Towards Automated Design of Riboswitches

Experimental screening and selection pipelines for the discovery of novel riboswitches are expensive, time-consuming, and inefficient. Using computational methods to reduce the number of candidates for the screen could drastically decrease these costs. However, existing computational approaches do not fully satisfy all requirements for the design of such initial screening libraries. In this work, we present a new method, libLEARNA, capable of providing RNA focus libraries of diverse variable-length qualified candidates. Our novel structure-based design approach considers global properties as well as desired sequence and structure features. We demonstrate the benefits of our method by designing theophylline riboswitch libraries, following a previously published protocol, and yielding 30% more unique high-quality candidates.Comment: 9 pages, Accepted at the 2023 ICML Workshop on Computational Biolog

Assessing Non-Invasive Liver Function in Patients With Intestinal Failure Receiving Total Parenteral Nutrition-Results From the Prospective PNLiver Trial

Liver abnormalities in intestinal failure (IF) patients receiving parenteral nutrition (PN) can progress undetected by standard laboratory tests to intestinal failure associated liver disease (IFALD). The aim of this longitudinal study is to evaluate the ability of non-invasive liver function tests to assess liver function following the initiation of PN. Twenty adult patients with IF were prospectively included at PN initiation and received scheduled follow-up assessments after 6, 12, and 24 months between 2014 and 2019. Each visit included liver assessment (LiMAx [Liver Maximum Capacity] test, ICG [indocyanine green] test, FibroScan), laboratory tests (standard laboratory test, NAFLD [non-alcoholic fatty liver disease] score, FIB-4 [fibrosis-4] score), nutritional status (bioelectrical impedance analysis, indirect calorimetry), and quality of life assessment. The patients were categorized post-hoc based on their continuous need for PN into a reduced parenteral nutrition (RPN) group and a stable parenteral nutrition (SPN) group. While the SPN group (n = 9) had significantly shorter small bowel length and poorer nutritional status at baseline compared to the RPN group (n = 11), no difference in liver function was observed between the distinct groups. Over time, liver function determined by LiMAx did continuously decrease from baseline to 24 months in the SPN group but remained stable in the RPN group. This decrease in liver function assessed with LiMAx in the SPN group preceded deterioration of all other investigated liver function tests during the study period. Our results suggest that the liver function over time is primarily determined by the degree of intestinal failure. Furthermore, the LiMAx test appeared more sensitive in detecting early changes in liver function in comparison to other liver function tests

Effects of Flexibility in Coarse-Grained Models for Bovine Serum Albumin and Immunoglobulin G

We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm

Effects of DPP-4 Inhibitors on the Heart in a Rat Model of Uremic Cardiomyopathy

BACKGROUND: Uremic cardiomyopathy contributes substantially to mortality in chronic kidney disease (CKD) patients. Glucagon-like peptide-1 (GLP-1) may improve cardiac function, but is mainly degraded by dipeptidyl peptidase-4 (DPP-4). METHODOLOGY/PRINCIPAL FINDINGS: In a rat model of chronic renal failure, 5/6-nephrectomized [5/6N] rats were treated orally with DPP-4 inhibitors (linagliptin, sitagliptin, alogliptin) or placebo once daily for 4 days from 8 weeks after surgery, to identify the most appropriate treatment for cardiac dysfunction associated with CKD. Linagliptin showed no significant change in blood level AUC(0-∞) in 5/6N rats, but sitagliptin and alogliptin had significantly higher AUC(0-∞) values; 41% and 28% (p = 0.0001 and p = 0.0324), respectively. No correlation of markers of renal tubular and glomerular function with AUC was observed for linagliptin, which required no dose adjustment in uremic rats. Linagliptin 7 µmol/kg caused a 2-fold increase in GLP-1 (AUC 201.0 ng/l*h) in 5/6N rats compared with sham-treated rats (AUC 108.6 ng/l*h) (p = 0.01). The mRNA levels of heart tissue fibrosis markers were all significantly increased in 5/6N vs control rats and reduced/normalized by linagliptin. CONCLUSIONS/SIGNIFICANCE: DPP-4 inhibition increases plasma GLP-1 levels, particularly in uremia, and reduces expression of cardiac mRNA levels of matrix proteins and B-type natriuretic peptides (BNP). Linagliptin may offer a unique approach for treating uremic cardiomyopathy in CKD patients, with no need for dose-adjustment

Methods for investigating allele frequencies and distribution in the acetolactate-synthase (ALS) gene in target-site-resistant Echinochloa crus-galli

