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1.
Nucleic Acids Res ; 2024 Apr 13.
Article in English | MEDLINE | ID: mdl-38613387

ABSTRACT

Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.

2.
bioRxiv ; 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38105973

ABSTRACT

Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.

3.
Front Digit Health ; 5: 1183319, 2023.
Article in English | MEDLINE | ID: mdl-37560198

ABSTRACT

Background: Adolescence is a vulnerable developmental period, characterized by high rates of mental health concerns, yet few adolescents receive treatment. Public libraries support adolescents by providing them with access to teen programming, technological resources, and have recently been providing mental health services. Digital mental health (DMH) services may help libraries provide scalable mental health solutions for their adolescent patrons and could be well positioned to address the mental health needs of historically underrepresented racial and ethnic (HURE) adolescents; however, little research has been conducted on the compatibility of DMH services with adolescent patron mental health needs or resource needs of library workers supporting them. Methods: The research team formed a partnership with a public library, which serves a large HURE adolescent population. We conducted needs assessment and implementation readiness interviews with 17 library workers, including leadership, librarians, and workers with specialized areas of practice. Interview questions focused on library infrastructure, as well as library needs and preferences around the design and implementation of DMH services for adolescents. We used the Consolidated Framework for Implementation Research as guiding implementation determinant framework to code and analyze the interview transcripts. Results: Our findings revealed library workers play an important role in guiding patrons to desired resources and share a goal of implementing adolescent DMH resources into the library and elevating marginalized adolescents' voices. Existing library resources, such as the library's role as a safe space for adolescents in the community, close relationships with external and community organizations, and availability of no-cost technological resources, could help facilitate the implementation of DMH services. Barriers related to community buy-in, mental health stigma, and library worker confidence in supporting adolescent mental health could affect service implementation. Conclusions: Our findings suggest public libraries are highly promising settings to deploy DMH services for adolescents. We identified important determinants that may impact the implementation of DMH services in public library settings. Special considerations are needed to design services to meet the mental health needs of HURE adolescent populations and those adolescents' most experiencing health inequities.

4.
J Exp Med ; 220(9)2023 09 04.
Article in English | MEDLINE | ID: mdl-37382893

ABSTRACT

Mucosal-associated invariant T (MAIT) cells use canonical semi-invariant T cell receptors (TCR) to recognize microbial riboflavin precursors displayed by the antigen-presenting molecule MR1. The extent of MAIT TCR crossreactivity toward physiological, microbially unrelated antigens remains underexplored. We describe MAIT TCRs endowed with MR1-dependent reactivity to tumor and healthy cells in the absence of microbial metabolites. MAIT cells bearing TCRs crossreactive toward self are rare but commonly found within healthy donors and display T-helper-like functions in vitro. Experiments with MR1-tetramers loaded with distinct ligands revealed significant crossreactivity among MAIT TCRs both ex vivo and upon in vitro expansion. A canonical MAIT TCR was selected on the basis of extremely promiscuous MR1 recognition. Structural and molecular dynamic analyses associated promiscuity to unique TCRß-chain features that were enriched within self-reactive MAIT cells of healthy individuals. Thus, self-reactive recognition of MR1 represents a functionally relevant indication of MAIT TCR crossreactivity, suggesting a potentially broader role of MAIT cells in immune homeostasis and diseases, beyond microbial immunosurveillance.


Subject(s)
Mucosal-Associated Invariant T Cells , Humans , Cell Membrane , Cell Communication , Cross Reactions , DNA Repair , Histocompatibility Antigens Class I , Minor Histocompatibility Antigens
5.
Animals (Basel) ; 13(6)2023 Mar 10.
Article in English | MEDLINE | ID: mdl-36978554

