Toarcian oceanic anoxic event: An assessment of global causes using belemnite C isotope records

Two hypotheses have been proposed to explain simultaneous large negative excursions (up to 7% PeeDee belemnite) in bulk carbonate (delta(13)C(carb)) and organic carbon isotope records (delta(13)C(org)) from black shales marking the Toarcian oceanic anoxic event (T-OAE). The first explanation envisions recycling of dissolved inorganic carbon (DIC) with a light isotopic signature into the photic zone from the lower levels of a salinity-stratified water mass, essentially requiring a regional paleoceanographic driver of the carbon cycle. The second involves the rapid and massive dissociation of methane from gas hydrates that effectively renders the T-OAE a global perturbation of the carbon cycle. We present C isotope records from belemnites (delta(13)C(bel)) sampled from two localities, calibrated with high-resolution ammonite biostratigraphy and Sr isotope stratigraphy, in Yorkshire (England) and Dotternhausen (Germany), that can be used to assess which model best explains the observed changes in carbon isotopes. Our records of the delta(13)C composition of belemnite calcite do not show the large negative C isotope excursions shown by coeval records of delta(13)C in sedimentary organic matter or bulk sedimentary carbonate. It follows that isotopically light carbon cannot have dominated the ocean-atmosphere carbon reservoir during the Toarcian OAE, as would be required were the methane release hypothesis correct. On the basis of an evaluation of available carbon isotope records we discuss a model in which the recycling of DIC from the deeper levels of a stratified water body, and shallowing of anoxic conditions into the photic zone, can explain all isotopic profiles. In particular, the model accounts for the higher C isotope values of belemnites that are characteristic of open ocean, well-mixed conditions, and the lower C isotope values of neritic phytoplankton communities that recorded the degree of density stratification and shallowing of anoxia in the photic zone

Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition

\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.Mycobacterium tuberculosis, the causative agent of tuberculosis, is a growing threat to global health, with recent efforts towards its eradication being reversed in the wake of the COVID-19 pandemic. Increasing resistance to gyrase-targeting second-line fluoroquinolone antibiotics indicates the necessity to develop both novel therapeutics and our understanding of M. tuberculosis growth during infection. ParDE toxin–antitoxin systems also target gyrase and are regulated in response to both host-associated and drug-induced stress during infection. Here, we present microbiological, biochemical, structural, and biophysical analyses exploring the ParDE1 and ParDE2 systems of M. tuberculosis H37Rv. The structures reveal conserved modes of toxin–antitoxin recognition, with complex-specific interactions. ParDE1 forms a novel heterohexameric ParDE complex, supported by antitoxin chains taking on two distinct folds. Curiously, ParDE1 exists in solution as a dynamic equilibrium between heterotetrameric and heterohexameric complexes. Conditional remodelling into higher order complexes can be thermally driven in vitro. Remodelling induces toxin release, tracked through concomitant inhibition and poisoning of gyrase activity. Our work aids our understanding of gyrase inhibition, allowing wider exploration of toxin–antitoxin systems as inspiration for potential therapeutic agents

Differential Allocation Revisited: When Should Mate Quality Affect Parental Investment?

This is the final version of the article. Available from University of Chicago Press via the DOI in this record.Differential allocation (DA) is the adaptive adjustment of reproductive investment (up or down) according to partner quality. A lack of theoretical treatments has led to some confusion in the interpretation of DA in the empirical literature. We present a formal framework for DA that highlights the nature of reproductive benefits versus costs for females mated to males of different quality. Contrary to popular belief, analytical and stochastic dynamic models both show that additive benefits of male quality on offspring fitness have no effect on optimal levels of female investment and thus cannot produce DA. Instead, if offspring fitness is affected multiplicatively by male quality, or male quality affects the female cost function, DA is expected because of changes in the marginal benefits or costs of extra investment. Additive male quality effects on the female cost function can cause a novel form of weak DA, because reduced costs can slightly favor current over future reproduction. Combinations of these distinct effects in more realistic model scenarios can explain various patterns of positive and negative DA reported for different species and mating systems. Our model therefore sheds new light on the diversity of empirical results by providing a strong conceptual framework for the DA hypothesis.This work was supported by the Research Council of Norway through its Young Talented Researchers funding scheme FRIMEDBIO, project number 240008 to I.I.R., and partly through its Centres of Excellence funding scheme, project number 223257, to Centre for Biodiversity Dynamics at the Norwegian University of Science and Technology. B.K. is funded by a Leverhulme Trust Early Career Research Fellowship (ECF 2015-273)

