Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing

Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s−1 and a processivity of >10.5 kb at 25°C

Why 'scaffolding' is the wrong metaphor : the cognitive usefulness of mathematical representations.

The metaphor of scaffolding has become current in discussions of the cognitive help we get from artefacts, environmental affordances and each other. Consideration of mathematical tools and representations indicates that in these cases at least (and plausibly for others), scaffolding is the wrong picture, because scaffolding in good order is immobile, temporary and crude. Mathematical representations can be manipulated, are not temporary structures to aid development, and are refined. Reflection on examples from elementary algebra indicates that Menary is on the right track with his ‘enculturation’ view of mathematical cognition. Moreover, these examples allow us to elaborate his remarks on the uniqueness of mathematical representations and their role in the emergence of new thoughts.Peer reviewe

On the equivalence of strong formulations for capacitated multi-level lot sizing problems with setup times

Several mixed integer programming formulations have been proposed for modeling capacitated multi-level lot sizing problems with setup times. These formulations include the so-called facility location formulation, the shortest route formulation, and the inventory and lot sizing formulation with (l,S) inequalities. In this paper, we demonstrate the equivalence of these formulations when the integrality requirement is relaxed for any subset of binary setup decision variables. This equivalence has significant implications for decomposition-based methods since same optimal solution values are obtained no matter which formulation is used. In particular, we discuss the relax-and-fix method, a decomposition-based heuristic used for the efficient solution of hard lot sizing problems. Computational tests allow us to compare the effectiveness of different formulations using benchmark problems. The choice of formulation directly affects the required computational effort, and our results therefore provide guidelines on choosing an effective formulation during the development of heuristic-based solution procedures

Aggregation of Aqueous Kaolin Suspensions in the Presence of Cationic Polyelectrolytes, Anionic Polyelectrolytes and their Mixtures

The influence of anionic, cationic synthetic polyelectrolytes and their mixtures on the aggregation of kaolin hydrosuspension has been studied by means of spectrophotometry, electrophoresis and dynamic light scattering (DLS). An enhancement of the flocculating property of the cationic polyelectrolyte FO 4650 in accordance with its consumption increases from 0.77 mg/g to 7.7 mg/g has been found. At these conditions the relative size of floccules (R) increases from 1.0 to 13.0. The increase of the flocculating property accordingly to the increasing charge of anionic polyelectrolyte is observed in mixtures of cationic and anionic polyelectrolytes. The time dependences of R in presence of the weakly charged cationic polyelectrolyte mixtures reach a plateau region. This can be associated with the formation of electrostatic contacts between the solid surface and the polymer mixtures, as well as with stabilizing equilibrium conformation of macromolecules. It has been found that mixtures of oppositely charged polyelectrolytes lead to more efficient aggregation of particles than individual polyelectrolytes. This process is enhanced by the introduction primarily of the cationic polyelectrolyte and then the anionic one (R = 6‒10). Use of the preformulated mixtures of polymers leads to the marked increase in degree of particle aggregation (R = 12). The reason is an interaction of kaolin particles with inter-polymer complex formed by electrostatic attraction of oppositely charged polyelectrolytes

A computational analysis of lower bounds for big bucket production planning problems

In this paper, we analyze a variety of approaches to obtain lower bounds for multi-level production planning problems with big bucket capacities, i.e., problems in which multiple items compete for the same resources. We give an extensive survey of both known and new methods, and also establish relationships between some of these methods that, to our knowledge, have not been presented before. As will be highlighted, understanding the substructures of difficult problems provide crucial insights on why these problems are hard to solve, and this is addressed by a thorough analysis in the paper. We conclude with computational results on a variety of widely used test sets, and a discussion of future research

Novel glucose-lowering drugs and the risk of acute kidney injury in routine care: the Stockholm CREAtinine Measurements (SCREAM) project

