Decolonizing Feminism: From Reproductive Abuse to Reproductive Justice

This paper asks why reproductive gains have sometimes amounted to reproductive abuse for Indigenous women in Canada. Guided by an intersectional and decolonial approach, it provides a historical material critique of the individualized rights discourse and reformist goals that tend to underlay feminist struggles in Canada. It explores how western feminism might support decolonization and reproductive justice.stice. Résumé Cet article demande pourquoi les gains en matière de reproduction se sont parfois traduits par des abus en matière de reproduction pour les femmes autochtones au Canada. Guidé par une approche intersectionnelle et décoloniale, il fournit une critique matérielle historique du discours sur les droits individualisés et des objectifs réformistes qui ont tendance à sous-tendre les luttes féministes au Canada. Il explore comment le féminisme occidental pourrait soutenir la décolonisation et la justice reproductive

Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates

Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases

Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes

International audienceBackground: Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secreted and transmembrane 1 (Sectm1) are neighbors but are not homologs. Sectm1 is involved in immunity and its molecular phylogeny is unknown. Methods: Using multiple alignments of complete protein sequences (MACS), we inferred Tex19 and Sectm1 molecular phylogenies. Protein conserved regions were identified and folds were predicted. Finally, expression patterns were studied across tissues and species using RNA-seq public data and RT-PCR. Results: We present 2 high quality alignments of 58 Tex19 and 58 Sectm1 protein sequences from 48 organisms. First, both genes are eutherian-specific, i.e., exclusively present in mammals except monotremes (platypus) and marsupials. Second, Tex19 and Sectm1 have both duplicated in Sciurognathi and Bovidae while they have remained as single copy genes in all further placental mammals. Phylogenetic concordance between both genes was significant (p-value < 0.05) and supported co-evolution and functional relationship. At the protein level, Tex19 exhibits 3 conserved regions and 4 invariant cysteines. In particular, a CXXC motif is present in the N-terminal conserved region. Sectm1 exhibits 2 invariant cysteines and an Ig-like domain. Strikingly, Tex19 C-terminal conserved region was lost in Haplorrhini primates while a Sectm1 C-terminal extra domain was acquired. Finally, we have determined that Tex19 and Sectm1 expression levels anti-correlate across the testis of several primates (ρ = −0.72) which supports anti-regulation. Conclusions: Tex19 and Sectm1 co-evolution and anti-regulated expressions support a strong functional relationship between both genes. Since Tex19 operates a control on TE and Sectm1 plays a role in immunity, Tex19 might suppress an immune response directed against cells that show TE activity in eutherian reproductive tissues

Generalized solvent boundary potential for computer simulations

Copyright 2001 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.1336570.A general approach has been developed to allow accurate simulations of a small region part of a large macromolecular system while incorporating the influence of the remaining distant atoms with an effective boundary potential. The method is called the Generalized Solvent Boundary Potential (GSBP). By representing the surrounding solvent as a continuum dielectric, both the solvent-shielded static field from the distant atoms of the macromolecule and the reaction field from the dielectricsolvent acting on the atoms in the region of interest are included. The static field is calculated once, using the finite-difference Poisson–Boltzmann (PB) equation, and the result is stored on a discrete grid for efficient simulations. The solventreaction field is developed using a basis-set expansion whose coefficients correspond to generalized electrostatic multipoles. A matrix representing the reaction field Green’s function between those generalized multipoles is calculated only once using the PB equation and stored for efficient simulations. In the present work, the formalism is applied to both spherical and orthorhombic simulation regions for which orthonormal basis-sets exist based on spherical harmonics or cartesian Legendre polynomials. The GSBP method is also tested and illustrated with simple model systems and two detailed atomic systems: the active site region of aspartyl-tRNA synthetase (spherical region) and the interior of the KcsA potassium channel (orthorhombic region). Comparison with numerical finite-difference PB calculations shows that GSBP can accurately describe all long-range electrostatic interactions and remain computationally inexpensive

Electrostatic free energy calculations using the generalized solvent boundary potential method

