20000 research outputs found
Sort by
scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs
No full textGlobal changes in DNA methylation are observed in development and disease, and single-cell analyses are highlighting the heterogeneous regulation of these processes. However, technical challenges associated with single-cell analysis of DNA methylation limit these studies. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of average DNA methylation levels. By targeting high-copy SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of loci covered in each scTEM-seq library. Parallel transcriptome analysis is also performed to link global DNA methylation estimates with gene expression. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary AML cells. Our method reveals global DNA methylation heterogeneity induced by decitabine treatment of KG1a cells associated with altered expression of immune process genes. We also compare global DNA methylation estimates to expression of transposable elements and find a predominance of negative correlations. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated cells. By linking global DNA methylation heterogeneity with transcription, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond
Testicular heat stress, a historical perspective and two postulates for why male germ cells are heat sensitive
No full textHerein, we compare the different experimental regimes used to induce testicular heat stress and summarise their impact on sperm production and male fertility. Irrespective of the protocol used, scrotal heat stress causes loss of sperm production. This is first seen 1–2 weeks post heat stress, peaking 4–5 weeks thereafter. The higher the temperature, or the longer the duration of heat, the more pronounced germ cell loss becomes, within extreme cases this leads to azoospermia. The second, and often underappreciated impact of testicular hyperthermia is the production of poor-quality spermatozoa. Typically, those cells that survive hyperthermia develop into morphologically abnormal and poorly motile spermatozoa. While both apoptotic and non-apoptotic pathways are known to contribute to hyperthermic germ cell loss, the mechanisms leading to formation of poor-quality sperm remain unclear. Mechanistically, it is unlikely that testicular hyperthermia affects messenger RNA (mRNA) abundance, as a comparison of four different mammalian studies shows no consistent single gene changes. Using available evidence, we propose two novel models to explain how testicular hyperthermia impairs sperm formation. Our first model suggests aberrant alternative splicing, while the second model proposes a loss of RNA repression. Importantly, neither model requires consistent changes in RNA species
A Survey on Enhanced Power Graphs of Finite Groups
No full textWe survey known results on enhanced power graphs of finite groups. Open problems, questions and suggestions for future work are also included
Type III polyketide biosynthesis in cyanobacteria
No full textType III polyketide synthases (PKSs) are small homodimeric enzymes responsible for the biosynthesis of a wide range of ecologically and industrially relevant compounds. They carry out the decarboxylative Clasien condensation of extender substrate molecules to a covalently bound starter substrate in an iterative way. Type III PKSs have mainly been studied in plants and heterotrophic bacteria. This thesis aimed to investigate the distribution and diversity of type III PKS biosynthesis pathways and products in cyanobacteria, photosynthetic bacteria renowned for their production of bioactive compounds. Phylogenetic analysis of type III PKS biosynthesis gene clusters from published cyanobacterial genomes showed that they have evolved into three distinct classes – one class similar to (7.7)paracyclophane-like biosynthesis gene clusters, one class similar to hierridin biosynthesis gene clusters and a novel class associated with cytochrome b5 genes. In silico structural analysis of representative protein models and previously elucidated crystal structurers showed distinct differences between bacterial, plant, fungal and cyanobacterial type III PKSs. Two novel type III PKS biosynthesis gene clusters were prioritized for further analysis; the 3.6 kb, four ORF rms gene cluster from Raphidiopsis mediterranea Skuja FSS1-150/1, which uniquely encodes a prenyltransferase, and the 26 kb 12 ORF mks cluster from Microcystis aeruginosa PCC 7806, a hybrid type I/III PKS gene cluster, inversely regulated to microcystin (hepatotoxin) biosynthesis. The type III PKS encoded within the rms cluster (RmsB) was heterologously expressed and purified to homogeneity for in vitro biochemical studies. The results showed that RmsB utilises long acyl-CoAs as substrates. Interestingly, mutagenesis of the active site residues did not abolish activity. Instead, the substrate specificity changed from myristoyl-CoA to decanoyl-CoA. This suggests that RmsB uses a different reaction mechanism to plant and bacterial type III PKSs. We subsequently cloned the entire rms cluster and heterologously expressed it in E. coli to investigate the metabolites being produced. LC-MS analysis showed that the engineered E. coli strain produces four novel compounds, including a prenylated herridin. The type III PKS encoded within the mks cluster (MksG), was heterologously expressed and purified to homogeneity for in vitro biochemical studies. The