Hühnerhirse (Echinochloa crus-galli) gewinnt als Ungras im Maisanbau zunehmend an Bedeutung. Einseitiger Einsatz von ALS-Inhibitoren erzeugt einen Selektionsdruck, der zu vermehrtem Auftreten von Resistenzen führt. Häufig handelt es sich um Target-Site-Resistenzen (TSR) mit Punktmutationen an den Positionen Ala-122, Pro-197 oder Trp-574 des ALS-Gens. Dieses liegt in der hexaploiden Hühnerhirse in drei homologen Varianten vor. Gängige PCR-Verfahren ermöglichen nur eine gemeinsame Analyse aller Genvarianten, wodurch ein großer Teil des Informationsgehalts verloren geht. Für eine fundierte Aussage müssen die Genvarianten getrennt analysiert werden. Ein methodischer Ansatz war die allel-spezifische PCR. Hierfür wurden DNA-Polymorphismen zwischen den drei ALS-Genvarianten genutzt, um diese separat bei Position 574 hochspezifisch zu amplifizieren und zu sequenzieren. Die schwierige Struktur und geringe Polymorphismen verhinderten den Einsatz der allel-spezifischen PCR an den Positionen 122 und 197. Hier wurden die drei Genvarianten gemeinsam amplifiziert und anschließend in einem mehrstufigen Ansatz mit Restriktionsenzymen spezifisch verdaut. Nach Separation, Aufreinigung und Reamplifikation der Fragmente wurden die einzelnen Genvarianten durch Pyrosequenzierung analysiert. So konnten an Position Ala-122 in allen ALS-Homologen heterozygote Mutationen nachgewiesen werden, bei Pro-197 und Trp-574 dagegen heterozygote bzw. homozygote Mutationen nur bei ALS3. Durch die Etablierung dieser Methoden können nun Resistenzmuster in Populationen von Echinochloa crus-galli detaillierter untersucht und wichtige Daten zu deren Ausbreitungsdynamik gewonnen werden.Barnyardgrass (Echinochloa crus-galli) is an important weed in maize. Rising selection pressure due to intensive use of ALS-inhibitors leads to an increase of resistances, of which target site resistances at positions Ala-122, Pro-197 and Trp-574 of ALS gene are a common result. Three homologous variants of this gene are present within the hexaploid barnyardgrass. Standard PCR cannot differentiate between variants, giving a rough overview of mutations, but not the exact location. For well-founded evaluation, the variants must be analyzed separately. One way to do so is allele-specific PCR. Using DNA polymorphisms differing the variants from each other, specific amplification was performed at position 574. Insufficient polymorphisms at positions 122 and 197 called for another approach. A large fragment including all three variants was created and subsequently digested repeatedly to get specific segments for each variant. Segments were separated, cleaned, re-amplified and finally analyzed by pyrosequencing. Thus, it was possible to find heterozygous mutations at position Ala-122 for all ALS homologues. For Pro-197 and Trp-574 mutations (heterozygous as well as homozygous) were found only in variant ALS3. By establishment of the described methods resistance patterns within populations of Echinochloa crus-galli can be reviewed more closely, giving better insight to dynamics of spreading

The Novel Phosphodiesterase 9A Inhibitor BI 409306 Increases Cyclic Guanosine Monophosphate Levels in the Brain, Promotes Synaptic Plasticity, and Enhances Memory Function in Rodents.

N-methyl-d-aspartate (NMDA) receptor-dependent long-term potentiation (LTP) is an established cellular model underlying learning and memory, and involves intracellular signaling mediated by the second messenger cyclic guanosine monophosphate (cGMP). As phosphodiesterase (PDE)9A selectively hydrolyses cGMP in areas of the brain related to cognition, PDE9A inhibitors may improve cognitive function by enhancing NMDA receptor-dependent LTP. This study aimed to pharmacologically characterize BI 409306, a novel PDE9A inhibitor, using in vitro assays and in vivo determination of cGMP levels in the brain. Further, the effects of BI 409306 on synaptic plasticity evaluated by LTP in ex vivo hippocampal slices and on cognitive performance in rodents were also investigated. In vitro assays demonstrated that BI 409306 is a potent and selective inhibitor of human and rat PDE9A with mean concentrations at half-maximal inhibition (IC50) of 65 and 168 nM. BI 409306 increased cGMP levels in rat prefrontal cortex and cerebrospinal fluid and attenuated a reduction in mouse striatum cGMP induced by the NMDA-receptor antagonist MK-801. In ex vivo rat brain slices, BI 409306 enhanced LTP induced by both weak and strong tetanic stimulation. Treatment of mice with BI 409306 reversed MK-801-induced working memory deficits in a T-maze spontaneous-alternation task and improved long-term memory in an object recognition task. These findings suggest that BI 409306 is a potent and selective inhibitor of PDE9A. BI 409306 shows target engagement by increasing cGMP levels in brain, facilitates synaptic plasticity as demonstrated by enhancement of hippocampal LTP, and improves episodic and working memory function in rodents. SIGNIFICANCE STATEMENT: This preclinical study demonstrates that BI 409306 is a potent and selective PDE9A inhibitor in rodents. Treatment with BI 409306 increased brain cGMP levels, promoted long-term potentiation, and improved episodic and working memory performance in rodents. These findings support a role for PDE9A in synaptic plasticity and cognition. The potential benefits of BI 409306 are currently being investigated in clinical trials

Viscosity and Diffusion: Crowding and Salt Effects in Protein Solutions

We report on a joint experimental-theoretical study of collective diffusion in, and static shear viscosity of solutions of bovine serum albumin (BSA) proteins, focusing on the dependence on protein and salt concentration. Data obtained from dynamic light scattering and rheometric measurements are compared to theoretical calculations based on an analytically treatable spheroid model of BSA with isotropic screened Coulomb plus hard-sphere interactions. The only input to the dynamics calculations is the static structure factor obtained from a consistent theoretical fit to a concentration series of small-angle X-ray scattering (SAXS) data. This fit is based on an integral equation scheme that combines high accuracy with low computational cost. All experimentally probed dynamic and static properties are reproduced theoretically with an at least semi-quantitative accuracy. For lower protein concentration and low salinity, both theory and experiment show a maximum in the reduced viscosity, caused by the electrostatic repulsion of proteins. The validity range of a generalized Stokes-Einstein (GSE) relation connecting viscosity, collective diffusion coefficient, and osmotic compressibility, proposed by Kholodenko and Douglas [PRE 51, 1081 (1995)] is examined. Significant violation of the GSE relation is found, both in experimental data and in theoretical models, in semi-dilute systems at physiological salinity, and under low-salt conditions for arbitrary protein concentrations