Copyright 2002 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics and may be found at http://dx.doi.org/10.1063/1.1507108.Free energyperturbation (FEP) calculations using all-atom molecular dynamics simulations with a large number of explicit solvent molecules are a powerful approach to study ligand–macromolecule association processes at the atomic level. One strategy to carry out FEP calculations efficiently and reduce computational time is to consider the explicit dynamics of only a small number of atoms in a localized region around the ligand. Such an approximation is motivated by the observation that the factors governing binding specificity are dominated by interactions in the vicinity of the ligand. However, a straightforward truncation of the system may yield inaccurate results as the influence exerted by the remote regions of the macromolecule and the surrounding solvent through long-range electrostatic effects may be significant. To obtain meaningful results, it is important to incorporate the influence of the remote regions of the ligand–macromolecule complex implicitly using some effective potential. The generalized solvent boundary potential (GSBP) that was developed recently [W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)] is an efficient computational method to represent the long-range electrostaticinteractions arising from remote (outer) regions in simulations of a localized (inner) region with a small number of explicit atoms. In the present work, FEP calculations combined with GSBP are used to illustrate the importance of these long-range electrostatic factors in estimation of the charging free energy of an aspartate ligand bound to the aspartyl-tRNA synthetase. Calculations with explicit spherical simulation inner regions of different radii are used to test the accuracy of the GSBP method and also illustrate the importance of explicit protein and solvent dynamics in the free energy estimation. The influence of the represented outer region is tested using separate simulations in which the reaction field and/or the protein static field are excluded. Both components are shown to be essential to obtain quantitatively meaningful results. The ability of implicitly treating the influence of protein fluctuations in the outer region using a protein dielectric constant is examined. It is shown that accurate charging free energy calculations can be performed for this system with a spherical region of 15 to 20 Å radius, which roughly corresponds to 1500–3500 moving atoms. The results indicate that GSBP in combination with FEP calculations is a precise and efficient approach to include long-range electrostatic effects in the study of ligand binding to large macromolecules

Post-translational modifications in DNA topoisomerase 2α highlight the role of a eukaryote-specific residue in the ATPase domain

Type 2 DNA topoisomerases (Top2) are critical components of key protein complexes involved in DNA replication, chromosome condensation and segregation, as well as gene transcription. The Top2 were found to be the main targets of anticancer agents, leading to intensive efforts to understand their functional and physiological role as well as their molecular structure. Post-translational modifications have been reported to influence Top2 enzyme activities in particular those of the mammalian Top2α isoform. In this study, we identified phosphorylation, and for the first time, acetylation sites in the human Top2α isoform produced in eukaryotic expression systems. Structural analysis revealed that acetylation sites are clustered on the catalytic domains of the homodimer while phosphorylation sites are located in the C-terminal domain responsible for nuclear localization. Biochemical analysis of the eukaryotic-specific K168 residue in the ATPase domain shows that acetylation affects a key position regulating ATP hydrolysis through the modulation of dimerization. Our findings suggest that acetylation of specific sites involved in the allosteric regulation of human Top2 may provide a mechanism for modulation of its catalytic activity.Fil: Bedez, Claire. Université de Strasbourg; FranciaFil: Lotz, Christophe. Université de Strasbourg; FranciaFil: Batisse, Claire. Université de Strasbourg; FranciaFil: Broeck, Arnaud Vanden. Université de Strasbourg; FranciaFil: Stote, Roland H.. Université de Strasbourg; FranciaFil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Pradeau-Aubreton, Karine. Université de Strasbourg; FranciaFil: Ruff, Marc. Université de Strasbourg; FranciaFil: Lamour, Valérie. Université de Strasbourg; Franci

N-methyl-D-aspartate receptors in the basolateral amygdala are required for both acquisition and expression of conditional fear in rats

Three experiments examined the effects of intra-amygdaloid infusions of an N-methyl-D-aspartate (NMDA) receptor antagonist, D,L-2-amino-5-phosphonovalerate (APV), on contextual fear conditioning in rats. In Experiment 1, APV infusion into the basolateral amygdala (BLA), before training, disrupted the acquisition of contextual fear. In Experiment 2, APV produced a disruption of both the acquisition and expression of contextual fear. This blockade of contextual fear was not state dependent, not due to a shift in footshock sensitivity, and not the result of increased motor activity in APV-treated rats. In Experiment 3, fear conditioning was not affected by a posttraining APV infusion into the BLA. These results indicate that NMDA receptors in the BLA are necessary for both the acquisition and expression of Pavlovian fear conditioning to contextual cues in rats.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/56217/1/marenBN96apv.pd