results showed that MksG can utilize a range of acyl-CoAs to produce diverse metabolites. Heterologous expression of the entire mks cluster in E. coli resulted in the production of multiple novel compounds, when analysed via HPLC, however, only two compounds could be identified by subsequent LC-MS analysis. One being a methyl-alkylresorcinol and the other being a proposed dimerisation of this compound. The process of 2 dimerisation is still unknown as the mks cluster does not contain the canonical genes for dimerisation. Overall, the results from this thesis have expanded knowledge of this understudied group of enzymes, including the distribution, diversity, structure, reaction mechanisms, substrate specificity, and reaction products of cyanobacterial type III PKSs from two distinct phylogenetic lineages. This knowledge can be used to drive the research within this field and to identify novel compounds of ecological and biotechnological relevance
Testing the acceptability of stillbirth awareness messages in an SMS program for fathers
No full textIssue addressed: To raise expectant fathers' awareness of risk factors for stillbirth. Methods: A set of brief text messages was developed addressing recognised risk factors for stillbirth: avoidance of maternal cigarette smoking, maternal going to sleep on side messaging, awareness of the importance of noticing and reporting changes in foetal movement and fathers' involvement in shared decision making for timing of birth. Eight messages were inserted into the SMS4dads pilot program being conducted by NSW Health. Feedback on the messages was requested. Participants rated the quality of the messages on a three-point Likert scale and provided comments. Results: Overall, 2528 messages were sent to 626 fathers' mobile phones, 45% of fathers replied with 666 ratings and 115 comments evaluating the texts. The quantitative ratings indicated substantial overall approval of the messages. Within the coding category “Evaluation of Message Content,” three themes described fathers' reactions and feelings about the smoking, movement, side sleeping and birth timing messages: “important-good information,” “not appropriate/anxiety provoking” and “not relevant-obvious.” Three themes reflecting the attributes of the messages within the “Service Quality” category were “need more information,” “complements public health” and “child voice fit.” Conclusions: Results indicate that the messages are an acceptable way to provide information and suggested actions addressing stillbirth risk factors to fathers-to-be. So what?: Fathers' awareness of the risk factors for stillbirth can assist mothers to take appropriate actions for a healthy birth. Information on risk factors can be provided to fathers via a father-focused text messaging service
Along‐orbit analysis of GRACE Follow‐On inter‐satellite laser ranging measurements for sub‐monthly surface mass variations
No full textWe examined the sensitivity of GRACE Follow-On (GRACE-FO) laser ranging interferometer (LRI) measurements to sub-monthly time-variable gravity (TVG) signals caused by transient, high-frequency mass changes in the Earth system. GRACE-FO LRI provides complementary inter-satellite ranging measurements with higher precision over a wider range of frequencies than the baseline K-band microwave ranging system. The common approach for studying mass variation relies on the inverted TVG or mascon solutions over a period of, for example, one month or 10 days which are adversely affected by temporal aliasing and/or smoothing. In this article, we present the alternative along-orbit analysis methodology in terms of line-of-sight gravity difference (LGD) to fully exploit the higher precision LRI measurements for examination of sub-monthly mass changes. The discrepancy between “instantaneous” LGD LRI observations and monthly-mean LGD (from Level-2 data) at satellite altitude indicates the sub-monthly gravitational variability not captured by monthly-mean solutions. In conjunction with the satellite ocean altimetry observations, high-frequency non-tidal atmosphere and ocean models, and hydrology models, we show that the LGD LRI observations detect the high-frequency oceanic mass variability in the Argentine Basin and the Gulf of Carpentaria, and sub-monthly variations in surface (river) water in the Amazon Basin. We demonstrate the benefits gained from repeat ground track analysis of GRACE-FO LRI data in the case of the Amazon surface water flow. The along-orbit analysis methodology based on LGD LRI time series presented here is especially suitable for quantifying temporal and spatial evolution of extreme, rapidly changing mass variations
What do we know about the experience of seclusion in a forensic setting? An integrative literature review
