Single-stranded DNA binding protein hitches a ride with the Escherichia coli YoaA-χ helicase.

The Escherichia coli XPD/Rad3-like helicase, YoaA, and DNA polymerase III subunit, χ, are involved in E. coli DNA damage tolerance and repair. YoaA and χ promote tolerance to the DNA chain-terminator, 3 -azidothymidine (AZT), and together form the functional helicase complex, YoaA-χ. How YoaA-χ contributes to DNA damage tolerance is not well understood. E. coli single-stranded DNA binding protein (SSB) accumulates at stalled replication forks, and the SSB-χ interaction is required to promote AZT tolerance via an unknown mechanism. YoaA-χ and SSB interactions were investigated in vitro to better understand this DNA damage tolerance mechanism, and we discovered YoaA-χ and SSB have a functional interaction. SSB confers a substrate-specific effect on the helicase activity of YoaA-χ, barely affecting YoaA-χ on an overhang DNA substrate but inhibiting YoaA-χ on forked DNA. A paralog helicase, DinG, unwinds SSB-bound DNA in a similar manner to YoaA-χ on the substrates tested. Through use of ensemble experiments, we believe SSB binds behind YoaA-χ relative to the DNA ds/ss junction and show via single-molecule assays that SSB translocates along ssDNA with YoaA-χ. This is, to our knowledge, the first demonstration of a mechanoenzyme pulling SSB along ssDNA.

Implementation of the Eat, Sleep, and Console Model of Care: A Quality Improvement Project.

A Southeastern, 741-bed acute care, Magnet designated teaching hospital and level III B NICU identified assessment and treatment concerns for Neonatal Opioid Withdrawal Syndrome (NOWS). In March 2020, a quality improvement project led to a multidisciplinary team formation to determine the effectiveness of the Eat, Sleep, Console (ESC) model of care in reducing the length of treatment (LOT) and length of stay (LOS) for neonates experiencing NOWS rather than use of the Finnegan Neonatal Abstinence Syndrome Scoring tool. The results concluded a decrease in the average LOT from 19.2 to 2.5 days and the average LOS from 23.9 to 9.3 days for those admitted directly into the ESC model of care on postpartum vs previous direct admission to the NICU. A group samples t-test showed there was a statistically significant decrease in LOS for ESC patients (p < .001) and LOT for ESC patients (p <001).

Improving Communication for Surgical Patients With Cancer With Limited English Proficiency.

Understanding disease processes, treatments, and special needs for surgical patients with cancer with limited English proficiency (LEP) can promote safe and accurate care. To ensure healthcare equity for patients at a large c.

Characterization of the Escherichia coli XPD/Rad3 iron-sulfur helicase YoaA in complex with the DNA polymerase III clamp loader subunit chi (χ).

Escherichia coli YoaA aids in the resolution of DNA damage that halts DNA synthesis in vivo in conjunction with χ, an accessory subunit of DNA polymerase III. YoaA and χ form a discrete complex separate from the DNA polymerase III holoenzyme, but little is known about how YoaA and χ work together to help the replication fork overcome damage. Although YoaA is predicted to be an iron-sulfur helicase in the XPD/Rad3 helicase family based on sequence analysis, the biochemical activities of YoaA have not been described. Here, we characterize YoaA and show that purified YoaA contains iron. YoaA and χ form a complex that is stable through three chromatographic steps, including gel filtration chromatography. When overexpressed in the absence of χ, YoaA is mostly insoluble. In addition, we show the YoaA-χ complex has DNA-dependent ATPase activity. Our measurement of the YoaA-χ helicase activity illustrates for the first time YoaA-χ translocates on ssDNA in the 5' to 3' direction and requires a 5' single-stranded overhang, or ssDNA gap, for DNA/DNA unwinding. Furthermore, YoaA-χ preferentially unwinds forked duplex DNA that contains both 3' and 5' single-stranded overhangs versus duplex DNA with only a 5' overhang. Finally, we demonstrate YoaA-χ can unwind damaged DNA that contains an abasic site or damage on 3' ends that stall replication extension. These results are the first biochemical evidence demonstrating YoaA is a bona fide iron-sulfur helicase, and we further propose the physiologically relevant form of the helicase is YoaA-χ.

