Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

Calculating binding free energies with quan-tum-mechanical (QM) methods is notoriously time-consum-ing. In this work, we studied whether such calculations can beaccelerated by using nonequilibrium (NE) moleculardynamics simulations employing Jarzynski’s equality. Westudied the binding of nine cyclic carboxylate ligands to theocta-acid deep-cavity host from the SAMPL4 challenge withthe reference potential approach. The binding free energieswere first calculated at the molecular mechanics (MM) levelwith free energy perturbation using the generalized Amberforce field with restrained electrostatic potential charges forthe host and the ligands. Then the free energy corrections for going from the MM Hamiltonian to a hybrid QM/MM Hamiltonian were estimated by averaging over many short NE molecular dynamics simulations. In the QM/MM calculations, the ligand was described at the semiempirical PM6-DH+ level. We show that this approach yields MM → QM/MM free energy corrections that agree with those from other approaches within statistical uncertainties. The desired precision can be obtained by running a proper number of independent NE simulations. For the systems studied in this work, a total simulation length of 20 ps was appropriate for most of the ligands, and 36−324 simulations were necessary in order to reach a precision of 0.3 kJ/ mol

Identification and Expression Patterns of Three Vitellogenin Genes and Their Roles in Reproduction of the Alligatorweed Flea Beetle Agasicles hygrophila (Coleoptera: Chrysomelidae)

The alligatorweed flea beetle Agasicles hygrophila is an insect used for biological control of the aquatic weed Alternanthera philoxeroides (alligatorweed). Because these insects are oviparous, synthesis, and transportation of yolk proteins is integral to reproduction. Vitellin, the chief protein constituent in egg yolk, is mainly synthesized in the fat body and its synthesis is regulated by the transcript levels of Vitellogenin (Vg). In our study, we first cloned and characterized three Vg genes from A. hygrophila and quantified the expression levels of these Vgs in different tissues and developmental stages by RT-qPCR. Analysis of the full-length cDNA sequences of the three A. hygrophila Vg genes revealed that the open reading frames of AhVg1, AhVg2, and AhVg3 were 5175, 5346, and 5385 bp, encoding 1724, 1781, and 1794 amino acids, respectively. RT-qPCR analysis revealed that these three AhVgs have similar expression patterns; expression in the fat body was significantly higher than that in other tissues, and the highest expression was observed in the adult developmental stage. RNA interference was used to explore the functions of the AhVgs. A. hygrophila female adults injected with dsRNA targeting the AhVg genes showed decreased AhVg gene expression. Down regulation of all three AhVgs significantly affected ovary development, reduced egg laying capacity, and reduced the egg hatch rate compared with the control groups. Our findings provide the basis for further study of the functions of Vg genes in other insect species

Does the Use of Antidepressants Accelerate the Disease Progress in Creutzfeldt–Jakob Disease Patients With Depression? A Case Report and A Systematic Review

Background: Creutzfeldt–Jakob disease (CJD) is a fatal neurodegenerative disorder characterized by rapidly progressive dementia. Growing evidence suggests that antidepressant usage was associated with dementia. Given the commonality of depression in CJD, it is necessary to investigate the effect of antidepressants on CJD.Methods: First, we report a case of sporadic CJD (sCJD) with depression where the condition worsened rapidly after using a serotonin and noradrenaline reuptake inhibitor (SNRI) antidepressant. Second, a systematic literature survey was conducted to investigate the effect of antidepressants on the survival time of sCJD patients with depression. Thirteen cases plus our case were included for qualitative analysis. Twelve subjects were included in the Kaplan–Meier survival and Cox regression analysis. Finally, we provide a postulation of pathophysiological mechanism in CJD.Results: The median survival time of all patients was 6.0 months, of which patients with SNRIs were significantly shorter than those with first-generation antidepressants (2.0 vs. 6.0 months; log rank, P = .008) and relatively shorter than those with nonselective serotonin reuptake inhibitors (SSRIs; 4.0 vs. 6.0 months; log rank, P = .090). In comparison with first-generation antidepressants, the use of SNRIs [hazard ratio (HR), 23.028; 95% confidence interval (CI), 1.401 to 378.461; P = .028] remained independently associated with shorter survival time.Conclusions: The use of antidepressants, especially SNRIs, was associated with a shorter survival time of sCJD patients. The possible changes in neurotransmitters should be emphasized. Scientifically, this study may provide insights into the mechanism of CJD. Clinically, it may contribute to the early diagnosis of CJD

Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens

The analysis of gene expression patterns during ovarian follicle development will advance our understanding of avian reproductive physiology and make it possible to improve laying performance. To gain insight into the molecular regulation of ovarian development, a systematic profiling of miRNAs and mRNAs at four key stages was conducted, using ovarian tissues from hens at 60 days of age (A), 100 days (B), 140 days-not yet laying (C), and 140 days-laying (D). Comparisons of consecutive stages yielded 73 differentially expressed miRNAs (DEMs) (14 for B vs. A, 8 for C vs. B, and 51 for D vs. C) and 2596 differentially expressed genes (DEGs) (51 for B vs. A, 20 for C vs. B, and 2579 for D vs. C). In addition, 174 DEMs (22 for C vs. A, 74 for D vs. A, and 78 for D vs. B) and 3205 DEGs (118 for C vs. A, 2284 for D vs. A, and 2882 for D vs. B) were identified between nonconsecutive stages. Some DEGs are involved in the Wnt and TGF-beta signaling pathways, which are known to affect ovarian development and ovulation. An integrative analysis of the miRNA and mRNA profiles identified 3166 putative miRNA-mRNA regulatory pairs containing 84 DEMs and 1047 DEGs. Functional annotation of the networks provides strong evidence that the miRNA regulatory networks may play vital roles in ovarian development and ovulation. Ten DEMs and 10 genes were validated by real-time quantitative PCR. The candidate miRNA-mRNA pairs gga-miR-200a-3p-SFRP4, gga-miR-101-3p-BMP5, gga-miR-32-5p-FZD4, and gga-miR-458b-5p-CTNNB1 potentially associated with ovarian development

Spatio-temporal divergence in the responses of Finland's boreal forests to climate variables

Spring greening in boreal forest ecosystems has been widely linked to increasing temperature, but few studies have attempted to unravel the relative effects of climate variables such as maximum temperature (TMX), minimum temperature (TMN), mean temperature (TMP), precipitation (PRE) and radiation (RAD) on vegetation growth at different stages of growing season. However, clarifying these effects is fundamental to better understand the relationship between vegetation and climate change. This study investigated spatio-temporal divergence in the responses of Finland's boreal forests to climate variables using the plant phenology index (PPI) calculated based on the latest Collection V006 MODIS BRDF-corrected surface reflectance products (MCD43C4) from 2002 to 2018, and identified the dominant climate variables controlling vegetation change during the growing season (May-September) on a monthly basis. Partial least squares (PLS) regression was used to quantify the response of PPI to climate variables and distinguish the separate impacts of different variables. The study results show the dominant effects of temperature on the PPI in May and June, with TMX, TMN and TMP being the most important explanatory variables for the variation of PPI depending on the location, respectively. Meanwhile, drought had an unexpectedly positive impact on vegetation in few areas. More than 50 % of the variation of PPI could be explained by climate variables for 68.5 % of the entire forest area in May and 87.7 % in June, respectively. During July to September, the PPI variance explained by climate and corresponding spatial extent rapidly decreased. Nevertheless, the RAD was found be the most important explanatory variable to July PPI in some areas. In contrast, the PPI in August and September was insensitive to climate in almost all of the regions studied. Our study gives useful insights on quantifying and identifying the relative importance of climate variables to boreal forest, which can be used to predict the possible response of forest under future warming.Peer reviewe

Recent Progress in the Correlative Structured Illumination Microscopy

The super-resolution imaging technique of structured illumination microscopy (SIM) enables the mixing of high-frequency information into the optical transmission domain via light-source modulation, thus breaking the optical diffraction limit. Correlative SIM, which combines other techniques with SIM, offers more versatility or higher imaging resolution than traditional SIM. In this review, we first briefly introduce the imaging mechanism and development trends of conventional SIM. Then, the principles and recent developments of correlative SIM techniques are reviewed. Finally, the future development directions of SIM and its correlative microscopies are presented

Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

Relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host were calculated at the combined density-functional theory and molecular mechanics (DFT/MM) level of theory. The DFT calculations employed the BLYP functional and the 6-31G∗ basis set for the ligand. We employed free-energy perturbations (FEP) with the reference-potential approach and used molecular dynamics (MD) simulations with the semiempirical quantum mechanical (SQM) PM6-DH+ method for the ligand as an intermediate level between MM and DFT/MM to improve the convergence. Thus, the relative binding free energy of two ligands was first calculated at the MM level by an alchemical transformation from one ligand to another in both the bound and unbound states. Then, for each ligand the free-energy correction for going from the MM to the SQM/MM potentials was calculated using explicit SQM/MM MD simulations. Finally, the free-energy correction for going from the SQM/MM to the DFT/MM potentials was estimated with FEP without running any DFT/MM simulations. Instead, the free energy was calculated by single-step exponential averaging (ssEA) or employing the cumulant approximation to the second order (CA). The results show that CA converges much better than ssEA, and with 500-4500 DFT/MM single-point energy calculations, converged free energies with a precision of 0.3 kJ/mol can be obtained. These free energies reproduce the experimental binding free energy differences with a mean absolute deviation of 3.4 kJ/mol, a correlation (R 2 ) of 0.97, and correct signs for all of the eight free-energy differences. This is appreciably better than the results obtained at the SQM/MM level of theory and also slightly better than those obtained with MM. We show that the convergence of the SQM/MM → DFT/MM perturbations can be monitored by the use of Wu and Kofke's bias metric and by the standard deviation of the difference between the SQM/MM and DFT/MM energies. Finally, we show that the use of the intermediate SQM/MM MD simulations improves the convergence of the free energies by a factor of at least two, compared to doing direct MM → DFT/MM perturbations