Loss of the Thioredoxin Reductase Trr1 Suppresses the Genomic Instability of Peroxiredoxin tsa1 Mutants

The absence of Tsa1, a key peroxiredoxin that scavenges H₂O₂ in Saccharomyces cerevisiae, causes the accumulation of a broad spectrum of mutations. Deletion of TSA1 also causes synthetic lethality in combination with mutations in RAD51 or several key genes involved in DNA double-strand break repair. In the present study, we propose that the accumulation of reactive oxygen species (ROS) is the primary cause of genome instability of tsa1Δ cells. In searching for spontaneous suppressors of synthetic lethality of tsa1Δ rad51Δ double mutants, we identified that the loss of thioredoxin reductase Trr1 rescues their viability. The trr1Δ mutant displayed a Can^R mutation rate 5-fold lower than wild-type cells. Additional deletion of TRR1 in tsa1Δ mutant reduced substantially the Can^R mutation rate of tsa1Δ strain (33-fold), and to a lesser extent, of rad51Δ strain (4-fold). Loss of Trr1 induced Yap1 nuclear accumulation and over-expression of a set of Yap1-regulated oxido-reductases with antioxidant properties that ultimately re-equilibrate intracellular redox environment, reducing substantially ROS-associated DNA damages. This trr1Δ -induced effect was largely thioredoxin-dependent, probably mediated by oxidized forms of thioredoxins, the primary substrates of Trr1. Thioredoxin Trx1 and Trx2 were constitutively and strongly oxidized in the absence of Trr1. In trx1Δ trx2Δ cells, Yap1 was only moderately activated; consistently, the trx1Δ trx2Δ double deletion failed to efficiently rescue the viability of tsa1Δ rad51Δ. Finally, we showed that modulation of the dNTP pool size also influences the formation of spontaneous mutation in trr1Δ and trx1Δ trx2Δ strains. We present a tentative model that helps to estimate the respective impact of ROS level and dNTP concentration in the generation of spontaneous mutations.     

Severe bacterial neonatal infections in Madagascar,Senegal, and Cambodia: A multicentric community-based cohort study

BackgroundSevere bacterial infections (SBIs) are a leading cause of neonatal deaths in low- and middle-income countries (LMICs). However, most data came from hospitals, which do not include neonates who did not seek care or were treated outside the hospital. Studies from the community are scarce, and few among those available were conducted with high-quality microbiological techniques. The burden of SBI at the community level is therefore largely unknown. We aimed here to describe the incidence, etiology, risk factors, and antibiotic resistance profiles of community-acquired neonatal SBI in 3 LMICs.Methods and findingsThe BIRDY study is a prospective multicentric community-based mother and child cohort study and was conducted in both urban and rural areas in Madagascar (2012 to 2018), Cambodia (2014 to 2018), and Senegal (2014 to 2018). All pregnant women within a geographically defined population were identified and enrolled. Their neonates were actively followed from birth to 28 days to document all episodes of SBI. A total of 3,858 pregnant women (2,273 (58.9%) in Madagascar, 814 (21.1%) in Cambodia, and 771 (20.0%) in Senegal) were enrolled in the study, and, of these, 31.2% were primigravidae. Women enrolled in the urban sites represented 39.6% (900/2,273), 45.5% (370/814), and 61.9% (477/771), and those enrolled in the rural sites represented 60.4% (1,373/2,273), 54.5% (444/814), and 38.1% (294/771) of the total in Madagascar, Cambodia, and Senegal, respectively. Among the 3,688 recruited newborns, 49.6% were male and 8.7% were low birth weight (LBW). The incidence of possible severe bacterial infection (pSBI; clinical diagnosis based on WHO guidelines of the Integrated Management of Childhood Illness) was 196.3 [95% confidence interval (CI) 176.5 to 218.2], 110.1 [88.3 to 137.3], and 78.3 [59.5 to 103] per 1,000 live births in Madagascar, Cambodia, and Senegal, respectively. The incidence of pSBI differed between urban and rural sites in all study countries. In Madagascar, we estimated an incidence of 161.0 pSBI per 1,000 live births [133.5 to 194] in the urban site and 219.0 [192.6 to 249.1] pSBI per 1,000 live births in the rural site (p = 0.008). In Cambodia, estimated incidences were 141.1 [105.4 to 189.0] and 85.3 [61.0 to 119.4] pSBI per 1,000 live births in urban and rural sites, respectively (p = 0.025), while in Senegal, we estimated 103.6 [76.0 to 141.2] pSBI and 41.5 [23.0 to 75.0] pSBI per 1,000 live births in urban and rural sites, respectively (p = 0.006). The incidences of culture-confirmed SBI were 15.2 [10.6 to 21.8], 6.5 [2.7 to 15.6], and 10.2 [4.8 to 21.3] per 1,000 live births in Madagascar, Cambodia, and Senegal, respectively, with no difference between urban and rural sites in each country. The great majority of early-onset infections occurred during the first 3 days of life (72.7%). The 3 main pathogens isolated were Klebsiella spp. (11/45, 24.4%), Escherichia coli (10/45, 22.2%), and Staphylococcus spp. (11/45, 24.4%). Among the 13 gram-positive isolates, 5 were resistant to gentamicin, and, among the 29 gram-negative isolates, 13 were resistant to gentamicin, with only 1 E. coli out of 10 sensitive to ampicillin. Almost one-third of the isolates were resistant to both first-line drugs recommended for the management of neonatal sepsis (ampicillin and gentamicin). Overall, 38 deaths occurred among neonates with SBI (possible and culture-confirmed SBI together). LBW and foul-smelling amniotic fluid at delivery were common risk factors for early pSBI in all 3 countries. A main limitation of the study was the lack of samples from a significant proportion of infants with pBSI including 35 neonatal deaths. Without these samples, bacterial infection and resistance profiles could not be confirmed.ConclusionsIn this study, we observed a high incidence of neonatal SBI, particularly in the first 3 days of life, in the community of 3 LMICs. The current treatment for the management of neonatal infection is hindered by antimicrobial resistance. Our findings suggest that microbiological diagnosis of SBI remains a challenge in these settings and support more research on causes of neonatal death and the implementation of early interventions (e.g., follow-up of at-risk newborns during the first days of life) to decrease the burden of neonatal SBI and associated mortality and help achieve Sustainable Development Goal 3.