The Escherichia coli clamp loader rapidly remodels SSB on DNA to load clamps.

Single-stranded DNA binding proteins (SSBs) avidly bind ssDNA and yet enzymes that need to act during DNA replication and repair are not generally impeded by SSB, and are often stimulated by SSB. Here, the effects of Escherichia coli SSB on the activities of the DNA polymerase processivity clamp loader were investigated. SSB enhances binding of the clamp loader to DNA by increasing the lifetime on DNA. Clamp loading was measured on DNA substrates that differed in length of ssDNA overhangs to permit SSB binding in different binding modes. Even though SSB binds DNA adjacent to single-stranded/double-stranded DNA junctions where clamps are loaded, the rate of clamp loading on DNA was not affected by SSB on any of the DNA substrates. Direct measurements of the relative timing of DNA-SSB remodeling and enzyme-DNA binding showed that the clamp loader rapidly remodels SSB on DNA such that SSB has little effect on DNA binding rates. However, when SSB was mutated to reduce protein-protein interactions with the clamp loader, clamp loading was inhibited by impeding binding of the clamp loader to DNA. Thus, protein-protein interactions between the clamp loader and SSB facilitate rapid DNA-SSB remodeling to allow rapid clamp loader-DNA binding and clamp loading.

Strategies in supporting inclusive education for autistic students-A systematic review of qualitative research results.

Background and Aim: Strategies to modify and adjust the educational setting in mainstream education for autistic students are under-researched. Hence, this review aims to identify qualitative research results of adaptation and modification strategies to support inclusive education for autistic students at school and classroom levels. Method: In this systematic review, four databases were searched. Following the preferred PRISMA approach, 108 studies met the inclusion criteria, and study characteristics were reported. Synthesis of key findings from included studies was conducted to provide a more comprehensive and holistic understanding. Main Contribution: This article provides insights into a complex area via aggregating findings from qualitative research a comprehensive understanding of the phenomena is presented. The results of the qualitative analysis indicate a focus on teachers' attitudes and students' social skills in research. Only 16 studies were at the classroom level, 89 were at the school level, and three studies were not categorized at either classroom or school level. A research gap was identified regarding studies focusing on the perspectives of autistic students, environmental adaptations to meet the students' sensitivity difficulties, and how to enhance the students' inclusion regarding content taught and knowledge development from a didactic perspective. Conclusions and Implications: Professional development that includes autism-specific understanding and strategies for adjusting and modifying to accommodate autistic students is essential. This conclusion may direct school leaders when implementing professional development programs. A special didactical perspective is needed to support teachers' understanding of challenges in instruction that autistic students may encounter.

Cellular and molecular characterization of two novel asparagine synthetase gene mutations linked to asparagine synthetase deficiency.

Asparagine synthetase (ASNS) catalyzes synthesis of asparagine (Asn) and Glu from Asp and Gln in an ATP-dependent reaction. Asparagine synthetase deficiency (ASNSD) results from biallelic mutations in the ASNS gene. Affected children exhibit congenital microcephaly, continued brain atrophy, seizures, and often premature mortality. However, the underlying mechanisms are unclear. This report describes a compound heterozygotic ASNSD child with two novel mutations in the ASNS gene, c.1118G>T (paternal) and c.1556G>A (maternal), that lead to G373V or R519H ASNS variants. Structural mapping suggested that neither variant participates directly in catalysis. Growth of cultured fibroblasts from either parent was unaffected in Asn-free medium, whereas growth of the child's cells was suppressed by about 50%. Analysis of Asn levels unexpectedly revealed that extracellular rather than intracellular Asn correlated with the reduced proliferation during incubation of the child's cells in Asn-free medium. Our attempts to ectopically express the G373V variant in either HEK293T or JRS cells resulted in minimal protein production, suggesting instability. Protein expression and purification from HEK293T cells revealed reduced activity for the R519H variant relative to WT ASNS. Expression of WT ASNS in ASNS-null JRS cells resulted in nearly complete rescue of growth in Asn-free medium, whereas we observed no proliferation for the cells expressing either the G373V or R519H variant. These results support the conclusion that the coexpression of the G373V and R519H ASNS variants leads to significantly reduced Asn synthesis, which negatively impacts cellular growth. These observations are consistent with the ASNSD phenotype.

