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Book: Biomedical sciences

Iles, Ray K. / Docherty, Suzanne M.

essential laboratory medicine

2012

Author's details	ed. by Ray K. Iles ; Suzanne M. Docherty
Keywords	Pathology, Clinical / methods ; Clinical Laboratory Techniques ; Labormedizin
Subject	Labordiagnostik ; Medizinische Labortechnik ; Laboratoriumsdiagnostik ; Laboratoriumsmedizin
Language	English
Size	XIII, 424 S. : zahlr. Ill., graph. Darst.
Publisher	Wiley-Blackwell
Publishing place	Oxford u.a.
Publishing country	Great Britain
Document type	Book
Note	Includes bibliographical references and index
HBZ-ID	HT017097276
ISBN	978-0-470-99775-8 ; 978-0-470-99774-1 ; 9781119950929 ; 9781119962410 ; 9781119962427 ; 0-470-99775-3 ; 0-470-99774-5 ; 1119950929 ; 1119962412 ; 1119962420
Database	Catalogue ZB MED Medicine, Health

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2012 A 299	order for loan	Magazin

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Article ; Online: A How to Guide: Clinical Population Test Development and Authorization of MALDI-ToF Mass Spectrometry-Based Screening Tests for Viral Infections.

Iles, Ray K / Iles, Jason K / Zmuidinaite, Raminta / Roberts, Michael

Viruses

2022 Volume 14, Issue 9

Abstract: Applying MALDI-ToF mass spectrometry as a clinical diagnostic test for viruses is different from that of bacteria, fungi and other micro-organisms. This is because the systems biology of viral infections, the size and chemical nature of specific viral ... ...

Abstract	Applying MALDI-ToF mass spectrometry as a clinical diagnostic test for viruses is different from that of bacteria, fungi and other micro-organisms. This is because the systems biology of viral infections, the size and chemical nature of specific viral proteins and the mass spectrometry biophysics of how they are quantitated are fundamentally different. The analytical challenges to overcome when developing a clinical MALDI-ToF mass spectrometry tests for a virus, particularly human pathogenic enveloped viruses, are sample enrichment, virus envelope disruption, optimal matrix formulation, optimal MALDI ToF MS performance and optimal spectral data processing/bioinformatics. Primarily, the instrument operating settings have to be optimized to match the nature of the viral specific proteins, which are not compatible with setting established when testing for bacterial and many other micro-organisms. The capacity to be a viral infection clinical diagnostic instrument often stretches current mass spectrometers to their operational design limits. Finally, all the associated procedures, from sample collection to data analytics, for the technique have to meet the legal and operational requirement for often high-throughput clinical testing. Given the newness of the technology, clinical MALDI ToF mass spectrometry does not fit in with standard criteria applied by regulatory authorities whereby numeric outputs are compared directly to similar technology tests that have already been authorized for use. Thus, CLIA laboratory developed test (LDT) criteria have to be applied. This article details our experience of developing a SAR-CoV-2 MALDI-ToF MS test suitable for asymptomatic carrier infection population screening.
MeSH term(s)	Bacteria/chemistry ; COVID-19 ; Humans ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Viral Proteins ; Virus Diseases/diagnosis ; Viruses
Chemical Substances	Viral Proteins
Language	English
Publishing date	2022-09-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091958
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Current Advancements in Noninvasive Profiling of the Embryo Culture Media Secretome.

Zmuidinaite, Raminta / Sharara, Fady I / Iles, Ray K

International journal of molecular sciences

2021 Volume 22, Issue 5

Abstract: There have been over 8 million babies born through in vitro fertilization (IVF) and this number continues to grow. There is a global trend to perform elective single embryo transfers, avoiding risks associated with multiple pregnancies. It is therefore ... ...

