with de novo pathogenic variants in DHDDS and provided the first systematic description of the clinical features and long-term outcome of this new neurodevelopmental and neurodegenerative disorder. The functional impact of the identified variants was explored by yeast complementation system and enzymatic assay. Patients presented during infancy or childhood with a variable association of neurodevelopmental disorder, generalized epilepsy, action myoclonus/cortical tremor, and ataxia. Later in the disease course they experienced a slow neurological decline with the emergence of hyperkinetic and/or hypokinetic movement disorder, cognitive deterioration, and psychiatric disturbances. Storage of lipidic material and altered lysosomes were detected in myelinated fibers and fibroblasts, suggesting a dysfunction of the lysosomal enzymatic scavenger machinery. Serum glycoprotein hypoglycosylation was not detected and, in contrast to retinitis pigmentosa and other congenital disorders of glycosylation involving dolichol metabolism, the urinary dolichol D18/D19 ratio was normal. Mapping the disease-causing variants into the protein structure revealed that most of them clustered around the active site of the DHDDS subunit. Functional studies using yeast complementation assay and in vitro activity measurements confirmed that these changes affected the catalytic activity of the cis-PTase and showed growth defect in yeast complementation system as compared with the wild-type enzyme and retinitis pigmentosa-associated protein. In conclusion, we characterized a distinctive neurodegenerative disorder due to de novo DHDDS variants, which clinically belongs to the spectrum of genetic progressive encephalopathies with myoclonus. Clinical and biochemical data from this cohort depicted a condition at the intersection of congenital disorders of glycosylation and inherited storage diseases with several features akin to of progressive myoclonus epilepsy such as neuronal ceroid lipofuscinosis and other lysosomal disorders.
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| 2. |
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Creci, Simone, 1992, et al.
(author)
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Acidity as Descriptor for Methanol Desorption in B-, Ga- and Ti-MFI Zeotypes
- 2021
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In: Catalysts. - : MDPI AG. - 2073-4344. ; 11:1, s. 1-12
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Journal article (peer-reviewed)abstract
- The isomorphous substitution of Si with metals other than Al in zeotype frameworks allows for tuning the acidity of the zeotype and, therefore, to tailor the catalyst's properties as a function of the desired catalytic reaction. In this study, B, Ga, and Ti are incorporated in the MFI framework of silicalite samples and the following series of increasing acidity is observed: Ti-silicalite < B-silicalite < Ga-silicalite. It is also observed that the lower the acidity of the sample, the easier the methanol desorption from the zeotype surface. In the target reaction, namely the direct conversion of methane to methanol, methanol extraction is affected by the zeotype acidity. Therefore, the results shown in this study contribute to a more enriched knowledge of this reaction.
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| 5. |
- Creci, Simone, 1992, et al.
(author)
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Methoxy ad-species in MFI zeotypes during methane exposure and methanol desorption followed by in situ IR spectroscopy
- 2021
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In: Catalysis Today. - : Elsevier BV. - 0920-5861. ; 369, s. 123-128
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Journal article (peer-reviewed)abstract
- The formation and evolution of methoxy ad-species in MFI zeotypes after CH4 exposure, and during temperature programmed desorption of CH3OH have been investigated in situ with diffuse reflectance Fourier transform infrared spectroscopy. Fe and/or Al atoms have been incorporated in framework position prior to crystallization and the influence of the resulting acidity on CH4 activation and CH3OH desorption has been examined. The results show that the presence of Fe promotes CH4 activation and that methanol is more strongly bound to the zeotype in the presence of Al. Because CH4 activation and CH3OH extraction are two of the key steps in the direct conversion of methane to methanol, our results indicate that Al-free zeotypes containing Fe atoms pinpoint important catalyst design parameters needed for this reaction.
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| 6. |
- Martinelli, Anna, 1978, et al.
(author)
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Local anisotropy in single crystals of zeotypes with the MFI framework structure evidenced by polarised Raman spectroscopy
- 2020
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In: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 22:3, s. 1640-1654
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Journal article (peer-reviewed)abstract
- Polarised Raman spectroscopy is used to characterise the local structure in single crystals of zeotypes, namely silicalite-1 and ZSM-5, which share the MFI framework structure. Attributes favourable for applying polarised Raman spectroscopy are the orthogonal axes of these single crystals and their size, i.e. 10 to 30 micrometers in all three directions. We show that the intensity of certain vibrational modes in silicalite-1 depends on the polarisation of the incident light, reflecting the anisotropic character of the molecular bonds contributing to these vibrations. Using these observations, and by estimating the depolarisation ratio (rho) and the pseudo-order factor (f), we propose a more accurate assignment of the Raman active modes. More precisely, Raman intensities peaked at 294, 360, 383 and 472 cm(-1) are attributed to bending modes in 10-, 6-, 5- and 4-membered rings, respectively. In the region of stretching modes, the vibration at 832 cm(-1) is assigned to Si-O-Si bonds shared between 5-membered rings, which have an orientation parallel to the a-axis of the crystal. By virtue of having a strongly polarised character, the modes at 472 and 832 cm(-1) can be used as orientational indicators. The proposed assignment is supported by the good agreement between experimental and simulated polar plots, where Raman intensities are plotted as a function of the polarisation angle of the incident light. Finally, upon partial substitution of Si atoms by Al, the crystalline structure is maintained and almost no spectroscopic changes are observed. The only significant difference is the increased width of most vibrational modes, which is consistent with the local lower symmetry. This is also seen in the angular dependence of selected vibrational modes that compared to the case of pure silicalite-1 appear less polarised. In the Raman spectrum of ZSM-5 a new feature at 974 cm(-1) is observed, which we attribute to Al-OH stretching. In the high frequency range, the O-H stretching modes are observed which arise from the Si-O(H)-Al Bronsted acid sites. The intensity of the characteristic mode at 3611 cm(-1) reveals an anisotropic character as well, which is in line with previous findings from solid state NMR that Al atoms distribute nonrandomly within the MFI framework structure.
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