Symptoms, Surgical Events, and Length of Stay of Surgical Oncology Outpatients.

PURPOSE: This study examined the incidence of postanesthesia symptoms, postoperative events, and length of stay (LOS) for surgical oncology outpatients in Phase II recovery during three time periods: before, one-month post, and one-year after the implementation of revised PACU I to PACU II transfer procedures and discharge criteria. DESIGN: Data for this retrospective analysis was obtained from the organizations' electronic medical records during the timeframe April 3, 2017 through August 5, 2018 after enhanced PACU I to PACU II transfer procedures were implemented on June 5, 2017. Records of surgical outpatients transferred from PACU I to PACU II who received regional pain control or preoperative anti-emetics were excluded from the analysis. METHODS: Study approval was obtained through the Institutional Review Board [#19-308]. The records [n = 1091] were sorted and analyzed according to symptoms, events, and length of recovery. Incidence of symptoms, use of IV fluids, and medications administered in PACU II was tabulated for each time-period. Kruskal-Wallis tests were used to detect differences in length of stay variables across the three time periods. FINDINGS: A significant decrease in PACU II LOS was observed following the implementation of revised PACU I to PACU II transfer criteria (P< .001). Although blood pressure changes decreased between each time period: 1.4% (T-1), 0.3% (T-2), and 0.2% (T-3), postanesthesia symptoms [dizziness, pain, and nausea] decreased from T-1 to T-2, with a small increase in T-3. The use of fentanyl and continuous IV fluids decreased between all time periods. CONCLUSIONS: Monitoring key variables related to patient outcomes involving LOS and symptom management ensures sustained practice changes, improves care, and optimizes surgical outpatient experience.

The SOS Error-Prone DNA Polymerase V Mutasome and ß-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis.

In the mid 1970s, Miroslav Radman and Evelyn Witkin proposed that Escherichia coli must encode a specialized error-prone DNA polymerase (pol) to account for the 100-fold increase in mutations accompanying induction of the SOS regulon. By the late 1980s, genetic studies showed that SOS mutagenesis required the presence of two "UV mutagenesis" genes, umuC and umuD, along with recA. Guided by the genetics, decades of biochemical studies have defined the predicted error-prone DNA polymerase as an activated complex of these three gene products, assembled as a mutasome, pol V Mut = UmuD'2C-RecA-ATP. Here, we explore the role of the ß-sliding processivity clamp on the efficiency of pol V Mut-catalyzed DNA synthesis on undamaged DNA and during translesion DNA synthesis (TLS). Primer elongation efficiencies and TLS were strongly enhanced in the presence of ß. The results suggest that ß may have two stabilizing roles: its canonical role in tethering the pol at a primer-3'-terminus, and a possible second role in inhibiting pol V Mut's ATPase to reduce the rate of mutasome-DNA dissociation. The identification of umuC, umuD, and recA homologs in numerous strains of pathogenic bacteria and plasmids will ensure the long and productive continuation of the genetic and biochemical journey initiated by Radman and Witkin.

Alternative complexes formed by the Escherichia coli clamp loader accessory protein HolC (x) with replication protein HolD (ψ) and repair protein YoaA.

