In and out of the Replication Factory

In this issue of Cell, Kitamura et al. (2006) use live-fluorescence microscopy to monitor individual genomic loci as they replicate in budding yeast. They confirm that DNA is recruited to replication factories and show that sister replication forks initiated from the same origin are held together within a single replication factory

Lyapunov Stability of First and Second Order GeCo and gBBKS Schemes

In this paper we investigate the stability properties of fixed points of the so-called gBBKS and GeCo methods, which belong to the class of non-standard schemes and preserve the positivity as well as all linear invariants of the underlying system of ordinary differential equations for any step size. The schemes are applied to general linear test equations and proven to be generated by $\mathcal C^1$-maps with locally Lipschitz continuous first derivatives. As a result, a recently developed stability theorem can be applied to investigate the Lyapunov stability of non-hyperbolic fixed points of the numerical method by analyzing the spectrum of the corresponding Jacobian of the generating map. In addition, if a fixed point is proven to be stable, the theorem guarantees the local convergence of the iterates towards it. In the case of first and second order gBBKS schemes the stability domain coincides with that of the underlying Runge--Kutta method. Furthermore, while the first order GeCo scheme converts steady states to stable fixed points for all step sizes and all linear test problems of finite size, the second order GeCo scheme has a bounded stability region for the considered test problems. Finally, all theoretical predictions from the stability analysis are validated numerically.Comment: 31 pages, 7 figure

Temporal separation of replication and recombination requires the intra-S checkpoint

In response to DNA damage and replication pausing, eukaryotes activate checkpoint pathways that prevent genomic instability by coordinating cell cycle progression with DNA repair. The intra-S-phase checkpoint has been proposed to protect stalled replication forks from pathological rearrangements that could result from unscheduled recombination. On the other hand, recombination may be needed to cope with either stalled forks or double-strand breaks resulting from hydroxyurea treatment. We have exploited fission yeast to elucidate the relationship between replication fork stalling, loading of replication and recombination proteins onto DNA, and the intra-S checkpoint. Here, we show that a functional recombination machinery is not essential for recovery from replication fork arrest and instead can lead to nonfunctional fork structures. We find that Rad22-containing foci are rare in S-phase cells, but peak in G2 phase cells after a perturbed S phase. Importantly, we find that the intra-S checkpoint is necessary to avoid aberrant strand-exchange events during a hydroxyurea block

Covalently Functionalized Sawdust for the Remediation of Phosphate from Agricultural Wastewater

Phosphate remediation from wastewater is rapidly becoming an ever more attractive process due to a combination of both the economic pressure of increasing phosphate scarcity and the environmental damage caused by untreated agricultural runoff. Ideally, remediated phosphate will be recoverable and would be able to be reused as fertilizer. Many different resins have been investigated, but due to the scale of the challenge, any feasible solution will involve the use of very inexpensive waste products as the solid support. Sawdust, functionalized with iron-binding ligands, is such a potential resin. Sawdust alone binds 0.3 g/kg of phosphate which is insufficient. Iron has a strong affinity for phosphate, making the formation of iron-phosphate bonds a promising avenue for the development of recyclable resins. Previously prepared iron-chitosan complexes bound 8.2 g/kg. However, as the price of chitosan has rapidly increased, alternatives are required. In this current study, the covalent modification of the sawdust using either carboxymethylcellulose-supported ligands, or direct functionalization of the sawdust can increase this to 40 g/kg using ethylene diamine as the iron-binding ligand. Binding decreases over repeated cycles of phosphate exposure and elution, but can be fully restored through regeneration using iron salts. The simple green synthesis of this material, and the iron-binding capability of the investigated ligands is discussed. These sawdust-based resins show promise as potential candidates for industrial-scale phosphate recovery efforts in the future

Perspective on Quantum Bubbles in Microgravity

Progress in understanding quantum systems has been driven by the exploration of the geometry, topology, and dimensionality of ultracold atomic systems. The NASA Cold Atom Laboratory (CAL) aboard the International Space Station has enabled the study of ultracold atomic bubbles, a terrestrially-inaccessible topology. Proof-of-principle bubble experiments have been performed on CAL with an rf-dressing technique; an alternate technique (dual-species interaction-driven bubbles) has also been proposed. Both techniques can drive discovery in the next decade of fundamental physics research in microgravity.Comment: 17 pages, 2 figure

Watch Me Play!: protocol for a feasibility study of a remotely delivered intervention to promote mental health resilience for children (ages 0–8) across UK early years and children’s services