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067

From L-Dopa to Dihydroxyphenylacetaldehyde: A Toxic Biochemical Pathway Plays a Vital Physiological Function in Insects

One protein in Aedes aegypti, classified into the aromatic amino acid decarboxylase (AAAD) family based on extremely high sequence homology (∼70%) with dopa decarboxylase (Ddc), was biochemically investigated. Our data revealed that this predicted AAAD protein use L-dopa as a substrate, as does Ddc, but it catalyzes the production of 3,4-dihydroxylphenylacetaldehyde (DHPAA) directly from L-dopa and apparently has nothing to do with the production of any aromatic amine. The protein is therefore named DHPAA synthase. This subsequently led to the identification of the same enzyme in Drosophila melanogaster, Anopheles gambiae and Culex quinquefasciatus by an initial prediction of putative DHPAA synthase based on sequence homology and subsequent verification of DHPAA synthase identity through protein expression and activity assays. DHPAA is highly toxic because its aldehyde group readily reacts with the primary amino groups of proteins, leading to protein crosslinking and inactivation. It has previously been demonstrated by several research groups that Drosophila DHPAA synthase was expressed in tissues that produce cuticle materials and apparent defects in regions of colorless, flexible cuticular structures have been observed in its gene mutants. The presence of free amino groups in proteins, the high reactivity of DHPAA with the free amino groups, and the genetically ascertained function of the Drosophila DHPAA synthase in the formation of colorless, flexible cuticle, when taken together, suggest that mosquito and Drosophila DHPAA synthases are involved in the formation of flexible cuticle through their reactive DHPAA-mediated protein crosslinking reactions. Our data illustrate how a seemingly highly toxic pathway can serve for an important physiological function in insects

Does publication bias inflate the apparent efficacy of psychological treatment for major depressive disorder? A systematic review and meta-analysis of US national institutes of health-funded trials

Background The efficacy of antidepressant medication has been shown empirically to be overestimated due to publication bias, but this has only been inferred statistically with regard to psychological treatment for depression. We assessed directly the extent of study publication bias in trials examining the efficacy of psychological treatment for depression. Methods and Findings We identified US National Institutes of Health grants awarded to fund randomized clinical trials comparing psychological treatment to control conditions or other treatments in patients diagnosed with major depressive disorder for the period 1972–2008, and we determined whether those grants led to publications. For studies that were not published, data were requested from investigators and included in the meta-analyses. Thirteen (23.6%) of the 55 funded grants that began trials did not result in publications, and two others never started. Among comparisons to control conditions, adding unpublished studies (Hedges’ g = 0.20; CI95% -0.11~0.51; k = 6) to published studies (g = 0.52; 0.37~0.68; k = 20) reduced the psychotherapy effect size point estimate (g = 0.39; 0.08~0.70) by 25%. Moreover, these findings may overestimate the "true" effect of psychological treatment for depression as outcome reporting bias could not be examined quantitatively. Conclusion The efficacy of psychological interventions for depression has been overestimated in the published literature, just as it has been for pharmacotherapy. Both are efficacious but not to the extent that the published literature would suggest. Funding agencies and journals should archive both original protocols and raw data from treatment trials to allow the detection and correction of outcome reporting bias. Clinicians, guidelines developers, and decision makers should be aware that the published literature overestimates the effects of the predominant treatments for depression

First GIS analysis of modern stone tools used by wild chimpanzees (Pan troglodytes verus) in Bossou, Guinea, West Africa

Stone tool use by wild chimpanzees of West Africa offers a unique opportunity to explore the evolutionary roots of technology during human evolution. However, detailed analyses of chimpanzee stone artifacts are still lacking, thus precluding a comparison with the earliest archaeological record. This paper presents the first systematic study of stone tools used by wild chimpanzees to crack open nuts in Bossou (Guinea-Conakry), and applies pioneering analytical techniques to such artifacts. Automatic morphometric GIS classification enabled to create maps of use wear over the stone tools (anvils, hammers, and hammers/anvils), which were blind tested with GIS spatial analysis of damage patterns identified visually. Our analysis shows that chimpanzee stone tool use wear can be systematized and specific damage patterns discerned, allowing to discriminate between active and passive pounders in lithic assemblages. In summary, our results demonstrate the heuristic potential of combined suites of GIS techniques for the analysis of battered artifacts, and have enabled creating a referential framework of analysis in which wild chimpanzee battered tools can for the first time be directly compared to the early archaeological record.Leverhulme Trust [IN-052]; MEXT [20002001, 24000001]; JSPS-U04-PWS; FCT-Portugal [SFRH/BD/36169/2007]; Wenner-Gren Foundation for Anthropological Researc