In a community-based, prospective cohort study, Bich-Tram Huynh and colleagues investigate the incidence and factors associated with several bacterial infections among neonates in rural and urban areas of three low-middle income countries.     

Cytochrome c3 Mutants of Desulfovibrio desulfuricans

To explore the physiological role of tetraheme cytochrome c₃ in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c₃ in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.     

Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.     

Cholecystokinin-Induced Desensitization, Receptor Phosphorylation, and Internalization in the CHP212 Neuroblastoma Cell Line

Abstract: Agonist stimulation of cells often results in desensitization of the response, to protect the cell from overstimulation. We have previously shown that the type A cholecystokinin (CCK) receptor on the pancreatic acinar cell and on the model CHO-CCKR cell line undergoes desensitization in response to CCK, with receptor phosphorylation and internalization playing key roles. Although these mechanisms contribute in a cell-specific manner, no analogous information exists for the CCK receptor expressed on neuronal cells, where in vivo data demonstrate a particularly sensitive response to CCK. The present study was designed to explore CCK receptor desensitization in the CHP212 neuroblastoma cell line, focusing on inositol 1,4,5-trisphosphate (IP₃) responses to CCK and on recognized molecular and cellular mechanisms of desensitization. CCK promptly stimulated IP₃ responses in these cells, with hormonal responsiveness rapidly and completely desensitized. Both receptor phosphorylation and internalization were observed to occur, with the former occurring most rapidly and likely being responsible for the earliest desensitization observed. Although the time course of receptor phosphorylation and dephosphorylation, and the groups of kinases involved in the neuroblastoma cell line, were most similar to those in the pancreatic cell, the movement of the agonist-bound receptor in these cells was quite different from that in the pancreatic cell and most similar to that in the CHO-CCKR cell line. This hybrid response supports the cell-specific nature of CCK receptor regulation and provides an important system to explore the molecular determinants of these processes.     

Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making

Humans stand out from other animals in that they are able to explicitly report on the reliability of their internal operations. This ability, which is known as metacognition, is typically studied by asking people to report their confidence in the correctness of some decision. However, the computations underlying confidence reports remain unclear. In this paper, we present a fully Bayesian method for directly comparing models of confidence. Using a visual two-interval forced-choice task, we tested whether confidence reports reflect heuristic computations (e.g. the magnitude of sensory data) or Bayes optimal ones (i.e. how likely a decision is to be correct given the sensory data). In a standard design in which subjects were first asked to make a decision, and only then gave their confidence, subjects were mostly Bayes optimal. In contrast, in a less-commonly used design in which subjects indicated their confidence and decision simultaneously, they were roughly equally likely to use the Bayes optimal strategy or to use a heuristic but suboptimal strategy. Our results suggest that, while people’s confidence reports can reflect Bayes optimal computations, even a small unusual twist or additional element of complexity can prevent optimality.     

Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models

Ensembling combines the predictions made by individual component base models with the goal of achieving a predictive accuracy that is better than that of any one of the constituent member models. Diversity among the base models in terms of predictions is a crucial criterion in ensembling. However, there are practical instances when the available base models produce highly correlated predictions, because they may have been developed within the same research group or may have been built from the same underlying algorithm. We investigated, via a case study on Fusarium head blight (FHB) on wheat in the U.S., whether ensembles of simple yet highly correlated models for predicting the risk of FHB epidemics, all generated from logistic regression, provided any benefit to predictive performance, despite relatively low levels of base model diversity. Three ensembling methods were explored: soft voting, weighted averaging of smaller subsets of the base models, and penalized regression as a stacking algorithm. Soft voting and weighted model averages were generally better at classification than the base models, though not universally so. The performances of stacked regressions were superior to those of the other two ensembling methods we analyzed in this study. Ensembling simple yet correlated models is computationally feasible and is therefore worth pursuing for models of epidemic risk.     

Oligodeoxynucleotides Embodying the Ambiguous Base Z, 5-Amino-imidazole-4-carboxamide

Abstract

Short oligomers containing 5-amino-1-(2-deoxy-β-D-ribofuranosyl)imidazole-4-carboxamide (dZ) were synthesized in solution using the phosphotriester methodology. Usual acyl groups were used for the canonical bases. For the exocyclic amino function of Z residue, the hydrogenolyzable benzyloxycarbonyl group was introduced.     

Fluid physico-chemical properties influence capture and diet in Nepenthes pitcher plants

Background and Aims Nepenthes pitcher plants have evolved modified leaves with slippery surfaces and enzymatic fluids that trap and digest prey, faeces and/or plant detritus. Although the fluid’s contribution to insect capture is recognized, the physico-chemical properties involved remain underexplored and may vary among species, influencing their diet type. This study investigates the contributions of acidity and viscoelasticity in the fluid’s capture efficiency of two ant and two fly species in four Nepenthes species with different nutrition strategies.Methods Four Nepenthes species were studied, namely N. rafflesiana, N. gracilis, N. hemsleyana and N. ampullaria. Fluid was collected from pitchers of varying ages from plants growing in the field and immediately transferred to glass vials, and individual ants (tribe Campotini, Fomicinae) and flies (Calliphora vomitoria and Drosophila melanogaster) were dropped in and observed for 5 min. Water-filled vials were used as controls. Survival and lifetime data were analysed using models applied to right-censored observations. Additional laboratory experiments were carried out in which C. vomitoria flies were immersed in pH-controlled aqueous solutions and observed for 5 min.Key Results Pitcher fluid differed among Nepenthes species as regards insect retention capacity and time-to-kill, with differences observed between prey types. Only the fluids of the reputedly insectivorous species were very acidic and/or viscoelastic and retained significantly more insects than the water controls. Viscoelastic fluids were fatal to flies and were able to trap the broadest diversity of insects. Younger viscoelastic fluids showed a better retention ability than older fluids, although with less rapid killing ability, suggesting that a chemical action follows a mechanical one. Insect retention increased exponentially with fluid viscoelasticity, and this happened more abruptly and at a lower threshold for flies compared with ants. Flies were more often retained if they fell into the traps on their backs, thus wetting their wings. Insect retention and death rate increased with fluid acidity, with a lower threshold for ants than for flies, and the time-to-kill decreased with increasing acidity. The laboratory experiments showed that fewer flies escaped from acidic solutions compared with water.Conclusions In addition to viscoelasticity, the pitcher’s fluid acidity and wetting ability influence the fate of insects and hence the diet of Nepenthes. The plants might select the prey that they retain by manipulating the secretion of H⁺ ions and polysaccharides in their pitcher fluid. This in turn might participate in possible adaptive radiation of this genus with regard to nutrient sequestration strategy. These plants might even structurally influence insect fall-orientation and capture-probability, inspiring biomimetic designs for pest control.