The potential for groundwater contamination along basin margins in the arid west: Alluvial fans and lake features

Many towns of the arid west were built upon alluvial fans and upon sites underlain by Pleistocene lake deposits. The objective of this study was to assess the potential impact of these activities of man upon groundwater quality within these geological features. Emphasis was placed on shallow groundwater quality after it was determined that deep groundwater is rarely contaminated at such sites. A reconnaissance of Utah and Nevada was made and four sites underlain by alluvial fans (Willard, Manti, Elsinore, and Spring City) and four sites underlain by lake shore deposits (Hyde Park, Fielding, Providence and Richmond) were selected in Utah for more detailed geologic, hydrologic, and water quality studies. Samples for water quality analyses were taken from existing wells and springs where available. At Hyde Park a shallow, small diameter well was constructed. Three groundwater sampling wells were constructed on the Willard Creek fan. Sites were selected to represent various degrees and types of land use. It was concluded that septic effluents, agricultural wastes, and other sources of man-made contamination can be hazards to shallow groundwater quality in alluvial fans and lake shore sediments. Mercury was found in concentrations exceeding the EPA drinking water standards at a few of the sites, but its source was probably natural. Nitrates and phosphates usually were the observable indicators of shallow groundwater contamination at the sites investigated, while coliform bacteria evidently are not transported appreciable distances underground and made poor indicators. The conclusions reached in this report are believed to be applicable to other areas of the arid west where similar geologic features and basin margin sediments occur

The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex

The MAGE (Melanoma-associated antigen) protein family members are structurally related to each other by a MAGEhomology domain comprised of 2 winged helix motifs WH/A and WH/B. This family specifically evolved in placental mammals although single homologs designated NSE3 (non-SMC element) exist in most eukaryotes. NSE3, together with its partner proteins NSE1 and NSE4 form a tight subcomplex of the structural maintenance of chromosomes SMC5–6 complex. Previously, we showed that interactions of the WH/B motif of the MAGE proteins with their NSE4/EID partners are evolutionarily conserved (including the MAGEA1-NSE4 interaction). In contrast, the interaction of the WH/A motif of NSE3 with NSE1 diverged in the MAGE paralogs. We hypothesized that the MAGE paralogs acquired new RING-finger containing partners through their evolution and form MAGE complexes reminiscent of NSE1-NSE3-NSE4 trimers. In this work, we employed the yeast 2-hybrid system to screen a human RING-finger protein library against several MAGE baits. We identified a number of potential MAGE-RING interactions and confirmed several of them (MDM4, PCGF6, RNF166, TRAF6, TRIM8, TRIM31, TRIM41) in co-immunoprecipitation experiments. Among these MAGE-RING pairs, we chose to examine MAGEA1-TRIM31 in detail and showed that both WH/A and WH/B motifs of MAGEA1 bind to the coiled-coil domain of TRIM31 and that MAGEA1 interaction stimulates TRIM31 ubiquitin-ligase activity. In addition, TRIM31 directly binds to NSE4, suggesting the existence of a TRIM31-MAGEA1-NSE4 complex reminiscent of the NSE1-NSE3-NSE4 trimer. These results suggest that MAGEA1 functions as a co-factor of TRIM31 ubiquitin-ligase and that the TRIM31-MAGEA1-NSE4 complex may have evolved from an ancestral NSE1-NSE3-NSE4 complex

A role of the Nse4 kleisin and Nse1/Nse3 KITE subunits in the ATPase cycle of SMC5/6

The SMC (Structural Maintenance of Chromosomes) complexes are composed of SMC dimers, kleisin and kleisin-interacting (HAWK or KITE) subunits. Mutual interactions of these subunits constitute the basal architecture of the SMC complexes. In addition, binding of ATP molecules to the SMC subunits and their hydrolysis drive dynamics of these complexes. Here, we developed new systems to follow the interactions between SMC5/6 subunits and the relative stability of the complex. First, we show that the N-terminal domain of the Nse4 kleisin molecule binds to the SMC6 neck and bridges it to the SMC5 head. Second, binding of the Nse1 and Nse3 KITE proteins to the Nse4 linker increased stability of the ATP-free SMC5/6 complex. In contrast, binding of ATP to SMC5/6 containing KITE subunits significantly decreased its stability. Elongation of the Nse4 linker partially suppressed instability of the ATP-bound complex, suggesting that the binding of the KITE proteins to the Nse4 linker constrains its limited size. Our data suggest that the KITE proteins may shape the Nse4 linker to fit the ATP-free complex optimally and to facilitate opening of the complex upon ATP binding. This mechanism suggests an important role of the KITE subunits in the dynamics of the SMC5/6 complexes