ABSTRACT

Domestic cats (Felis catus) are amongst the most destructive invasive vertebrates globally, depredating billions of native animals annually. The size and seasonal variation of their geographical "footprint" is key to understanding their effects on wildlife, particularly if they live near conservation areas. Here we report the first GPS-tracking studies of free-roaming owned cats in the city of Cape Town, South Africa. A total of 23 cats was tracked (14 cats in summer, 9 in winter) using miniature (22 g) GPS locators in 2010-2011. In summer, all cats living on the urban-edge (UE: n = 7) made extensive use of protected areas, while only one of seven urban (U) cats (>150 m from the edge) did so. In winter two of four UE and two of five U cats entered protected areas. Home ranges (95% kernel density estimates) were significantly larger in summer (3.00 ± 1.23 ha) than winter (0.87 ± 0.25 ha) and cats ventured further from their homes in summer (maximum 849 m) than in winter (max 298 m). The predation risk posed by caracal (Caracal caracal) may limit the time cats spend in protected areas, but our results suggest that cat buffers around conservation areas should be at least ~600 m wide to reduce impacts to native fauna.

6.
Methods Enzymol ; 673: 169-190, 2022.
Article in English | MEDLINE | ID: mdl-35965006

ABSTRACT

DNA helicases are involved in nearly all facets of genome integrity, and in humans, mutations in helicase-encoding genes are often linked to diseases of genomic instability. Two highly studied and evolutionarily conserved helicase families are the PIF1 and RecQ helicases. Enzymes in these families have known roles in DNA replication, recombination, and repair, as well as telomere maintenance, DNA recombination, and transcription. Although genetics, structural biology, and a variety of other techniques have been used to study these helicases, ensemble analyses of their basic biochemical activities such as DNA binding, ATP hydrolysis, and DNA unwinding have made significant contributions to our understanding of their physiological roles. Here, we present general methods to generate recombinant proteins from both helicase families, as well as standard biochemical assays to investigate their activities on DNA.


Subject(s)
DNA Replication , RecQ Helicases , DNA , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Repair , Genomic Instability , Humans , RecQ Helicases/genetics , RecQ Helicases/metabolism
7.
R Soc Open Sci ; 9(2): 220043, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35223069

ABSTRACT

As the demand for carbon-neutral energy sources increases, so does the need to understand the impacts that these technologies have on the environment. Here, we assess the potential consequences of additional mortality on an Endangered raptor recently exposed to wind farms for the first time, the Black Harrier Circus maurus, one of the world's rarest harriers. We conduct a population viability assessment using a Bayesian model integrating life-history information and annual reporting rates from detection/non-detection surveys from the South African Bird Atlas Project. Our model estimates a global population of approximately 1300 birds currently declining at 2.3% per year, and one that could collapse in under 100 years, if an average of three to five adult birds are killed annually. This level of mortality may soon exist, given the current rate of fatalities and the number of wind farms planned within the species' distribution. In addition, we find that the population is sensitive to changes in climate. Our results highlight the critical need for appropriate placement, and adaptive management of wind farms and other infrastructure causing harrier mortality. We also show how detection/non-detection data may be used to infer population dynamics and viability, when population counts are unavailable.

8.
Curr Genet ; 67(5): 761-767, 2021 Oct.
Article in English | MEDLINE | ID: mdl-33961099

ABSTRACT

RecQ family helicases are found in all domains of life and play roles in multiple processes that underpin genomic integrity. As such, they are often referred to as guardians or caretakers of the genome. Despite their importance, however, there is still much we do not know about their basic functions in vivo, nor do we fully understand how they interact in organisms that encode more than one RecQ family member. We recently took a multi-omics approach to better understand the Saccharomyces cerevisiae Hrq1 helicase and its interaction with Sgs1, with these enzymes being the functional homologs of the disease-linked RECQL4 and BLM helicases, respectively. Using synthetic genetic array analyses, immuno-precipitation coupled to mass spectrometry, and RNA-seq, we found that Hrq1 and Sgs1 likely participate in many pathways outside of the canonical DNA recombination and repair functions for which they are already known. For instance, connections to transcription, ribosome biogenesis, and chromatin/chromosome organization were uncovered. These recent results are briefly detailed with respect to current knowledge in the field, and possible follow-up experiments are suggested. In this way, we hope to gain a wholistic understanding of these RecQ helicases and how their mutation leads to genomic instability.


