Mechanics and dynamics of X-chromosome pairing at X inactivation

At the onset of X-chromosome inactivation, the vital process whereby female mammalian cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-inactivation center) regions. The mechanism inducing recognition and pairing of the X’s remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called "pairing sites") involved, we dissect the mechanical basis of Xic colocalization by using a statistical physics model. We show that soluble DNA-specific binding molecules, such as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes but only when their concentration, or chemical affinity, rises above a threshold value as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data

Contribution of rock glacier discharge to late summer and fall streamflow in the Uinta Mountains, Utah, USA

Water draining from rock glaciers in the Uinta Mountains of Utah (USA) was analyzed and compared with samples of groundwater and water from the primary stream in a representative 5000 ha drainage. Rock glacier water resembles snowmelt in the early summer but evolves to higher values of d-excess and greatly elevated Ca and Mg content as the melt season progresses. This pattern is consistent with models describing a transition from snowmelt to melting of seasonal ice to melting of perennial ice in the rock glacier interior in late summer and fall. Water derived from this internal ice appears to have been the source of ∼25 % of the streamflow in this study area during September of 2021. This result emphasizes the significant role that rock glaciers can play in the hydrology of high-elevation watersheds, particularly in summers following a winter with below-average snowpack.</p

Examining the variability of rock glacier meltwater in space and time in high-elevation environments of Utah, United States

Rock glaciers are common geomorphic features in alpine landscapes and comprise a potentially significant but poorly quantified water resource. This project focused on three complementary questions germane to rock glacier hydrology: 1) Does the composition of rock glacier meltwater vary from year to year? 2) How dependent is the composition of rock glacier meltwater on lithology? And 3) How does the presence of rock glaciers in a catchment change stream water chemistry? To address these questions, we deployed automated samplers to collect water from late June through mid-October 2022 in two rock-glacierized mountain ranges in Utah, United States characterized by different lithologies. In the Uinta Mountains of northern Utah, where bedrock is predominantly quartzite, water was collected at springs discharging from two rock glaciers previously shown to release water in late summer sourced from internal ice. In the La Sal Mountains of southeastern Utah, where trachyte bedrock is widespread, water was collected at a rock glacier spring, along the main stream in a watershed containing multiple rock glaciers, and from a stream in a watershed where rock glaciers are absent. Precipitation was also collected, and data loggers for water temperature and electric conductivity were deployed. Water samples were analyzed for stable isotopes with cavity ring-down spectroscopy and hydrochemistry with ICP-MS. Our data show that water discharging from rock glaciers in the Uinta Mountains exhibits a shift from a snowmelt source to an internal ice source over the course of the melt season that is consistent from year to year. We also found that the chemistry of rock glacier water in the two study areas is notably different in ways that can be linked back to their contrasting bedrock types. Finally, in the La Sal Mountains, the properties of water along the main stream in a rock-glacierized basin resemble the properties of water discharging from rock glaciers, and strongly contrast with the water in a catchment lacking rock glaciers. Collectively these results underscore the role of rock glaciers as an agent influencing the hydrochemistry of water in high-elevation stream systems

Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin

VanA-type resistance to glycopeptide antibiotics in clinical enterococci is regulated by the VanSARA two-component signal transduction system. The nature of the molecular ligand that is recognised by the VanSA sensory component has not hitherto been identified. Here we employ purified, intact and active VanSA membrane protein (henceforth referred to as VanS) in analytical ultracentrifugation experiments to study VanS oligomeric state and conformation in the absence and presence of vancomycin. A combination of sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge (SEDFIT, SEDFIT-MSTAR and MULTISIG analysis) showed that VanS in the absence of the ligand is almost entirely monomeric (molar mass M = 45.7 kDa) in dilute aqueous solution with a trace amount of high molar mass material (M ~ 200 kDa). The sedimentation coefficient s suggests the monomer adopts an extended conformation in aqueous solution with an equivalent aspect ratio of ~ (12+2). In the presence of vancomycin over a 33% increase in the sedimentation coefficient is observed with the appearance of additional higher s components, demonstrating an interaction, an observation consistent with our circular dichroism measurements. The two possible causes of this increase in s – either a ligand induced dimerization and/or compaction of the monomer are considered