Introduction Little is known about the comparative effects of sodium glucose cotransporter-2 inhibitors (SGLT2i), glucagon-like peptide-1 receptor agonists (GLP1-RA), or dipeptidyl peptidase-4 inhibitors (DPP-4i) on the risk of acute kidney injury (AKI) in routine care, which may differ from the controlled setting of trials.Methods Observational study comparing risks of AKI among new users of SGLT2i, GLP1-RA or DPP-4i in the region of Stockholm, Sweden, during 2008-2018. AKI was defined by ICD-10 codes and creatinine-based KDIGO criteria. We used inverse probability of treatment weighting (IPTW) to adjust for 60 potential confounders, weighted Kaplan-Meier curves and Cox regression to estimate hazard ratios and absolute risks.Results We included 17,407 participants who newly initiated DPP-4i (N = 10,605), GLP1-RA (N = 4448) or SGLT2i (N = 2354). Mean age was 63 years (39% women) and median (IQR) eGFR was 89 (73-100) ml/min/1.73 m(2). During a median follow-up of 2.5 years, 1411 participants experienced AKI. SGLT2i users had the lowest incidence rate of AKI, 18.3 [CI 95% 14.1-23.4] per 1000 person years, followed by GLP1-RA (22.5; 19.9-25.3) and DPP-4i (26.6; 25-28.2). The weighted 3-year absolute risk for AKI was 5.79% [3.63-8.52] in the SGLT2i group, compared with 7.03% [5.69-8.69] and 7.00% [6.43-7.58] in the GLP1-RA and DPP-4i groups, respectively. The adjusted hazard ratio was 0.73 [CI 95% 0.45-1.16] for SGLT2i vs. DPP-4i, and 0.98 [CI 95% 0.82-1.18] for GLP1-RA vs. DPP-4i.Conclusion This study of routine care patients initiating novel glucose-lowering drugs showed similar occurrence of AKI between therapies, and suggests lower risk for SGLT2i.Clinical epidemiolog

Corrigendum to ‘Dietary aflatoxin B1 (AFB1) reduces growth performance, impacting growth axis, metabolism, and tissue integrity in juvenile gilthead sea bream (Sparus aurata)’. Aquaculture, volume 533, 25 February 2021, 736189

The authors regret the errors in a few table references within the text. Specifically, it should reads as follows within the following subsections/ page: 3.2. Blood analysis (page 5)info:eu-repo/semantics/publishedVersio

Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection

This work is licensed under a Creative Commons Attribution 4.0 International License.Background Interrogation of site-specific CpG methylation in circulating tumor DNAs (ctDNAs) has been employed in a number of studies for early detection of breast cancer (BrCa). In many of these studies, the markers were identified based on known biology of BrCa progression, and interrogated using methyl-specific PCR (MSP), a technique involving bisulfite conversion, PCR, and qPCR. Methods In this report, we are demonstrating the development of a novel assay (Multiplex Bisulfite PCR-LDR-qPCR) which can potentially offer improvements to MSP, by integrating additional steps such as ligase detection reaction (LDR), methylated CpG target enrichment, carryover protection (use of uracil DNA glycosylase), and minimization of primer-dimer formation (use of ribose primers and RNAseH2). The assay is designed to for breast cancer-specific CpG markers identified through integrated analyses of publicly available genome-wide methylation datasets for 31 types of primary tumors (including BrCa), as well as matching normal tissues, and peripheral blood. Results Our results indicate that the PCR-LDR-qPCR assay is capable of detecting ~ 30 methylated copies of each of 3 BrCa-specific CpG markers, when mixed with excess amount unmethylated CpG markers (~ 3000 copies each), which is a reasonable approximation of BrCa ctDNA overwhelmed with peripheral blood cell-free DNA (cfDNA) when isolated from patient plasma. The bioinformatically-identified CpG markers are located in promoter regions of NR5A2 and PRKCB, and a non-coding region of chromosome 1 (upstream of EFNA3). Additional bioinformatic analyses would reveal that these methylation markers are independent of patient race and age, and positively associated with signaling pathways associated with BrCa progression (such as those related to retinoid nuclear receptor, PTEN, p53, pRB, and p27). Conclusion This report demonstrates the potential utilization of bisulfite PCR-LDR-qPCR assay, along with bioinformatically-driven biomarker discovery, in blood-based BrCa detection