Subject(s)
RecQ Helicases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Immunoprecipitation , Mass Spectrometry , RNA-Seq , RecQ Helicases/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics
9.
Eur J Health Econ ; 21(9): 1399-1410, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32930894

ABSTRACT

OBJECTIVES: We analyze the impact of the positioning of shifts (morning, afternoon, night) on worker absenteeism in a large German automobile plant. METHODS: Using a completely balanced panel of 153 organizational units over the 2-year-period 2009 to 2010 (i.e. 104 consecutive weeks with 15,912 unit-week-observations) we estimate a series of GLM and Fixed Effects models. RESULTS: Our main finding is that during afternoon shifts absence rates are significantly higher than during either morning or night shifts and that absence rates are particularly high during the afternoon shift immediately following the 3 weeks of consecutive night shifts. We attribute our first finding to the "social opportunity costs" of working and the second one to a "tax evasion effect". CONCLUSIONS: When designing new shift models, firms should try to anticipate their workers' reaction to avoid unintended incentives.


Subject(s)
Absenteeism , Models, Statistical , Work Schedule Tolerance , Automobiles , Germany , Humans , Time Factors
10.
ACS Infect Dis ; 5(10): 1688-1692, 2019 10 11.
Article in English | MEDLINE | ID: mdl-31478369

ABSTRACT

Monobactam antibiotic 1 is active against Gram-negative bacteria even though it has a higher molecular weight (MW) than the limit of 600 Da typically applied in designing such compounds. On the basis of 2D NMR data, the compound is able to adopt a compact conformation. The dimensions, projection area, and dipole moment derived from this conformation are compatible with porin permeation, as are locations of polar groups upon superimposition to the crystal structure of ampicillin bound to E. coli OmpF porin. Minimum inhibitory concentration (MIC) shifts in a porin knock-out strain are also consistent with 1 predominately permeating through porins. In conclusion, we describe a carefully characterized case of a molecule outside default design parameters where MW does not adequately represent the 3D shape more directly related to permeability. Leveraging 3D design criteria would open up additional chemical space currently underutilized due to limitations perceived in 2D.


Subject(s)
Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Gram-Negative Bacteria/drug effects , Monobactams/chemistry , Monobactams/pharmacology , Escherichia coli/drug effects , Escherichia coli Proteins/drug effects , Hydrophobic and Hydrophilic Interactions , Microbial Sensitivity Tests , Models, Molecular , Molecular Conformation , Molecular Weight , Permeability , Porins
11.
ACS Chem Biol ; 14(6): 1217-1226, 2019 06 21.
Article in English | MEDLINE | ID: mdl-31184469

ABSTRACT

Beta-lactams comprise one of the earliest classes of antibiotic therapies. These molecules covalently inhibit enzymes from the family of penicillin-binding proteins (PBPs), which are essential in construction of the bacterial cell wall. As a result, beta-lactams cause striking changes to cellular morphology, the nature of which varies by the range of PBPs simultaneously engaged in the cell. The traditional method of exploring beta-lactam polyspecificity is a gel-based binding assay which is low-throughput and typically is run  ex situ in cell extracts. Here, we describe a medium-throughput, image-based assay combined with machine learning methods to automatically profile the activity of beta-lactams in E. coli cells. By testing for morphological change across a panel of strains with perturbations to individual PBP enzymes, our approach automatically and quantifiably relates different beta-lactam antibiotics according to their preferences for individual PBPs in cells. We show the potential of our approach for guiding the design of novel inhibitors toward different PBP-binding profiles by predicting the mechanisms of two recently reported PBP inhibitors.


Subject(s)
Anti-Bacterial Agents/pharmacology , Escherichia coli/drug effects , beta-Lactams/pharmacology , Escherichia coli/metabolism , Machine Learning , Markov Chains , Microbial Sensitivity Tests , Penicillin-Binding Proteins/metabolism
12.
ACS Infect Dis ; 5(7): 1045-1051, 2019 07 12.
Article in English | MEDLINE | ID: mdl-30861342

ABSTRACT

Resistance in Gram-negative bacteria to ß-lactam drugs is mediated primarily by the expression of ß-lactamases, and co-dosing of ß-lactams with a ß-lactamase inhibitor (BLI) is a clinically proven strategy to address resistance. New ß-lactamases that are not impacted by existing BLIs are spreading and creating the need for development of novel broader spectrum BLIs. IID572 is a novel broad spectrum BLI of the diazabicyclooctane (DBO) class that is able to restore the antibacterial activity of piperacillin against piperacillin/tazobactam-resistant clinical isolates. IID572 is differentiated from other DBOs by its broad inhibition of ß-lactamases and the lack of intrinsic antibacterial activity.