Background: Half of mental health problems are established by the age of 14 years and 75% by 24 years. Early intervention and prevention of mental ill health are therefore vitally important. However, increased demand over recent years has meant that access to child mental health services is often restricted to those in severest need. Watch Me Play! (WMP) is an early intervention designed to support caregiver attunement and attention to the child to promote social-emotional well-being and thereby mental health resilience. Originally developed in the context of a local authority mental health service for children in care, it is now also delivered online as a low intensity, scalable, preventative intervention. Although WMP shows promise and is already used in some services, we do not yet know whether it is effective. Methods: A non-randomised single group feasibility study with embedded process evaluation. We propose to recruit up to 40 parents/carers of children aged 0–8 years who have been referred to early years and children’s services in the UK. WMP involves a parent watching the child play and talking to their child about their play (or for babies, observing and following signals) for up to 20 min per session. Some sessions are facilitated by a trained practitioner who provides prompts where necessary, gives feedback, and discusses the child’s play with the caregiver. Services will offer five facilitated sessions, and parents will be asked to do at least 10 additional sessions on their own with their child in a 5-week period. Feasibility outcomes examined are as follows: (i) recruitment, (ii) retention, (iii) adherence, (iv) fidelity of delivery, (v) barriers and facilitators of participation, (vi) intervention acceptability, (vii) description of usual care, and (viii) data collection procedures. Intervention mechanisms will be examined through qualitative interview data. Economic evaluation will be conducted estimating cost of the intervention and cost of service use for child and parents/carers quality-adjusted life years. Discussion: This study will address feasibility questions associated with progression to a future randomised trial of WMP. Trial registration: ISRCTN13644899. Registered on 14th April 2023

Cell Discovery / Cancer cell specific inhibition of Wnt/-catenin signaling by forced intracellular acidification

Use of the diabetes type II drug Metformin is associated with a moderately lowered risk of cancer incidence in numerous tumor entities. Studying the molecular changes associated with the tumor-suppressive action of Metformin we found that the oncogene SOX4, which is upregulated in solid tumors and associated with poor prognosis, was induced by Wnt/-catenin signaling and blocked by Metformin. Wnt signaling inhibition by Metformin was surprisingly specific for cancer cells. Unraveling the underlying specificity, we identified Metformin and other Mitochondrial Complex I (MCI) inhibitors as inducers of intracellular acidification in cancer cells. We demonstrated that acidification triggers the unfolded protein response to induce the global transcriptional repressor DDIT3, known to block Wnt signaling. Moreover, our results suggest that intracellular acidification universally inhibits Wnt signaling. Based on these findings, we combined MCI inhibitors with H+ ionophores, to escalate cancer cells into intracellular hyper-acidification and ATP depletion. This treatment lowered intracellular pH both in vitro and in a mouse xenograft tumor model, depleted cellular ATP, blocked Wnt signaling, downregulated SOX4, and strongly decreased stemness and viability of cancer cells. Importantly, the inhibition of Wnt signaling occurred downstream of -catenin, encouraging applications in treatment of cancers caused by APC and -catenin mutations.(VLID)270614

Anopheles gambiae PGRPLC-Mediated Defense against Bacteria Modulates Infections with Malaria Parasites

Recognition of peptidoglycan (PGN) is paramount for insect antibacterial defenses. In the fruit fly Drosophila melanogaster, the transmembrane PGN Recognition Protein LC (PGRP-LC) is a receptor of the Imd signaling pathway that is activated after infection with bacteria, mainly Gram-negative (Gram−). Here we demonstrate that bacterial infections of the malaria mosquito Anopheles gambiae are sensed by the orthologous PGRPLC protein which then activates a signaling pathway that involves the Rel/NF-κB transcription factor REL2. PGRPLC signaling leads to transcriptional induction of antimicrobial peptides at early stages of hemolymph infections with the Gram-positive (Gram+) bacterium Staphylococcus aureus, but a different signaling pathway might be used in infections with the Gram− bacterium Escherichia coli. The size of mosquito symbiotic bacteria populations and their dramatic proliferation after a bloodmeal, as well as intestinal bacterial infections, are also controlled by PGRPLC signaling. We show that this defense response modulates mosquito infection intensities with malaria parasites, both the rodent model parasite, Plasmodium berghei, and field isolates of the human parasite, Plasmodium falciparum. We propose that the tripartite interaction between mosquito microbial communities, PGRPLC-mediated antibacterial defense and infections with Plasmodium can be exploited in future interventions aiming to control malaria transmission. Molecular analysis and structural modeling provided mechanistic insights for the function of PGRPLC. Alternative splicing of PGRPLC transcripts produces three main isoforms, of which PGRPLC3 appears to have a key role in the resistance to bacteria and modulation of Plasmodium infections. Structural modeling indicates that PGRPLC3 is capable of binding monomeric PGN muropeptides but unable to initiate dimerization with other isoforms. A dual role of this isoform is hypothesized: it sequesters monomeric PGN dampening weak signals and locks other PGRPLC isoforms in binary immunostimulatory complexes further enhancing strong signals