Abstract	There have been over 8 million babies born through in vitro fertilization (IVF) and this number continues to grow. There is a global trend to perform elective single embryo transfers, avoiding risks associated with multiple pregnancies. It is therefore important to understand where current research of noninvasive testing for embryos stands, and what are the most promising techniques currently used. Furthermore, it is important to identify the potential to translate research and development into clinically applicable methods that ultimately improve live birth and reduce time to pregnancy. The current focus in the field of human reproductive medicine is to develop a more rapid, quantitative, and noninvasive test. Some of the most promising fields of research for noninvasive assays comprise cell-free DNA analysis, microscopy techniques coupled with artificial intelligence (AI) and omics analysis of the spent blastocyst media. High-throughput proteomics and metabolomics technologies are valuable tools for noninvasive embryo analysis. The biggest advantages of such technology are that it can differentiate between the embryos that appear morphologically identical and has the potential to identify the ploidy status noninvasively prior to transfer in a fresh cycle or before vitrification for a later frozen embryo transfer.
MeSH term(s)	Artificial Intelligence ; Blastocyst/cytology ; Culture Media/metabolism ; Embryo Culture Techniques/methods ; Embryo Transfer/methods ; Embryo, Mammalian/cytology ; Female ; Fertilization in Vitro/methods ; Humans ; Pregnancy
Chemical Substances	Culture Media
Language	English
Publishing date	2021-03-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22052513
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Article ; Online: MALDI-ToF Mass Spectra Phenomic Analysis for Human Disease Diagnosis Enabled by Cutting-Edge Data Processing Pipelines and Bioinformatics Tools.

Pais, Ricardo J / Iles, Ray K / Zmuidinaite, Raminta

Current medicinal chemistry

2021 Volume 28, Issue 32, Page(s) 6532–6547

Abstract: Current methods for diagnosing human disease are still incapable of rapidly and accurately screening for multiple diseases simultaneously on a large scale, and at an affordable price. MALDI-ToF mass spectrometry is an ultra-sensitive, ultra-fast, lowcost, ...

Abstract	Current methods for diagnosing human disease are still incapable of rapidly and accurately screening for multiple diseases simultaneously on a large scale, and at an affordable price. MALDI-ToF mass spectrometry is an ultra-sensitive, ultra-fast, lowcost, high-throughput technology that has the potential to achieve this goal, allowing human phenotype characterization and thus phenomic screening for multiple disease states. In this review, we will discuss the main advances achieved so far, putting forward targeted applications of MALDI-ToF mass spectrometry in the service of human disease detection. This review focuses on the methodological workflow as MALDI-ToF data processing for phenomic analysis, using state-of-the-art bioinformatic pipelines and software tools. The role of mathematical modelling, machine learning, and artificial intelligence algorithms for disease screening are considered. Moreover, we present some previously developed tools for disease diagnostics and screening based on MALDI-ToF analysis. We discuss the remaining challenges that are ahead when implementing MALDI-ToF into clinical laboratories. Differentiating a standard profile from a single disease phenotype is challenging, but the potential to simultaneously run multiple algorithm screens for different disease phenotypes may only be limited by computing power once this initial hurdle is overcome. The ability to explore the full potential of human clinical phenomics may be closer than imagined; this review gives an insight into the benefits this technology may reap for the future of clinical diagnostics.
MeSH term(s)	Artificial Intelligence ; Computational Biology ; Humans ; Machine Learning ; Phenomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Language	English
Publishing date	2021-06-17
Publishing country	United Arab Emirates
Document type	Journal Article ; Review
ZDB-ID	1319315-6
ISSN	1875-533X ; 0929-8673
ISSN (online)	1875-533X
ISSN	0929-8673
DOI	10.2174/0929867327666201027154257
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Article: A How to Guide: Clinical Population Test Development and Authorization of MALDI-ToF Mass Spectrometry-Based Screening Tests for Viral Infections

