Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald–Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2–4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.     

Germination response of Arabian desert species to gibberellic acid and potassium nitrate seed treatment

Abstract

Desert plant species commonly use seed dormancy to prevent germination during unfavorable environmental conditions and thus increase the probability of seedling survival. Seed dormancy presents a challenge for restoration ecology, particularly in desert species for which our knowledge of dormancy regulation is limited. In the present study the effect of gibberellic acid (GA₃) and potassium nitrate (KNO₃) on seed dormancy release was investigated on eight Arabian desert species. Both treatments significantly enhanced the germination of most species tested. GA₃ was more effective than KNO₃ in enhancing germination percentage, reducing mean germination time and synchronizing the germination in most of the studied species. Light requirement during germination was species-specific, but in general the presence of light promoted germination more effectively when combined with KNO₃ and GA₃. The wide variation in dormancy and germination requirements among the tested species is indicative of distinct germination niches, which might assist their co-existence in similar habitat/environmental conditions. Seed pre-treatments that optimize germination in this habitat must therefore be assessed for individual species to improve the outcomes of ecological restoration.     

Loss of A-type lamin expression compromises nuclear envelope integrity leading to muscular dystrophy

The nuclear lamina is a protein meshwork lining the nucleoplasmic face of the inner nuclear membrane and represents an important determinant of interphase nuclear architecture. Its major components are the A- and B-type lamins. Whereas B-type lamins are found in all mammalian cells, A-type lamin expression is developmentally regulated. In the mouse, A-type lamins do not appear until midway through embryonic development, suggesting that these proteins may be involved in the regulation of terminal differentiation. Here we show that mice lacking A-type lamins develop to term with no overt abnormalities. However, their postnatal growth is severely retarded and is characterized by the appearance of muscular dystrophy. This phenotype is associated with ultrastructural perturbations to the nuclear envelope. These include the mislocalization of emerin, an inner nuclear membrane protein, defects in which are implicated in Emery-Dreifuss muscular dystrophy (EDMD), one of the three major X-linked dystrophies. Mice lacking the A-type lamins exhibit tissue-specific alterations to their nuclear envelope integrity and emerin distribution. In skeletal and cardiac muscles, this is manifest as a dystrophic condition related to EDMD.     

On the structure and initial parameter identification of Gaussian RBF networks

We consider the efficient initialization of structure and parameters of generalized Gaussian radial basis function (RBF) networks using fuzzy decision trees generated by fuzzy ID3 like induction algorithms. The initialization scheme is based on the proposed functional equivalence property of fuzzy decision trees and generalized Gaussian RBF networks. The resulting RBF network is compact, easy to induce, comprehensible, and has acceptable classification accuracy with stochastic gradient descent learning algorithm.     

The C-terminal domain of dimeric serine hydroxymethyltransferase plays a key role in stabilization of the quaternary structure and cooperative unfolding of protein: domain swapping studies with enzymes having high sequence identity

The serine hydroxymethyltransferase from Bacillus subtilis (bsSHMT) and B. stearothermophilus (bstSHMT) are both homodimers and share approximately 77% sequence identity; however, they show very different thermal stabilities and unfolding pathways. For investigating the role of N- and C-terminal domains in stability and unfolding of dimeric SHMTs, we have swapped the structural domains between bs- and bstSHMT and generated the two novel chimeric proteins bsbstc and bstbsc, respectively. The chimeras had secondary structure, tyrosine, and pyridoxal-5'-phosphate microenvironment similar to that of the wild-type proteins. The chimeras showed enzymatic activity slightly higher than that of the wild-type proteins. Interestingly, the guanidium chloride (GdmCl)-induced unfolding showed that unlike the wild-type bsSHMT, which undergoes dissociation of native dimer into monomers at low guanidium chloride (GdmCl) concentration, resulting in a non-cooperative unfolding of enzyme, its chimera bsbstc, having the C-terminal domain of bstSHMT was resistant to low GdmCl concentration and showed a GdmCl-induced cooperative unfolding from native dimer to unfolded monomer. In contrast, the wild-type dimeric bstSHMT was resistant to low GdmCl concentration and showed a GdmCl-induced cooperative unfolding, whereas its chimera bstbsc, having the C- terminal domain of bsSHMT, showed dissociation of native dimer into monomer at low GdmCl concentration and a GdmCl-induced non-cooperative unfolding. These results clearly demonstrate that the C-terminal domain of dimeric SHMT plays a vital role in stabilization of the oligomeric structure of the native enzyme hence modulating its unfolding pathway.     

Bioremediation of PAH-contaminated soil by composting: A case study

Composting technique was used for bioremediation of industrial soil originating from a former tar-contaminated site. The composting process was regulated by aeration to keep optimal temperature gradient and concentrations of O₂ and CO₂ inside the composting pile. The efficiency of bioremediation was evaluated by performing analysis of 11 individual three- to six-ring unsubstituted aromatic hydrocarbons (PAH) and estimating of changes in ecotoxicity of the contaminated soil. After 42 d of composting, PAH with 3–4 rings were removed from 42 to 68%, other higher-molar mass PAH from 35 to 57%. Additional 100 d of compost maturation in open-air field did not result in a further decrease of PAH. Ecotoxicity tests performed with bioluminescent bacteriaVibrio fischerii showed a decrease in toxicity both after composting and maturation phases. However, toxicity tests on mustard-seed germination did not reveal any significant changes during composting and maturation phases.     