Coping with Time-Varying Demand When Setting Staffing Requirements for a Service System

We review queueing-theory methods for setting staffing requirements in service systems where customer demand varies in a predictable pattern over the day. Analyzing these systems is not straightforward, because standard queueing theory focuses on the long-run steady-state behavior of stationary models. We show how to adapt stationary queueing models for use in nonstationary environments so that time-dependent performance is captured and staffing requirements can be set. Relatively little modification of straightforward stationary analysis applies in systems where service times are short and the targeted quality of service is high. When service times are moderate and the targeted quality of service is still high, time-lag refinements can improve traditional stationary independent period-by-period and peak-hour approximations. Time-varying infinite-server models help develop refinements, because closed-form expressions exist for their time-dependent behavior. More difficult cases with very long service times and other complicated features, such as end-of-day effects, can often be treated by a modified-offered-load approximation, which is based on an associated infinite-server model. Numerical algorithms and deterministic fluid models are useful when the system is overloaded for an extensive period of time. Our discussion focuses on telephone call centers, but applications to police patrol, banking, and hospital emergency rooms are also mentioned

Srs2 mediates PCNA-SUMO-dependent inhibition of DNA repair synthesis

Completion of DNA replication needs to be ensured even when challenged with fork progression problems or DNA damage. PCNA and its modifications constitute a molecular switch to control distinct repair pathways. In yeast, SUMOylated PCNA (S-PCNA) recruits Srs2 to sites of replication where Srs2 can disrupt Rad51 filaments and prevent homologous recombination (HR). We report here an unexpected additional mechanism by which S-PCNA and Srs2 block the synthesis-dependent extension of a recombination intermediate, thus limiting its potentially hazardous resolution in association with a cross-over. This new Srs2 activity requires the SUMO interaction motif at its C-terminus, but neither its translocase activity nor its interaction with Rad51. Srs2 binding to S-PCNA dissociates Polδ and Polη from the repair synthesis machinery, thus revealing a novel regulatory mechanism controlling spontaneous genome rearrangements. Our results suggest that cycling cells use the Siz1-dependent SUMOylation of PCNA to limit the extension of repair synthesis during template switch or HR and attenuate reciprocal DNA strand exchanges to maintain genome stability. © 2013 European Molecular Biology Organization

Rad52 SUMOylation affects the efficiency of the DNA repair

Homologous recombination (HR) plays a vital role in DNA metabolic processes including meiosis, DNA repair, DNA replication and rDNA homeostasis. HR defects can lead to pathological outcomes, including genetic diseases and cancer. Recent studies suggest that the post-translational modification by the small ubiquitin-like modifier (SUMO) protein plays an important role in mitotic and meiotic recombination. However, the precise role of SUMOylation during recombination is still unclear. Here, we characterize the effect of SUMOylation on the biochemical properties of the Saccharomyces cerevisiae recombination mediator protein Rad52. Interestingly, Rad52 SUMOylation is enhanced by single-stranded DNA, and we show that SUMOylation of Rad52 also inhibits its DNA binding and annealing activities. The biochemical effects of SUMO modification in vitro are accompanied by a shorter duration of spontaneous Rad52 foci in vivo and a shift in spontaneous mitotic recombination from single-strand annealing to gene conversion events in the SUMO-deficient Rad52 mutants. Taken together, our results highlight the importance of Rad52 SUMOylation as part of a ‘quality control’ mechanism regulating the efficiency of recombination and DNA repair

CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation

CRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation

Space transfer vehicle concepts and requirements study, phase 2

This final report is a compilation of the Phase 1 and Phase 2 study findings and is intended as a Space Transfer Vehicle (STV) 'users guide' rather than an exhaustive explanation of STV design details. It provides a database for design choices in the general areas of basing, reusability, propulsion, and staging; with selection criteria based on cost, performance, available infrastructure, risk, and technology. The report is organized into the following three parts: (1) design guide; (2) STV Phase 1 Concepts and Requirements Study Summary; and (3) STV Phase 2 Concepts and Requirements Study Summary. The overall objectives of the STV study were to: (1) define preferred STV concepts capable of accommodating future exploration missions in a cost-effective manner; (2) determine the level of technology development required to perform these missions in the most cost effective manner; and (3) develop a decision database of programmatic approaches for the development of an STV concept

Molecular basis for PrimPol recruitment to replication forks by RPA

DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multi-functional replicative enzyme called Primase-Polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPolʼs recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPolʼs mode of recruitment to stalled forks to facilitate repriming and restart