Iles, Ray K. / Iles, Jason K. / Zmuidinaite, Raminta / Roberts, Michael

Viruses. 2022 Sept. 03, v. 14, no. 9

2022

Abstract	Applying MALDI-ToF mass spectrometry as a clinical diagnostic test for viruses is different from that of bacteria, fungi and other micro-organisms. This is because the systems biology of viral infections, the size and chemical nature of specific viral proteins and the mass spectrometry biophysics of how they are quantitated are fundamentally different. The analytical challenges to overcome when developing a clinical MALDI-ToF mass spectrometry tests for a virus, particularly human pathogenic enveloped viruses, are sample enrichment, virus envelope disruption, optimal matrix formulation, optimal MALDI ToF MS performance and optimal spectral data processing/bioinformatics. Primarily, the instrument operating settings have to be optimized to match the nature of the viral specific proteins, which are not compatible with setting established when testing for bacterial and many other micro-organisms. The capacity to be a viral infection clinical diagnostic instrument often stretches current mass spectrometers to their operational design limits. Finally, all the associated procedures, from sample collection to data analytics, for the technique have to meet the legal and operational requirement for often high-throughput clinical testing. Given the newness of the technology, clinical MALDI ToF mass spectrometry does not fit in with standard criteria applied by regulatory authorities whereby numeric outputs are compared directly to similar technology tests that have already been authorized for use. Thus, CLIA laboratory developed test (LDT) criteria have to be applied. This article details our experience of developing a SAR-CoV-2 MALDI-ToF MS test suitable for asymptomatic carrier infection population screening.
Keywords	bioinformatics ; biophysics ; carrier state ; data analysis ; matrix-assisted laser desorption-ionization mass spectrometry ; pathogens ; spectral analysis ; viruses
Language	English
Dates of publication	2022-0903
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091958
Database	NAL-Catalogue (AGRICOLA)

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Article: Direct Detection of Glycated Human Serum Albumin and Hyperglycosylated IgG3 in Serum, by MALDI-ToF Mass Spectrometry, as a Predictor of COVID-19 Severity.

Iles, Ray K / Iles, Jason K / Lacey, Jonathan / Gardiner, Anna / Zmuidinaite, Raminta

Diagnostics (Basel, Switzerland)

2022 Volume 12, Issue 10

Abstract: The prefusion spike protein of SARS-CoV-2 binds advanced glycation end product (AGE)-glycated human serum albumin (HSA) and a higher mass (hyperglycosylated/glycated) immunoglobulin (Ig) G3, as determined by matrix assisted laser desorption mass ... ...

Abstract	The prefusion spike protein of SARS-CoV-2 binds advanced glycation end product (AGE)-glycated human serum albumin (HSA) and a higher mass (hyperglycosylated/glycated) immunoglobulin (Ig) G3, as determined by matrix assisted laser desorption mass spectrometry (MALDI-ToF). We set out to investigate if the total blood plasma of patients who had recovered from acute respiratory distress syndrome (ARDS) as a result of COVID-19, contained more glycated HSA and higher mass (glycosylated/glycated) IgG3 than those with only clinically mild or asymptomatic infections. A direct serum dilution, and disulphide bond reduction, method was developed and applied to plasma samples from SARS-CoV-2 seronegative (
Language	English
Publishing date	2022-10-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics12102521
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Degree of immunoglobulin kappa light chain glycosylation of anti-spike SARS CoV-2 antibodies correlates with COVID-19 severity

Grigaite, Raminta / Iles, Jason K / Harding, Stephen / Patel, Roshani / Wallis, Gregg / Iles, Ray K

medRxiv

Abstract: Glycosylation of antibodies and the effects this has on inflammatory responses has concentrated predominately on the study of glycosylation moieties found in the Fc region of heavy chains. Light chain glycosylation and their ratios are relatively ... ...