No full textSeclusion is used in forensic and general mental health settings to protect a person or others from harm. However, seclusion can result in trauma-related harm and re-traumatization with little known about the experience of seclusion for consumers in forensic mental health settings from their perspectives. This article explores consumer experiences of seclusion in forensic mental health settings and explores the differences between female and male experiences of seclusion. Five electronic databases were systematically searched using keywords and variations of experience, attitude, seclusion, coercion, forensic mental health, and forensic psychiatry. Inclusion criteria were original peer-reviewed studies conducted in adult forensic mental health settings reporting data on the experiences of or attitudes towards seclusion. Seven studies met the criteria for inclusion and a quality assessment was undertaken. Results found consumers in forensic mental health settings perceive seclusion to be harmful, a punishment for their behaviour, and largely a negative experience that impacts their emotional health. Some consumers report positive experiences of seclusion. Differences in the experience of seclusion for females and males are unclear. Further research is required to understand the experience of seclusion for women in forensic mental health settings. Identification and consideration of differences in the experience of seclusion for males and females may assist in identifying sex-specific interventions and may inform policy and practices to eliminate or reduce the trauma associated with seclusion use
Investigating myotoxicity following Australian red-bellied black snake (Pseudechis porphyriacus) envenomation
No full textBackground: Myotoxicity is one of the common clinical manifestations of red-bellied black snake (Pseudechis porphyriacus) envenomation characterised by elevated creatine kinase (CK) concentrations of greater than 1000 U/L. This study aimed to investigate the occurrence of myotoxicity in patients following envenomation. Methods/Principal findings: Patient characteristics and serial blood samples (timed venom concentrations and CK concentrations, pre- and post- antivenom) from 114 patients (median age 41, 2-90y; 80 male) were extracted from the Australian Snakebite Project database. Patients were categorised into three groups based on peak CK concentrations [no myotoxicity (10,000 U/L)]. The odds of (mild or severe) myotoxicity was lower in patients that received early antivenom (within 6 hours post-bite) compared to those that received late or no antivenom (odd ratio was 0.186; 95% confidence interval, 0.052–0.664). A population pharmacokinetic-pharmacodynamic (PKPD) model was developed to describe the relationship between the time course of venom (a mixture of toxins) and effect (elevated CK). In addition, a kinetic-pharmacodynamic (KPD) model was developed to describe the relationship between time course of a theoretical toxin and effect. Model development and parameter estimation was performed using NONMEM v7.3. No single set of parameter values from either the PKPD or KPD models were found that could accurately describe the time course of different levels of severity of myotoxicity. The predicted theoretical toxin half-life from the KPD model was 11 ± 3.9 hours compared to the half-life of venom of 5.3 ± 0.36 hours. This indicates that the putative causative toxin’s concentration-time profile does not parallel that of venom. Conclusion: Early antivenom administration reduces the incidence of myotoxicity. The venom concentration profile does not appear to be the driver for myotoxicity following envenomation. Additional factors that affect the sensitivity of the patient to snake venom/toxins must be explored to understand the relationship with myotoxicity
Towards a proportionist social work ethics: a Habermasian perspective
No full textIn this paper, we offer an innovative alternative to the deontological and utilitarian approaches which tend to dominate social work ethics, instead proposing a proportionist ethics drawing on the work of Jürgen Habermas. Flyvberg (1998) claims that Habermas ‘distanced himself from phronesis and neo-Aristotelianism’, both of which he is purported to have ‘rhetorically . . . associated with neo-conservatism’ (p. 225) and Varela (1992) places Habermas squarely in the Kantian tradition. In this paper, we present an alternative interpretation of Habermas’s ethical stance, which is based on our perception of him as a keen observer of and commentator on modern life, not least about human intersubjective relations and communication, and our practical attempts to deal with the intractable problems of difference in an increasingly pluralistic world. Moreover, we see a form of proportionist thinking in Habermas which suggests a close alignment with Aristotelianism and, indeed, Thomism. For social work, an approach of this sort seems particularly urgent as the field tends increasingly towards, on the one hand, technological, rule bound, deontological frameworks, such as codes of ethics and ethics audits (Reamer, 2001) and, on the other hand, ideologically based ethics of care approaches, both of which tend to stultification and obstruction of the practical action appropriate to the age
Coupled Brinkman and Kozeny–Carman model for railway ballast washout using the finite element method
No full textThis study investigates the use of a nonlinear model based on the penalisation approach to couple fluid flow and porous media flow. The problem is formulated using a unified Brinkman equation on the domain with a nonlinear permeability which is given a function of porosity, which in turn is governed by an advection equation. The permeability is assumed to be governed by the Kozeny–Carman equation which relates the permeability with the average grain size and porosity. The model is solved using an adaptive finite element method in space and the method of characteristics in time. Finally, numerical examples are provided to illustrate the model and discuss possible extensions