Subject(s)
Azabicyclo Compounds/chemical synthesis , Gram-Negative Bacteria/drug effects , beta-Lactamase Inhibitors/chemical synthesis , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Azabicyclo Compounds/chemistry , Azabicyclo Compounds/pharmacology , Drug Resistance, Microbial/drug effects , Drug Stability , Gram-Negative Bacteria/enzymology , Microbial Sensitivity Tests , Molecular Structure , beta-Lactamase Inhibitors/chemistry , beta-Lactamase Inhibitors/pharmacology
13.
PLoS One ; 14(1): e0210756, 2019.
Article in English | MEDLINE | ID: mdl-30653592

ABSTRACT

Annual movements have been widely described for birds migrating across the Americas and between Eurasia and Africa, yet relatively little information exists for intra-African migrants. Identifying the areas used throughout a species annual cycle by understanding migratory patterns and settlement areas during breeding and non-breeding seasons is essential for conservation initiatives. Here, we describe for the first time, the migratory patterns and settlement areas of an endangered raptor endemic to Southern Africa, the Black Harrier (Circus maurus). From 2008 to 2015, thirteen breeding adult Black Harriers were trapped in south-western South Africa and fitted either with a GPS-GSM or with a PTT tracker device. Adults were monitored for 365 ± 198 days (range: 56-819 days) revealing great individual variability in annual movements. Most Black Harriers performed an unusual West-East migration from their breeding areas, but routes of all migrating individuals covered the entire southern land area of South Africa and Lesotho. The distance travelled averaged 814 ± 324 km, but unlike many other species, migrants travelled faster during post-breeding (i.e. austral summer) (207.8 ± 113.2 km.day-1) than during pre-breeding (i.e. austral winter/spring) migrations (143.8 ± 32.2 km.day-1). Although most marked individuals displayed movements similar to those that bred following pre-breeding migrations, only two of thirteen were confirmed as breeders the year after being tagged. This suggests that individuals may sometimes take a sabbatical year in reproduction, although this requires confirmation. Most tagged birds died on migration or during the non-breeding season. Adults frequently returned to the same non-breeding settlement areas, and often used up to 3 different locations an average of about 200 km apart. On the other hand, there was wide variation in distance between subsequent reproductive events. We discuss the implications of our study for the conservation of Black Harriers and more broadly for intra-African bird migrants.


Subject(s)
Animal Migration , Birds/physiology , Endangered Species , Animals , Breeding , Conservation of Natural Resources , Female , Geographic Information Systems , Lesotho , Male , Remote Sensing Technology , Reproduction , Seasons , South Africa
14.
ACS Infect Dis ; 5(3): 394-405, 2019 03 08.
Article in English | MEDLINE | ID: mdl-30624052

ABSTRACT

The Gram-negative bacterial permeability barrier, coupled with efflux, raises formidable challenges to antibiotic drug discovery. The absence of efficient assays to determine compound penetration into the cell and impact of efflux makes the process resource-intensive, small-scale, and lacking much success. Here, we present BacPK: a label-free, solid phase extraction-mass spectrometry (SPE-MS)-based assay that measures total cellular compound accumulation in Escherichia coli. The BacPK assay is a 96-well accumulation assay that takes advantage of 9 s/sample SPE-MS throughput. This enables the analysis of each compound in a four-point dose-response in isogenic strain pairs along with a no-cell control and 16-point external standard curve, all in triplicate. To validate the assay, differences in accumulation were examined for tetracycline (Tet) and two analogs, confirming that close analogs can differ greatly in accumulation. Tet cellular accumulation was also compared for isogenic strains exhibiting Tet resistance due to the expression of an efflux pump (TetA) or ribosomal protection protein (TetM), confirming only TetA affected cellular Tet accumulation. Finally, using a diverse set of antibacterial compounds, we confirmed the assay's ability to quantify differences in accumulation for isogenic strain pairs with efflux or permeability alterations that are consistent with differences in susceptibility seen for the compounds.