Efficient and faithful replication of DNA is essential for all organisms. However, the replication fork frequently encounters barriers that need to be overcome to ensure cell survival and genetic stability. Cells must carefully balance and regulate replication vs. repair reactions. In Escherichia coli, the replisome consists of the DNA polymerase III holoenzyme, including DNA polymerase, proofreading exonuclease, processivity clamp and clamp loader, as well as a fork helicase, DnaB and primase, DnaG. We provide evidence here that one component of the clamp loader complex, HolC (or χ) plays a dual role via its ability to form 2 mutually exclusive complexes: one with HolD (or ψ) that recruits the clamp-loader and hence the DNA polymerase holoenzyme and another with helicase-like YoaA protein, a DNA-damage inducible repair protein. By yeast 2 hybrid analysis, we show that two residues of HolC, F64 and W57, at the interface in the structure with HolD, are required for interaction with HolD and for interaction with YoaA. Mutation of these residues does not interfere with HolC's interaction with single-strand DNA binding protein, SSB. In vivo, these mutations fail to complement the poor growth and sensitivity to azidothymidine, a chain-terminating replication inhibitor. In support of the notion that these are exclusive complexes, co-expression of HolC, HolD and YoaA, followed by pulldown of YoaA, yields a complex with HolC but not HolD. YoaA fails to pulldown HolC-F64A. We hypothesize that HolC, by binding with SSB, can recruit the DNA polymerase III holoenzyme through HolD, or an alternative repair complex with YoaA helicase.

Professional Development for Enhancing Autism Spectrum Disorder Awareness in Preschool Professionals.

The current study describes the design, implementation, and analysis of a professional development programme using a Lesson Study model to enhance awareness in preschool professionals regarding inclusive education for children with autism spectrum disorder. The mixed method approach included pre- and post-intervention questionnaires, audio-recordings of group seminars, and an interview. The results indicated an increase in autism awareness among the professionals, suggesting that professionals changed their practice as a result of the programme. This was particularly clear regarding making adjustments to the learning environment and taking measures to prevent challenging situations. In addition to describing the implementation of a professional development programme in a preschool, this paper emphasises the importance of appropriate conditions for such initiatives.

Potassium Glutamate and Glycine Betaine Induce Self-Assembly of the PCNA and ß-Sliding Clamps.

Sliding clamps are oligomeric ring-shaped proteins that increase the efficiency of DNA replication. The stability of the Escherichia coli ß-clamp, a homodimer, is particularly remarkable. The dissociation equilibrium constant of the ß-clamp is of the order of 10 pM in buffers of moderate ionic strength. Coulombic electrostatic interactions have been shown to contribute to this remarkable stability. Increasing NaCl concentration in the assay buffer results in decreased dimer stability and faster subunit dissociation kinetics in a way consistent with simple charge-screening models. Here, we examine non-Coulombic ionic effects on the oligomerization properties of sliding clamps. We determined relative diffusion coefficients of two sliding clamps using fluorescence correlation spectroscopy. Replacing NaCl by KGlu, the primary cytoplasmic salt in E. coli, results in a decrease of the diffusion coefficient of these proteins consistent with the formation of protein assemblies. The UV-vis spectrum of the ß-clamp labeled with tetramethylrhodamine shows the characteristic absorption band of dimers of rhodamine when KGlu is present in the buffer. This suggests that KGlu induces the formation of assemblies that involve two or more rings stacked face-to-face. Results can be quantitatively explained on the basis of unfavorable interactions between KGlu and the functional groups on the protein surface, which drive biomolecular processes that bury exposed surface. Similar results were obtained with the Saccharomyces cerevisiae PCNA sliding clamp, suggesting that KGlu effects are not specific to the ß-clamp. Clamp association is also promoted by glycine betaine, a zwitterionic compound that accumulates intracellularly when E. coli is exposed to high concentrations of extracellular solute. Possible biological implications are discussed.

Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.