Informed Conditioning on Clinical Covariates Increases Power in Case-Control Association Studies

Genetic case-control association studies often include data on clinical covariates, such as body mass index (BMI), smoking status, or age, that may modify the underlying genetic risk of case or control samples. For example, in type 2 diabetes, odds ratios for established variants estimated from low–BMI cases are larger than those estimated from high–BMI cases. An unanswered question is how to use this information to maximize statistical power in case-control studies that ascertain individuals on the basis of phenotype (case-control ascertainment) or phenotype and clinical covariates (case-control-covariate ascertainment). While current approaches improve power in studies with random ascertainment, they often lose power under case-control ascertainment and fail to capture available power increases under case-control-covariate ascertainment. We show that an informed conditioning approach, based on the liability threshold model with parameters informed by external epidemiological information, fully accounts for disease prevalence and non-random ascertainment of phenotype as well as covariates and provides a substantial increase in power while maintaining a properly controlled false-positive rate. Our method outperforms standard case-control association tests with or without covariates, tests of gene x covariate interaction, and previously proposed tests for dealing with covariates in ascertained data, with especially large improvements in the case of case-control-covariate ascertainment. We investigate empirical case-control studies of type 2 diabetes, prostate cancer, lung cancer, breast cancer, rheumatoid arthritis, age-related macular degeneration, and end-stage kidney disease over a total of 89,726 samples. In these datasets, informed conditioning outperforms logistic regression for 115 of the 157 known associated variants investigated (P-value = 1×10−9). The improvement varied across diseases with a 16% median increase in χ2 test statistics and a commensurate increase in power. This suggests that applying our method to existing and future association studies of these diseases may identify novel disease loci

A Mississippian black shale record of redox oscillation in the Craven Basin, UK

Early diagenetic redox oscillation processes have been rarely recognised in the ancient rock record but potentially exert an important control on mineral authigenesis, hydrocarbon prospectivity and supply of metals and/or reduced S as part of associated mineral systems. The upper unit of the Mississippian Bowland Shale Formation is a candidate record of diagenetic redox oscillation processes because it was deposited under a relatively high sediment accumulation rate linked to a large delta system, and under dominantly anoxic and intermittently sulphidic bottom-water conditions. In order to characterise the syngenetic and early diagenetic processes, sedimentological and geochemical data were integrated through the Upper Bowland Shale at three sites in the Craven Basin (Lancashire, UK). Organic matter (OM) comprises a mixture of Type II, II-S, II/III and III OM. ‘Redox zones’ are defined by patterns of Fe-speciation and redox-sensitive trace element enrichment and split into two groups. ‘Sulphidic’ zones (EUX, AN-III, AN-I and AN-IT) represent sediments deposited under conditions of at least intermittently active sulphate-reduction in bottom-waters. ‘Non-sulphidic’ zones (OX-RX, OX-F and OX) represent sediments deposited under non-sulphidic (oxic to ferruginous anoxic) bottom-waters. Operation of a shelf-to-basin ‘reactive Fe’ (FeHR) shuttle, moderated by sea level fluctuation and delta proximity, controlled the position and stability of redoxclines between zones of Fe and sulphate reduction, and methanogenesis. Early diagenetic redoxclines were capable of migration through the shallow sediment column relatively quickly, in response to sea level fluctuation. Preservation of syngenetic and early diagenetic geochemical signals shows redoxclines between Fe and sulphate reduction, and the upper boundary of sulphate-methane transition zone, were positioned within decimetres (i.e., 10 s cm) of seabed. Falling sea level and increasing FeHR supply is recognised as a switch from zones EUX (high sea level), AN-III and ultimately AN-I and AN-IT (low sea level). Zone AN-I defines the operation of ‘redox oscillation’, between zones of Fe and sulphate reduction in shallow porewaters, associated with enhanced degradation of OM and complete dissolution of primary carbonate. Preservation of OM and carbonate, in this system, was a function of changing bottom and pore water redox processes. Redox oscillation operated in a siliciclastic, prodeltaic environment associated with a relatively high sediment accumulation rate and high loadings of labile organic matter and metal oxides. These findings are important for understanding Late Palaeozoic black shales in the context of hydrocarbon and mineral systems