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121 results on '"Monahan, L."'

1. Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.

Author

Gaio, D, Anantanawat, K, To, J, Liu, M, Monahan, L, Darling, AE, Gaio, D, Anantanawat, K, To, J, Liu, M, Monahan, L, and Darling, AE

Abstract

We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.

Published
2022

2. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance

Author

Yasir M, Turner AK, Bastkowski S, Baker D, Page AJ, Telatin A, Phan M-D, Monahan L, Savva GM, Darling A, Webber MA, and Charles IG

Subjects
Bioinformatics, 06 Biological Sciences, 11 Medical and Health Sciences
Abstract

Understanding the genetic basis for a phenotype is a central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking for conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which are not amenable to disruption. To overcome this limitation, we developed a new version of "TraDIS" (transposon directed insertion-site sequencing) that we term "TraDIS-Xpress" that combines an inducible promoter into the transposon cassette. This allows controlled overexpression and repression of all genes owing to saturation of inserts adjacent to all open reading frames as well as conventional inactivation. We applied TraDIS-Xpress to identify responses to the biocide triclosan across a range of concentrations. Triclosan is endemic in modern life, but there is uncertainty about its mode of action with a concentration-dependent switch from bacteriostatic to bactericidal action unexplained. Our results show a concentration-dependent response to triclosan with different genes important in survival between static and cidal exposures. These genes include those previously reported to have a role in triclosan resistance as well as a new set of genes, including essential genes. Novel genes identified as being sensitive to triclosan exposure include those involved in barrier function, small molecule uptake, and integrity of transcription and translation. We anticipate the approach we show here, by allowing comparisons across multiple experimental conditions of TraDIS data, and including essential genes, will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.

Published
2020

4. Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids

Author

Roy Chowdhury, P, Fourment, M, DeMaere, MZ, Monahan, L, Merlino, J, Gottlieb, T, Darling, AE, and Djordjevic, SP

Subjects
Time Factors, DNA Transposable Elements, Chromosome Mapping, Microbiology, Phylogeny, Plasmids
Abstract

© 2019 Elsevier Inc. IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.

Published
2019

6. Hackflex: low cost Illumina sequencing library construction for high sample counts

Author

Gaio, D, To, J, Liu, M, Monahan, L, Anantanawat, K, Darling, A, Gaio, D, To, J, Liu, M, Monahan, L, Anantanawat, K, and Darling, A

Abstract

We developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50/sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.

Published
2019

7. Evaluation of ddRADseq for reduced representation metagenome sequencing

Author

Darling, AE, Liu, M, Worden, P, Monahan, L, Demaere, M, Burke, C, Djordjevic, S, Charles, I, Darling, AE, Liu, M, Worden, P, Monahan, L, Demaere, M, Burke, C, Djordjevic, S, and Charles, I

Abstract

Background ‘Who is doing what’ is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. Results We assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling. Conclusion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

Published
2017

9. Re-engaging the adolescent religion imagination

Author

Janssen, J.A.P.J., Prendergast, N., Monahan, L., Prendergast, N., and Monahan, L.

Subjects
Behaviour Change and Well-being, Re-imaging the catholic school
Abstract

Item does not contain fulltext

Published
2003

10. DOES PREOPERATIVE ECHOCARDIOGRAPHY PREDICT OUTCOME IN OCTOGENARIANS UNDERGOING CARDIAC SURGERY?

Author

Reddy, N, Smith, R H., Monahan, L, Scott, W C., De Leon, J R., and Lazar, Jason M.

Subjects
Echocardiography -- Evaluation -- Physiological aspects, Heart ventricle, Left -- Physiological aspects, Health, Evaluation, Physiological aspects
Abstract

Purpose: Left Ventricular (LV) function and mass carry prognostic importance in various cardiac disease states. Cardiac surgery is increasingly being performed in octogenarians. Because patients are preselected with preserved systolic [...]