Protein functional constraints are manifest as superfamily and functional-subgroup conserved residues, and as pairwise correlations. Deep Analysis of Residue Constraints (DARC) aids the visualization of these constraints, characterizes how they correlate with each other and with structure, and estimates statistical significance. This can identify determinants of protein functional specificity, as we illustrate for bacterial DNA clamp loader ATPases. These load ring-shaped sliding clamps onto DNA to keep polymerase attached during replication and contain one δ, three γ, and one δ' AAA+ subunits semi-circularly arranged in the order δ-γ1-γ2-γ3-δ'. Only γ is active, though both γ and δ' functionally influence an adjacent γ subunit. DARC identifies, as functionally-congruent features linking allosterically the ATP, DNA, and clamp binding sites: residues distinctive of γ and of γ/δ' that mutually interact in trans, centered on the catalytic base; several γ/δ'-residues and six γ/δ'-covariant residue pairs within the DNA binding N-termini of helices α2 and α3; and γ/δ'-residues associated with the α2 C-terminus and the clamp-binding loop. Most notable is a trans-acting γ/δ' hydroxyl group that 99% of other AAA+ proteins lack. Mutation of this hydroxyl to a methyl group impedes clamp binding and opening, DNA binding, and ATP hydrolysis-implying a remarkably clamp-loader-specific function.

Investigation of the Possible Pharmacologically Active Forms of the Nicotinic Acetylcholine Receptor Agonist Anabaseine.

Three major forms of the nicotinic agonist toxin anabaseine (cyclic iminium, cyclic imine and the monocationic open-chain ammonium-ketone) co-exist in almost equal concentrations at physiological pH. We asked the question: Which of these forms is pharmacologically active? First, we investigated the pH dependence of anabaseine inhibition of [3H]-methylcarbamylcholine binding at rat brain α4ß2 nicotinic acetylcholine receptors (nAChRs). These experiments indicated that one or both monocationic forms interact with the orthosteric binding site for ACh. However, since they occur at equal concentrations near physiological pH, we employed another approach, preparing a stable analog of each form and examining its agonist activities and binding affinities at several vertebrate brain and neuromuscular nAChRs. Only 2-(3-pyridyl)-1,4,5,6-tetrahydropyrimidine monohydrogen chloride (PTHP), the cyclic iminium analog, displayed nAChR potencies and binding affinities similar to anabaseine. The cyclic imine analog 2,3'-bipyridyl and the open-chain ammonium-ketone analog 5-methylamino-1-(3-pyridyl)-1-pentanone (MAPP), displayed ≤1% of the activity predicted if the one form was solely active. The lower potency of weakly basic 2,3'-bipyridyl can be explained by the presence of a small concentration of its monocationic form. Since the open chain ammonium-ketone monocationic form of anabaseine has some structural similarity to the neurotransmitter GABA, we also tested the ability of anabaseine and its 1,2-dehydropyrrolidinyl analog myosmine to activate a mammalian GABAA receptor, but no activity was detected. We conclude that the monocationic cyclic iminium is the form which avidly binds and activates vertebrate nAChRs.

Secretory granule protein chromogranin B (CHGB) forms an anion channel in membranes.

Regulated secretion is an intracellular pathway that is highly conserved from protists to humans. Granin family proteins were proposed to participate in the biogenesis, maturation and release of secretory granules in this pathway. However, the exact molecular mechanisms underlying the intracellular functions of the granin family proteins remain unclear. Here, we show that chromogranin B (CHGB), a secretory granule protein, inserts itself into membrane and forms a chloride-conducting channel. CHGB interacts strongly with phospholipid membranes through two amphipathic α helices. At a high local concentration, CHGB insertion in membrane causes significant bilayer remodeling, producing protein-coated nanoparticles and nanotubules. Fast kinetics and high cooperativity for anion efflux from CHGB vesicles suggest that CHGB tetramerizes to form a functional channel with a single-channel conductance of ∼125 pS (150/150 mM Cl-). The CHGB channel is sensitive to an anion channel blocker and exhibits higher anion selectivity than the other six known families of Cl- channels. Our data suggest that the CHGB subfamily of granin proteins forms a new family of organelle chloride channels.