Subject(s)
Escherichia coli/chemistry , Escherichia coli/metabolism , High-Throughput Screening Assays/methods , Mass Spectrometry/methods , Solid Phase Extraction/methods , Tetracycline/chemistry , Tetracycline/isolation & purification , Tetracycline/metabolism
15.
Chemosphere ; 219: 58-65, 2019 Mar.
Article in English | MEDLINE | ID: mdl-30529854

ABSTRACT

Annually, sand and gravel processing generates approximately 20 million tonnes of non-commercial by-product as fine silt particles (<63 µm) which constitutes approximately 20% of quarry production in the UK. This study is significant as it investigated the use of quarry silt as a sub-soil medium to partially substitute soil-forming materials whilst facilitating successful post-restoration crop establishment. In a glasshouse pot experiment, top-soil and sub-soil layering was simulated, generating an artificial sub-soil medium by mixing two quarry non-commercial by-products, i.e. silt and overburden. These were blended in three ratios (100:0, 70:30, 50:50). Pots were packed to two bulk densities (1.3 and 1.5 g cm-3) and sown with three cover crops used in the early restoration process namely winter rye (Secale cereale), white mustard (Sinapis alba) and a grassland seed mixture (Lolium perenne, Phleum pratense, Poa pratensis, Festuca rubra). Three weeks into growth, the first signs of nitrogen (N) deficiency were observed in mustard plants, with phosphorus (P) and potassium (K) deficiencies observed at 35 days. Rye exhibited minor N deficiency symptoms four weeks into growth, whilst the grassland mixture showed no deficiency symptoms. The 70:30 silt:overburden sub-soil blend resulted in significantly higher Root Mass Densities of grassland seed mixture and rye in the sub-soil layer as compared with the other blends. The innovation in this work is the detailed physical, chemical and biological characterisation of silt:overburden blends and effects on root development of plants commonly used in early restoration to bio-engineer soil structural improvements.


Subject(s)
Environmental Restoration and Remediation/methods , Silicon Dioxide/pharmacology , Soil/chemistry , Crops, Agricultural/metabolism , Nitrogen/deficiency , Phosphorus/deficiency , Plant Roots/growth & development , Poaceae/metabolism , Potassium Deficiency , United Kingdom
16.
Biochemistry ; 58(6): 788-798, 2019 02 12.
Article in English | MEDLINE | ID: mdl-30507159

ABSTRACT

Pin1 is an essential peptidyl-prolyl isomerase (PPIase) that catalyzes cis-trans prolyl isomerization in proteins containing pSer/Thr-Pro motifs. It has an N-terminal WW domain that targets these motifs and a C-terminal PPIase domain that catalyzes isomerization. Recently, Pin1 was shown to modify the conformation of phosphorylated histone H1 and stabilize the chromatin-H1 interaction by increasing its residence time. This Pin1-histone H1 interaction plays a key role in pathogen response, in infection, and in cell cycle control; therefore, anti-Pin1 therapeutics are an important focus for treating infections as well as cancer. Each of the H1 histones (H1.0-H1.5) contains several potential Pin1 recognition pSer/pThr-Pro motifs. To understand the Pin1-histone H1 interaction fully, we investigated how both the isolated WW domain and full-length Pin1 interact with three H1 histone substrate peptide sequences that were previously identified as important binding partners (H1.1, H1.4, and H1.5). NMR spectroscopy was used to measure the binding affinities and the interdomain dynamics upon binding to these sequences. We observed different KD values depending on the histone binding site, suggesting that energetics play a role in guiding the Pin1-histone interaction. While interdomain interactions vary between the peptides, we find no evidence for allosteric activation for the histone H1 substrates.