Published
1999

11. Bacterial Cell Division: The Mechanism and Its Precison

Author

Harry, E, Monahan, L, Thompson, L, Harry, E, Monahan, L, and Thompson, L

Abstract

The recent development of cell biology techniques for bacteria to allow visualization of fundamental processes in time and space, and their use in synchronous populations of cells, has resulted in a dramatic increase in our understanding of cell division and its regulation in these tiny cells. The first stage of cell division is the formation of a Z ring, composed of a polymerized tubulin-like protein, FtsZ, at the division site precisely at midcell. Several membrane-associated division proteins are then recruited to this ring to form a complex, the divisome, which causes invagination of the cell envelope layers to form a division septum. The Z ring marks the future division site, and the timing of assembly and positioning of this structure are important in determining where and when division will take place in the cell. Z ring assembly is controlled by many factors including negative regulatory mechanisms such as Min and nucleoid occlusion that influence Z ring positioning and FtsZ accessory proteins that bind to FtsZ directly and modulate its polymerization behavior. The replication status of the cell also influences the positioning of the Z ring, which may allow the tight coordination between DNA replication and cell division required to produce two identical newborn cells. © 2006 Elsevier Inc. All rights reserved.

Published
2006

47. Improving Adolescent Psychosocial Assessment through Standardized Patient Simulation: An Interdisciplinary Quality Improvement Initiative.

Author

Monahan L, Eaves CL, Watson JC, Friese J, McKenna L, and Estrada-Ibarra E

Subjects
Humans, Adolescent, Child, Quality Improvement, Clinical Competence, Communication, Patient Simulation, Internship and Residency
Abstract

Adolescent suicide and mental illness have increased at alarming rates. Healthcare professionals report a lack of skill and confidence in obtaining adolescent histories and managing confidential care due to limited training in residency. Nursing professional development practitioners face challenges of adequately preparing interdisciplinary healthcare providers to assess, identify, and intervene at all points of contact with adolescents. To increase the confidence in clinical communication skills and clinical competency, and to increase the number of social work referrals related to modifiable risk factors for adolescent patients, a Texas pediatric tertiary care center utilized standardized patient (SP) methodology to supplement traditional clinical experiences with communication-focused education based on the Home, Education, Eating, Activities, Drugs, Sexuality, Suicidality, and Safety (HEEADSSS) interviewing. This quality improvement (QI) pilot demonstrated the benefits of utilizing standardized patient methodology in communication-focused education based on the HEEADSSS interviewing. Following the SP simulations, confidence in clinical communication skills increased by 13%, clinical competency in performing comprehensive psychosocial interviews increased by 11%, use of HEEADSSS increased by 64%, and social work referrals increased by 89%. This interdisciplinary SP interviewing simulation pilot was beneficial in improving the 36 physician and nursing residents' ability to conduct psychosocial assessments for risk factors of suicidality among adolescents.

Published
2024
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48. Nursing Graduates' Preparedness for Practice: Substantiating the Call for Competency-Evaluated Nursing Education.

Author

McGarity T, Monahan L, Acker K, and Pollock W

Abstract

Practice readiness continues to be a challenge in healthcare. This was especially evident during the COVID-19 pandemic. This focused descriptive-correlational study examined nurses' perceived preparedness for practice during the pandemic. One hundred and eighty-four registered nurses (RN) responded to Qualtrics survey questions addressing the competencies they perceived they had and the competencies they felt they needed that would have better prepared them to care for patients during the COVID-19 pandemic. The results demonstrated that although these nurses felt competent in certain areas, they perceived that they needed more education in those same areas to feel better prepared. Bivariate correlations and linear regression analysis indicated that institutional competency development, education, and work experience influenced perceived competency.

Published
2023
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49. Distinct and shared therapeutic neural mechanisms of mindfulness-based and social support stress reduction groups in adults with autism spectrum disorder.

Author

Pagni BA, Hill E, Walsh MJM, Delaney S, Ogbeama D, Monahan L, Cook JR, Guerithault N, Dixon MV, Ballard L, and Braden BB

Subjects
Humans, Adult, Anxiety psychology, Anxiety Disorders, Stress, Psychological diagnostic imaging, Stress, Psychological therapy, Social Support, Mindfulness methods, Autism Spectrum Disorder diagnostic imaging, Autism Spectrum Disorder therapy
Abstract