Water temperature and pH influence olfactory sensitivity to pre-ovulatory and post-ovulatory ovarian pheromones in male Barilius bendelisis

The attractive response and sexual activity elicited by pre-ovulatory steroid sulphate and post-ovulatory 15K-PGF pheromones are greater in wild caught tubercular males and immature males which express breeding tubercles on the snout (at 12–13 days post androgen implant) than in non-tubercular and non-androgen implanted males of freshwater fishBarilius bendelisis. This shows that circulatory androgens exert an activational effect on olfactory receptors of male fish. Wild caught tubercular males and androgen implanted juvenile males exhibit a high responsiveness to steroid sulphate at the water temperature and pH which fish experience during the pre-spawning phase. The male’s sensitivity to 15K-PGF is almost equally high at the water temperature and pH which they experience in wild during the both pre-spawning and spawning periods. This suggests that the differential olfactory sensitivity to the two classes of pheromones in androgen implanted males is due to the varied temperature and pH of water, and that during the breeding season the male’s olfactory sensitivity to PGF pheromone is more widespread than to the steroidal pheromone. An increased and decreased olfactory sensitivity in mature males to sex pheromones and L-alanine respectively during the breeding phase is in agreement with the hypothesis that pheromonal stimuli dominate over feeding stimuli to promote spawning success.     

In vitro regeneration of roots of Phyla nodiflora and Leptadenia reticulata,and comparison of roots from cultured and natural plants for secondary metabolites

Adventitious roots, generated using leaf explants of P. nodiflora, and meristem explants of L. reticulata, were cultured on Murashige and Skoog (MS) medium supplemented with napthylacetic acid (2 microM) and indole butyric acid (3 microM) respectively. After 30 days, subculturing of roots in liquid MS medium with napthylacetic acid (1.5 microM) for P. nodiflora and indole butyric acid (3 microM) for L. reticulata afforded considerable increase in root mass. HPTLC profiles and microscopic examination of transverse sections of in vitro and naturally grown roots provided information on secondary metabolite accumulation vis-à-vis developmental stages of the root.     

Macrophage-colony-stimulating factor-induced activation of extracellular-regulated kinase involves phosphatidylinositol 3-kinase and reactive oxygen species in human monocytes

We previously reported that activation of the phosphatidylinositol (PI) 3-kinase pathway was important in M-CSF-induced monocyte survival. Because M-CSF also induces activation of the mitogen-activated protein (MAP) kinase extracellular-regulated kinase (Erk), we focused on dissecting the mechanism used by M-CSF to induce Erk activation in human monocytes. We found that, in addition to the MAP/Erk kinase inhibitor PD098059, the PI 3-kinase inhibitors LY294002 and wortmannin both suppressed Erk activation in M-CSF-treated monocytes, suggesting that 3-phosphorylated products of PI 3-kinase played a role in Erk activation. Investigating the biochemical pathways regulated by PI 3-kinase to activate Erk, we found that, in response to M-CSF, normal human monocytes induced reactive oxygen species (ROS), which were suppressed by the PI 3-kinase inhibitor wortmannin but not by the solvent control DMSO or the MAP/Erk kinase inhibitor PD098059. We next found that, in the absence of M-CSF, ROS could induce Erk activation in human monocytes. Exogenous H(2)O(2) induced Erk activation in human monocytes, which was suppressed by exogenous catalase. To determine whether ROS induced by M-CSF played a role in Erk activation, we found that N-acetylcysteine and diphenyleneiodonium both suppressed Erk activation in M-CSF-treated monocytes. Erk activation by M-CSF also seemed to play a role in cellular survival in monocytes. These data suggest that, in M-CSF-stimulated human monocytes, PI 3-kinase products and ROS production play a role in Erk activation and monocyte survival.     

Angiogenic factors and alveolar vasculature: development and alterations by injury in very premature baboons

Proper formation of the pulmonary microvasculature is essential for normal lung development and gas exchange. Lung microvascular development may be disrupted by chronic injury of developing lungs in clinical diseases such as bronchopulmonary dysplasia. We examined microvascular development, angiogenic growth factors, and endothelial cell receptors in a fetal baboon model of chronic lung disease (CLD). In the last third of gestation, the endothelial cell marker platelet endothelial cell adhesion molecule (PECAM)-1 increased 7.5-fold, and capillaries immunostained for PECAM-1 changed from a central location in airspace septa to a subepithelial location. In premature animals delivered at 67% of term and supported with oxygen and ventilation for 14 days, PECAM-1 protein and capillary density did not increase, suggesting failure to expand the capillary network. The capillaries of the CLD animals were dysmorphic and not subepithelial. The angiogenic growth factor vascular endothelial growth factor (VEGF) and its receptor fms-like tyrosine kinase receptor (Flt-1) were significantly decreased in CLD. Angiopoietin-1, another angiogenic growth factor, and its receptor tyrosine kinase with immunoglobulin and epidermal growth factor homology domains were not significantly changed. These data suggest that CLD impairs lung microvascular development and that a possible mechanism is disruption of VEGF and Flt-1 expression.