Biology subjects

Becker, S.

Publications and source records attributed to Becker, S..

78 records · Page 5Linked to original sources

bioRxiv2019

Imidazole-imidazole hydrogen bonding in the pH sensing Histidine sidechains of Influenza A M2

The arrangement of histidine sidechains in influenza A M2 tetramer determines their pKa values, which define pH controlled proton conduction critical to the virus lifecycle. Both water associated and hydrogen bonded Imidazole-Imidazolium histidine quaternary structures have been proposed, based on crystal structures, and NMR chemical shifts, respectively. Here we show, using the conduction domain construct of M2 in lipid bilayers, that the imidazole rings are hydrogen bonded even at a pH of 7.8 in the neutral charge state.\n\nAn intermolecular 8.9 {+/-} 0.3 Hz 2hJNN hydrogen bond is observed between H37 N{varepsilon} and N{delta} recorded in a fully protonated sample with 100 kHz magic-angle spinning. This interaction could not be detected in the drug-bound sample.

biophysics↗

bioRxiv2019

Serine-arginine protein kinase 1 regulates Ebola virus transcription

Ebola virus (EBOV) causes a severe and often fatal disease for which no approved vaccines or antivirals are currently available. EBOV transcription requires the sequential phosphorylation and dephosphorylation of the viral transcription factor VP30. While dephosphorylation is carried out by phosphatases PP2A and PP1, the VP30-specific kinase is unknown. Here, we report that serine-arginine protein kinase 1 and 2 (SRPK1 and SRPK2) phosphorylate serine-29 of VP30, which is located in an N-terminal R26xxS29 motif. Interaction with VP30 via the R26xxS29 motif recruits SRPK1 into EBOV-induced inclusion bodies, the sites of viral RNA synthesis and an inhibitor of SRPK1/SRPK2 downregulates primary viral transcription. When the SRPK1 recognition motif of VP30 was mutated in a recombinant EBOV, virus replication was severely impaired. It is presumed that the interplay between SRPK1 and PP2A in the EBOV inclusions provides a comprehensive regulatory circuit to ensure the activity of VP30 in EBOV transcription.

microbiology↗

bioRxiv2019

A live-cell imaging system for visualizing the transport of Marburg virus nucleocapsid-like structures

Live-cell imaging is a powerful tool for visualization of the spatio-temporal dynamics of living organisms. Although this technique is utilized to visualize nucleocapsid transport in Marburg virus (MARV)- or Ebola virus-infected cells, the experiments require biosafety level-4 (BSL-4) laboratories, which are restricted to trained and authorized individuals. To overcome this limitation, we developed a live-cell imaging system to visualize MARV nucleocapsid-like structures using fluorescence-conjugated viral proteins, which can be conducted outside BSL-4 laboratories. Our experiments revealed that nucleocapsid-like structures have similar transport characteristics to nucleocapsids observed in MARV-infected cells. This system provides a safe platform to evaluate antiviral drugs that inhibit MARV nucleocapsid transport.

molecular biology↗

bioRxiv2019

Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models

BackgroundLinear mixed-effects models (LMM) are a leading method in conducting genome-wide association studies (GWAS) but require residual maximum likelihood (REML) estimation of variance components, which is computationally demanding. Previous work has reduced the computational burden of variance component estimation by replacing direct matrix operations with iterative and stochastic methods and by employing loose tolerances to limit the number of iterations in the REML optimization procedure. Here, we introduce two novel algorithms, stochastic Lanczos derivative-free REML (SLDF_REML) and Lanczos first-order Monte Carlo REML (L_FOMC_REML), that exploit problem structure via the principle of Krylov subspace shift-invariance to speed computation beyond existing methods. Both novel algorithms only require a single round of computation involving iterative matrix operations, after which their respective objectives can be repeatedly evaluated using vector operations. Further, in contrast to existing stochastic methods, SLDF_REML can exploit precomputed genomic relatedness matrices (GRMs), when available, to further speed computation.\n\nResultsResults of numerical experiments are congruent with theory and demonstrate that interpreted-language implementations of both algorithms match or exceed existing compiled-language software packages in speed, accuracy, and flexibility.\n\nConclusionsBoth the SLDF_REML and L_FOMC_REML algorithms outperform existing methods for REML estimation of variance components for LMM and are suitable for incorporation into existing GWAS LMM software implementations.\n\nFull list of author information is available at the end of the article

bioinformatics↗

bioRxiv2019

Phantom limb pain intensity is associated with generalized hyperalgesia

After limb amputation, most amputees suffer from phantom limb pain (PLP). The mechanisms underlying this condition are complex and insufficiently understood. Altered somatosensory sensitivity (either heightened or lowered) might contribute to PLP. Recent studies have tested this assumption but mainly focused on the residual limb. However, altered somatosensation in PLP might be generalized. In this study, we applied quantitative sensory testing to 37 unilateral upper-limb amputees (23 with PLP, 14 without PLP) and 19 healthy controls. We assessed thresholds to heat pain (HPT), pressure pain (PPT), warmth detection (WDT), and two-point discrimination (2PDT) at the residual limb, a homologous point and the thenar of the intact limb, and both corners of the mouth. We did not find significant differences in any of the thresholds between the groups. However, higher PLP intensity was significantly related to lower HPT at all measured body sites except for the residual limb. At the residual limb, lower HPT were observed in more distal amputations and in amputees showing a higher degree of prosthesis use. Although WDT did by itself not significantly correlate with PLP intensity at any of the body sites, multiple regression analysis showed the highest multiple correlations with PLP intensity for a combination of high WDT and low HPT at the corners of the mouth. In this model, the combination of HPT and WDT shared 58% of the variance with PLP intensity. Other factors of potential importance, especially residual limb pain, were not significantly associated to any sensory threshold. We conclude that the intensity, but not the presence of PLP is positively associated with higher heat pain sensitivity. Since this association was observed at various, distributed body sites, we suggest that central mechanisms might be underlying such generalized hyperalgesia.

neuroscience↗

bioRxiv2018

Examining the Role of the Surfactant Family Member SFTA3 in Interneuron Specification

The transcription factor NKX2.1, expressed at high levels in the medial ganglionic eminence (MGE), is a master regulator of cortical interneuron progenitor development. To identify gene candidates with expression profiles similar to NKX2.1, previous transcriptome analysis of human embryonic stem cell (hESC)-derived MGE-like progenitors revealed SFTA3 as the strongest candidate. Quantitative real-time PCR analysis of hESC-derived NKX2.1-positive progenitors and transcriptome data available from the Allen Institute for Brain Science revealed comparable expression patterns for NKX2.1 and SFTA3 during interneuron differentiation in vitro and demonstrated high SFTA3 expression in the human MGE. Although SFTA3 has been well studied in the lung, the possible role of this surfactant protein in the MGE during embryonic development remains unexamined. To determine if SFTA3 plays a role in MGE specification, SFTA3-/- and NKX2.1 -/-hESC lines were generated using custom designed CRISPRs. We show that NKX2.1 KOs have a significantly diminished capacity to differentiate into MGE interneuron subtypes. SFTA3 KOs also demonstrated a somewhat reduced ability to differentiate down the MGE-like lineage, although not as severe relative to NKX2.1 deficiency. These results suggest NKX2.1 and SFTA3 are co-regulated genes, and that deletion of SFTA3 does not lead to a major change in the specification of MGE derivatives.

neuroscience↗