Subject(s)
Histones/metabolism , NIMA-Interacting Peptidylprolyl Isomerase/metabolism , Peptide Fragments/metabolism , Allosteric Regulation , Amino Acid Sequence , Binding Sites , Histones/chemical synthesis , Histones/chemistry , Humans , Magnetic Resonance Spectroscopy , NIMA-Interacting Peptidylprolyl Isomerase/chemistry , Peptide Fragments/chemical synthesis , Peptide Fragments/chemistry , Protein Binding , Protein Domains , Sequence Alignment
17.
J Med Chem ; 61(20): 9360-9370, 2018 10 25.
Article in English | MEDLINE | ID: mdl-30226381

ABSTRACT

This report summarizes the identification and synthesis of novel LpxC inhibitors aided by computational methods that leveraged numerous crystal structures. This effort led to the identification of oxazolidinone and isoxazoline inhibitors with potent in vitro activity against P. aeruginosa and other Gram-negative bacteria. Representative compound 13f demonstrated efficacy against P. aeruginosa in a mouse neutropenic thigh infection model. The antibacterial activity against K. pneumoniae could be potentiated by Gram-positive antibiotics rifampicin (RIF) and vancomycin (VAN) in both in vitro and in vivo models.


Subject(s)
Amidohydrolases/antagonists & inhibitors , Isoxazoles/chemistry , Isoxazoles/pharmacology , Oxazolidinones/chemistry , Oxazolidinones/pharmacology , Animals , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Drug Evaluation, Preclinical , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Mice , Microbial Sensitivity Tests , Models, Molecular , Molecular Conformation
18.
Article in English | MEDLINE | ID: mdl-30061293

ABSTRACT

The monobactam scaffold is attractive for the development of new agents to treat infections caused by drug-resistant Gram-negative bacteria because it is stable to metallo-ß-lactamases (MBLs). However, the clinically used monobactam aztreonam lacks stability to serine ß-lactamases (SBLs) that are often coexpressed with MBLs. LYS228 is stable to MBLs and most SBLs. LYS228 bound purified Escherichia coli penicillin binding protein 3 (PBP3) similarly to aztreonam (derived acylation rate/equilibrium dissociation constant [k2/Kd ] of 367,504 s-1 M-1 and 409,229 s-1 M-1, respectively) according to stopped-flow fluorimetry. A gel-based assay showed that LYS228 bound mainly to E. coli PBP3, with weaker binding to PBP1a and PBP1b. Exposing E. coli cells to LYS228 caused filamentation consistent with impaired cell division. No single-step mutants were selected from 12 Enterobacteriaceae strains expressing different classes of ß-lactamases at 8× the MIC of LYS228 (frequency, <2.5 × 10-9). At 4× the MIC, mutants were selected from 2 of 12 strains at frequencies of 1.8 × 10-7 and 4.2 × 10-9 LYS228 MICs were ≤2 µg/ml against all mutants. These frequencies compared favorably to those for meropenem and tigecycline. Mutations decreasing LYS228 susceptibility occurred in ramR and cpxA (Klebsiella pneumoniae) and baeS (E. coli and K. pneumoniae). Susceptibility of E. coli ATCC 25922 to LYS228 decreased 256-fold (MIC, 0.125 to 32 µg/ml) after 20 serial passages. Mutants accumulated mutations in ftsI (encoding the target, PBP3), baeR, acrD, envZ, sucB, and rfaI These results support the continued development of LYS228, which is currently undergoing phase II clinical trials for complicated intraabdominal infection and complicated urinary tract infection (registered at ClinicalTrials.gov under identifiers NCT03377426 and NCT03354754).


Subject(s)
Anti-Bacterial Agents/pharmacology , Escherichia coli/enzymology , Escherichia coli/genetics , Klebsiella pneumoniae/enzymology , Klebsiella pneumoniae/genetics , Monobactams/pharmacology , Aztreonam/pharmacology , Enterobacteriaceae/drug effects , Enterobacteriaceae/enzymology , Enterobacteriaceae/genetics , Escherichia coli/drug effects , Klebsiella pneumoniae/drug effects , Microbial Sensitivity Tests , Mutation/genetics , beta-Lactamases/genetics
19.
Article in English | MEDLINE | ID: mdl-30038040