Abstract	Glycosylation of antibodies and the effects this has on inflammatory responses has concentrated predominately on the study of glycosylation moieties found in the Fc region of heavy chains. Light chain glycosylation and their ratios are relatively understudied. Nevertheless, variable glycosylation and ratio of κ and λ light chains have been associated with worse prognosis in myeloma and in tissue deposition amyloidosis. The κ λ light chains, of antibodies binding to SARS-CoV2 nucleocapsid and spike protein were analysed, using MALDI-ToF MS, in respect to their intensity, ratios, glycosylation patterns and any pattern changes correlating with COVID-19 severity. The molecular masses and signal intensity of κ and λ glycosylated and non-glycosylated light chains were measured for immunoglobulins isolated from plasma of seropositive and seronegative health care workers (HCW), and convalescent patients who had suffered from acute respiratory distress syndrome (ARDS). Overall, there was no significant changes in κ to λ ratio of total IgG (via protein G capture) antibodies between the groups. A non-statistically significant trend towards λ light chains was found in antibodies against SARS CoV-2 Nucleocapsid and Spike proteins. However, detailed analysis of the molecular forms found a significant increase and bias towards un-glycosylated light chains and in particular un-glycosylated κ light chains, in antibodies against SAR-CoV-2 spike protein, from convalescent COVID-ARDS patients. Here we have demonstrated a bias towards un-glycosylated κ chains in anti-spike antibodies in those who suffered from ARDS as a result of SARS-CoV2 infection 3 months after recovery. How this relates to the immunopathology of COVID-19 requires further study.
Keywords	covid19
Language	English
Publishing date	2023-01-09
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.01.06.23284259
Database	COVID19

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Article ; Online: Exploring the relationship of sleep, cognition, and cortisol in sickle cell disease.

Kölbel, Melanie / Kirkham, Fenella J / Iles, Ray K / Stotesbury, Hanne / Halstead, Elizabeth / Brenchley, Celia / Sahota, Sati / Dimitriou, Dagmara

Comprehensive psychoneuroendocrinology

2022 Volume 10, Page(s) 100128

Abstract: Background: Neurocognitive impairment is common in people with Sickle Cell Disease (SCD) and evidence is accumulating that sleep disturbances play a role. The interaction between cortisol and sleep in the general population is associated with cognition ... ...

Abstract	Background: Neurocognitive impairment is common in people with Sickle Cell Disease (SCD) and evidence is accumulating that sleep disturbances play a role. The interaction between cortisol and sleep in the general population is associated with cognition as well as general wellbeing but there are few data in SCD. We aimed to understand the relationship between cortisol and sleep in individuals with SCD and explored associations with cognition. Methods: Forty-five participants of black heritage (SCD: N = 27, 9-29 years, 16 females; Controls: N = 18, 11-25 years, 13 females) were recruited from the community between 2018 - 2020. Participants completed standardized questionnaires about their sleep behaviour and wore actigraphy MotionWatch8 for 7 nights to assess nocturnal sleep patterns. Salivary cortisol samples were taken on wakening and 3 times after 14:00. Cognition was assessed using the Wechsler Intelligence Scales for children and adults. Results: People with SCD took longer to fall asleep and experienced greater wake bouts, mobile minutes and fragmented sleep compared to controls. Although non-significant, people with SCD experienced lower morning cortisol, with a flattened diurnal cortisol ratio compared to controls. Interestingly, SCD participants, but not controls, with low diurnal variation scored lowest on processing speed (PSI) and perceptual reasoning index (PRI). A moderator analysis revealed that the effect of morning cortisol and diurnal cortisol ratio on PRI by group health (i.e., SCD and healthy controls) depended on sleep quality. Discussion: Sleep and cortisol may play a crucial role in the expression of cognitive difficulties seen in SCD. This should be considered for the development of interventions to optimise cognitive functioning and sleep. This, in turn, could positively impact on secretion of cortisol and general health in SCD.
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article
ISSN	2666-4976
ISSN (online)	2666-4976
DOI	10.1016/j.cpnec.2022.100128
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Article ; Online: HILIC-MS-based shotgun metabolomic profiling of maternal urine at 9-23 weeks of gestation - establishing the baseline changes in the maternal metabolome.

Trivedi, Drupad K / Iles, Ray K

Biomedical chromatography : BMC

2015 Volume 29, Issue 2, Page(s) 240–245

Abstract: In this data-rich age it is no longer necessary to methodically isolate, characterize and measure specific molecules. What is important is to identify which of the hundreds or thousands of resolved and measured 'unknown' molecules are potentially ... ...