Background: Mindfulness-based stress reduction (MBSR) alleviates depression and anxiety in adults with autism spectrum disorder (ASD); however, underlying therapeutic neural mechanisms and mindfulness-specific effects have yet to be elucidated., Methods: We randomly assigned adults with ASD to MBSR or social support/education (SE). They completed questionnaires that assessed depression, anxiety, mindfulness traits, autistic traits and executive functioning abilities as well as a self-reflection functional MRI task. We used repeated-measures analysis of covariance (ANCOVA) to evaluate behavioural changes. To identify task-specific connectivity changes, we performed a generalized psychophysiological interactions (gPPI) functional connectivity (FC) analysis on regions of interest (ROIs; insula, amygdala, cingulum and prefrontal cortex [PFC]). We used Pearson correlations to explore brain-behaviour relationships., Results: Our final sample included 78 adults with ASD - 39 who received MBSR and 39 who received SE. Mindfulness-based stress reduction uniquely improved executive functioning abilities and increased mindfulness traits, whereas both MBSR and SE groups showed reductions in depression, anxiety and autistic traits. Decreases specific to MBSR in insula-thalamus FC were associated with anxiety reduction and increased mindfulness traits, including the trait "nonjudgment;" MBSR-specific decreases in PFC-posterior cingulate connectivity correlated with improved working memory. Both groups showed decreased amygdala-sensorimotor and medial-lateral PFC connectivity, which corresponded with reduced depression., Limitations: Larger sample sizes and neuropsychological evaluations are needed to replicate and extend these findings., Conclusion: Together, our findings suggest that MBSR and SE are similarly efficacious for depression, anxiety and autistic traits, whereas MBSR produced additional salutary effects related to executive functioning and mindfulness traits. Findings from gPPI identified shared and distinct therapeutic neural mechanisms, implicating the default mode and salience networks. Our results mark an early step toward the development of personalized medicine for psychiatric symptoms in ASD and offer novel neural targets for future neurostimulation research., Clinical Trial Registration: ClinicalTrials.gov identifier NCT04017793., Competing Interests: Competing interests: B. Pagni received support for article processing charges from the ASU Graduate Program Student Association’s Publication Grant. M. Walsh receives funding from the National Institute of Mental Health ( NIMH F31MH122107). M. Dixon received payment for execution of the program as part of this study. L. Ballard declares having received honoraria for facilitation of guided mind-fulness medications and educational presentations on mindfulness meditation., (© 2023 CMA Impact Inc. or its licensors.)

Published
2023
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50. Sex-related brain connectivity correlates of compensation in adults with autism: insights into female protection.

Author

Walsh MJM, Pagni B, Monahan L, Delaney S, Smith CJ, Baxter L, and Braden BB

Subjects
Male, Adult, Humans, Female, Magnetic Resonance Imaging methods, Brain diagnostic imaging, Brain Mapping methods, Neural Pathways diagnostic imaging, Autistic Disorder, Autism Spectrum Disorder diagnostic imaging
Abstract

The male preponderance in autism spectrum disorder (ASD) led to the hypothesis that aspects of female biology are protective against ASD. Females with ASD (ASD-F) report more compensatory behaviors (i.e. "camouflaging") to overcome ASD-related social differences, which may be a mechanism of protection. No studies have examined sex-related brain pathways supporting camouflaging in ASD-F, despite its potential to inform mechanisms underlying the ASD sex bias. We used functional connectivity (FC) to investigate "sex-atypical" and "sex-typical" FC patterns linked to camouflaging in adults with ASD and examined multimodal coherence of findings via structural connectometry. Exploratory associations with cognitive/emotional functioning examined the adaptive nature of FC patterns. We found (i) "sex-atypical" FC patterns linked to camouflaging in the hypothalamus and precuneus and (ii) "sex-typical" patterns in the right anterior cingulate and anterior parahippocampus. Higher hypothalamic FC with a limbic reward cluster also correlated with better cognitive control/emotion recognition. Structural connectometry validated FC results with consistent brain pathways/effect patterns implicated in ASD-F. In summary, "male-typical" and "female-typical" brain connectivity patterns support camouflaging in ASD-F in circuits implicated in reward, emotion, and memory retrieval. "Sex-atypical" results are consistent with fetal steroidogenic/neuroinflammatory hypotheses. However, female genetics/biology may contribute to "female-typical" patterns implicated in camouflaging., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.)

Published
2022
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