An influenza virus-inspired polymer system for the timed release of siRNA

Small interfering RNA silences specific genes by interfering with mRNA translation, and acts to modulate or inhibit specific biological pathways; a therapy that holds great promise in the cure of many diseases. However, the naked small interfering RNA is susceptible to degradation by plasma and tissue nucleases and due to its negative charge unable to cross the cell membrane. Here we report a new polymer carrier designed to mimic the influenza virus escape mechanism from the endosome, followed by a timed release of the small interfering RNA in the cytosol through a self-catalyzed polymer degradation process. Our polymer changes to a negatively charged and non-toxic polymer after the release of small interfering RNA, presenting potential for multiple repeat doses and long-term treatment of diseases

Antimicrobial resistance (AMR) nanomachines: mechanisms for fluoroquinolone and glycopeptide recognition, efflux and/or deactivation

In this review, we discuss mechanisms of resistance identified in bacterial agents Staphylococcus aureus and the enterococci towards two priority classes of antibiotics—the fluoroquinolones and the glycopeptides. Members of both classes interact with a number of components in the cells of these bacteria, so the cellular targets are also considered. Fluoroquinolone resistance mechanisms include efflux pumps (MepA, NorA, NorB, NorC, MdeA, LmrS or SdrM in S. aureus and EfmA or EfrAB in the enterococci) for removal of fluoroquinolone from the intracellular environment of bacterial cells and/or protection of the gyrase and topoisomerase IV target sites in Enterococcus faecalis by Qnr-like proteins. Expression of efflux systems is regulated by GntR-like (S. aureus NorG), MarR-like (MgrA, MepR) regulators or a two-component signal transduction system (TCS) (S. aureus ArlSR). Resistance to the glycopeptide antibiotic teicoplanin occurs via efflux regulated by the TcaR regulator in S. aureus. Resistance to vancomycin occurs through modification of the D-Ala-D-Ala target in the cell wall peptidoglycan and removal of high affinity precursors, or by target protection via cell wall thickening. Of the six Van resistance types (VanA-E, VanG), the VanA resistance type is considered in this review, including its regulation by the VanSR TCS. We describe the recent application of biophysical approaches such as the hydrodynamic technique of analytical ultracentrifugation and circular dichroism spectroscopy to identify the possible molecular effector of the VanS receptor that activates expression of the Van resistance genes; both approaches demonstrated that vancomycin interacts with VanS, suggesting that vancomycin itself (or vancomycin with an accessory factor) may be an effector of vancomycin resistance. With 16 and 19 proteins or protein complexes involved in fluoroquinolone and glycopeptide resistances, respectively, and the complexities of bacterial sensing mechanisms that trigger and regulate a wide variety of possible resistance mechanisms, we propose that these antimicrobial resistance mechanisms might be considered complex ‘nanomachines’ that drive survival of bacterial cells in antibiotic environments

Synthetic amphipathic peptides resembling apolipoproteins stimulate the release of human placental lactogen

Previous studies from our laboratory demonstrated native high density lipoproteins and apolipoproteins AI, AII, and CI, stimulate the release of human placental lactogen (hPL) from trophoblast cells in culture. To examine the mechanisms by which these apolipoproteins stimulate hPL release, we have studied hPL secretion in response to several synthetic peptide analogs of the amphipathic helical structure of the apolipoproteins. The magnitude of the stimulation of hPL release in response to the analog peptides correlated with the ability to displace apolipoproteins from high density lipoprotein and with other measures of phospholipid binding affinity such as the increase in alpha-helicity and the size of complexes formed between the peptide and phospholipid. The correlation of stimulatory ability and lipid affinity suggests that the action of the apolipoproteins on hPL release may be mediated through an interaction with plasma membrane phospholipids