Photophysical characterization of interchromophoric interactions between rhodamine dyes conjugated to proteins.

Rhodamine dyes in aqueous solution form non-fluorescent dimers with a plane-to-plane stacking geometry (H-dimers). The self-quenching properties of these dimers have been exploited to probe the conformation and dynamics of proteins using a variety of fluorescence approaches that require the interpretation of fluorescence intensities, lifetimes and fluctuations. Here, we report on a systematic study of the photophysical properties of three rhodamine dyes (tetramethylrhodamine, Alexa 488 and Alexa 546) covalently bound to the E. coli sliding clamp (ß clamp) with emphasis on the properties of the H-dimers that form when the dimeric protein is labeled with one dye at each side of the dimer interface. Overall, results are consistent with an equilibrium between non-emissive dimers and unstacked monomers that experience efficient dynamic quenching Protein constructs labeled with tetramethylrhodamine show the characteristic features of H-dimers in their absorption spectra and a c.a. 40-fold quenching of fluorescence intensity. The degree of quenching decreases when samples are labeled with a tetramethylrhodamine derivative bearing a six-carbon linker. H-dimers do not form in samples labeled with Alexa 488 and A546, but fluorescence is still quenched in these samples through a dynamic mechanism. These results should help researchers design and interpret fluorescence experiments that take advantage of the properties of rhodamine dimers in protein research.

Mechanism of opening a sliding clamp.

Clamp loaders load ring-shaped sliding clamps onto DNA where the clamps serve as processivity factors for DNA polymerases. In the first stage of clamp loading, clamp loaders bind and stabilize clamps in an open conformation, and in the second stage, clamp loaders place the open clamps around DNA so that the clamps encircle DNA. Here, the mechanism of the initial clamp opening stage is investigated. Mutations were introduced into the Escherichia coli ß-sliding clamp that destabilize the dimer interface to determine whether the formation of an open clamp loader-clamp complex is dependent on spontaneous clamp opening events. In other work, we showed that mutation of a positively charged Arg residue at the ß-dimer interface and high NaCl concentrations destabilize the clamp, but neither facilitates the formation of an open clamp loader-clamp complex in experiments presented here. Clamp opening reactions could be fit to a minimal three-step 'bind-open-lock' model in which the clamp loader binds a closed clamp, the clamp opens, and subsequent conformational rearrangements 'lock' the clamp loader-clamp complex in a stable open conformation. Our results support a model in which the E. coli clamp loader actively opens the ß-sliding clamp.

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli ß Sliding Clamp.

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli ß-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the ß-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states.

Solution structure of an "open" E. coli Pol III clamp loader sliding clamp complex.

Sliding clamps are opened and loaded onto primer template junctions by clamp loaders, and once loaded on DNA, confer processivity to replicative polymerases. Previously determined crystal structures of eukaryotic and T4 clamp loader-clamp complexes have captured the sliding clamps in either closed or only partially open interface conformations. In these solution structure studies, we have captured for the first time the clamp loader-sliding clamp complex from Escherichia coli using size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS). The data suggests the sliding clamp is in an open conformation which is wide enough to permit duplex DNA binding. The data also provides information about spatial arrangement of the sliding clamp with respect to the clamp loader subunits and is compared to complex crystal structures determined from other organisms.

Solution study of the Escherichia coli DNA polymerase III clamp loader reveals the location of the dynamic ψχ heterodimer.

Several X-ray crystal structures of the E. coli core clamp loader containing the five core (δ', δ, and three truncated γ) subunits have been determined, but they lack the ψ and χ subunits. We report the first solution structure of the complete seven-subunit clamp loader complex using small angle X-ray scattering. This structure not only provides information about the location of the χ and ψ subunits but also provides a model of the dynamic nature of the clamp loader complex.