ABSTRACT

LYS228 is a novel monobactam with potent activity against Enterobacteriaceae LYS228 is stable to metallo-ß-lactamases (MBLs) and serine carbapenemases, including Klebsiella pneumoniae carbapenemases (KPCs), resulting in potency against the majority of extended-spectrum ß-lactamase (ESBL)-producing and carbapenem-resistant Enterobacteriaceae strains tested. Overall, LYS228 demonstrated potent activity against 271 Enterobacteriaceae strains, including multidrug-resistant isolates. Based on MIC90 values, LYS228 (MIC90, 1 µg/ml) was ≥32-fold more active against those strains than were aztreonam, ceftazidime, ceftazidime-avibactam, cefepime, and meropenem. The tigecycline MIC90 was 4 µg/ml against the strains tested. Against Enterobacteriaceae isolates expressing ESBLs (n = 37) or displaying carbapenem resistance (n = 77), LYS228 had MIC90 values of 1 and 4 µg/ml, respectively. LYS228 exhibited potent bactericidal activity, as indicated by low minimal bactericidal concentration (MBC) to MIC ratios (MBC/MIC ratios of ≤4) against 97.4% of the Enterobacteriaceae strains tested (264/271 strains). In time-kill studies, LYS228 consistently achieved reductions in CFU per milliliter of 3 log10 units (≥99.9% killing) at concentrations ≥4× MIC for Escherichia coli and K. pneumoniae reference strains, as well as isolates encoding TEM-1, SHV-1, CTX-M-14, CTX-M-15, KPC-2, KPC-3, and NDM-1 ß-lactamases.


Subject(s)
Anti-Bacterial Agents/pharmacology , Enterobacteriaceae/drug effects , Monobactams/pharmacology , Azabicyclo Compounds/pharmacology , Aztreonam/pharmacology , Cefepime/pharmacology , Ceftazidime/pharmacology , Drug Combinations , Drug Resistance, Multiple, Bacterial/genetics , Enterobacteriaceae/genetics , Meropenem/pharmacology , Microbial Sensitivity Tests , Tigecycline/pharmacology , beta-Lactamases/genetics
20.
J Hydrol (Amst) ; 556: 211-219, 2018 Jan.
Article in English | MEDLINE | ID: mdl-29332951

ABSTRACT

This study delivers new insights into rainfall-induced seal formation through a novel approach in the use of X-ray Computed Tomography (CT). Up to now seal and crust thickness have been directly quantified mainly through visual examination of sealed/crusted surfaces, and there has been no quantitative method to estimate this important property. X-ray CT images were quantitatively analysed to derive formal measures of seal and crust thickness. A factorial experiment was established in the laboratory using open-topped microcosms packed with soil. The factors investigated were soil type (three soils: silty clay loam - ZCL, sandy silt loam - SZL, sandy loam - SL) and rainfall duration (2-14 min). Surface seal formation was induced by applying artificial rainfall events, characterised by variable duration, but constant kinetic energy, intensity, and raindrop size distribution. Soil porosities derived from CT scans were used to quantify the thickness of the rainfall-induced surface seals and reveal temporal seal micro-morphological variations with increasing rainfall duration. In addition, the water repellency and infiltration dynamics of the developing seals were investigated by measuring water drop penetration time (WDPT) and unsaturated hydraulic conductivity (Kun). The range of seal thicknesses detected varied from 0.6 to 5.4 mm. Soil textural characteristics and OM content played a central role in the development of rainfall-induced seals, with coarser soil particles and lower OM content resulting in thicker seals. Two different trends in soil porosity vs. depth were identified: i) for SL soil porosity was lowest at the immediate soil surface, it then increased constantly with depth till the median porosity of undisturbed soil was equalled; ii) for ZCL and SL the highest reduction in porosity, as compared to the median porosity of undisturbed soil, was observed in a well-defined zone of maximum porosity reduction c. 0.24-0.48 mm below the soil surface. This contrasting behaviour was related to different dynamics and processes of seal formation which depended on the soil properties. The impact of rainfall-induced surface sealing on the hydrological behaviour of soil (as represented by WDTP and Kun) was rapid and substantial: an average 60% reduction in Kun occurred for all soils between 2 and 9 min rainfall, and water repellent surfaces were identified for SZL and ZCL. This highlights that the condition of the immediate surface of agricultural soils involving rainfall-induced structural seals has a strong impact in the overall ability of soil to function as water reservoir.

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