Abstract	In this data-rich age it is no longer necessary to methodically isolate, characterize and measure specific molecules. What is important is to identify which of the hundreds or thousands of resolved and measured 'unknown' molecules are potentially associated with the pathophysiology of interest. We have taken LC-MS data from pregnancy urine and applied SIMCA P+ data analysis software in shotgun metabolomics to search the large amount of data for significant metabolite changes that occur in the transition from the first to early second trimester of pregnancy. Seventy-two individual urine samples were examined spanning 9-23 weeks of gestation. Three-hundred and eighty-three ions were identified and variations were mapped between profiles of different gestational age and the significance quantified. In urine collected during pregnancy, the transition from first to early second trimester revealed a relatively steady pattern of metabolites except for four that showed a dramatic fall in abundance as pregnancy progressed from the first to second trimester. The pattern of changes in urinary metabolites identified by Zwitterionic Hydrophilic Liquid Interaction Chromatography (ZIC-HILIC) coupled to mass spectrometry was evaluated and we established a baseline of changes from which a search for metabolomic markers associated with clinical pathologies of pregnancy can be made as a part of wider ultraomics study.
MeSH term(s)	Chromatography, Liquid/methods ; Female ; Humans ; Mass Spectrometry/methods ; Metabolome/physiology ; Metabolomics/methods ; Pregnancy
Language	English
Publishing date	2015-02
Publishing country	England
Document type	Journal Article
ZDB-ID	632848-9
ISSN	1099-0801 ; 0269-3879
ISSN (online)	1099-0801
ISSN	0269-3879
DOI	10.1002/bmc.3266
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Article ; Online: Shotgun metabolomic profiles in maternal urine identify potential mass spectral markers of abnormal fetal biochemistry - dihydrouracil and progesterone in the metabolism of Down syndrome.

Trivedi, Drupad K / Iles, Ray K

Biomedical chromatography : BMC

2015 Volume 29, Issue 8, Page(s) 1173–1183

Abstract: In Down syndrome (DS) in particular, the precise cellular mechanisms linking genotype to phenotype is not straightforward despite a clear mapping of the genetic cause. Metabolomic profiling might be more revealing in understanding molecular-cellular ... ...

Abstract	In Down syndrome (DS) in particular, the precise cellular mechanisms linking genotype to phenotype is not straightforward despite a clear mapping of the genetic cause. Metabolomic profiling might be more revealing in understanding molecular-cellular mechanisms of inborn errors of metabolism/syndromes than genomics alone and also result in new prenatal screening approaches. The urinary metabolome of 122 maternal urine from women with and without an aneuploid pregnancy (predominantly Down syndrome) were compared by both zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and reversed-phase liquid chromatography (RPLC) coupled to hybrid ion trap time of flight mass spectral analysis. ZIC-HILIC mass spectrometry resolved 10-fold more unique molecular ions than RPLC mass spectrometry, of which molecules corresponding to ions of m/z 114.07 and m/z 314.20 showed maternal urinary level changes that significantly coincided with the presence of a DS fetus. The ion of m/z 314.20 was identified as progesterone and m/z 114.07 as dihydrouracil. A metabolomics profiling-based maternal urinary screening test modelled from this separation data would detect approximately 87 and 60.87% (using HILIC-MS and RPLC-MS, respectively) of all DS pregnancies between 9 and 23 weeks of gestation with no false positives.
MeSH term(s)	Adult ; Biomarkers/metabolism ; Biomarkers/urine ; Chromatography, Reverse-Phase/methods ; Down Syndrome/diagnosis ; Down Syndrome/metabolism ; Down Syndrome/urine ; Female ; Fetus/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Metabolome ; Metabolomics/methods ; Pregnancy ; Prenatal Diagnosis ; Progesterone/metabolism ; Progesterone/urine ; Tandem Mass Spectrometry/methods ; Uracil/analogs & derivatives ; Uracil/metabolism ; Uracil/urine
Chemical Substances	Biomarkers ; dihydrouracil (016FR52RU5) ; Progesterone (4G7DS2Q64Y) ; Uracil (56HH86ZVCT)
Language	English
Publishing date	2015-08
Publishing country	England
Document type	Journal Article
ZDB-ID	632848-9
ISSN	1099-0801 ; 0269-3879
ISSN (online)	1099-0801
ISSN	0269-3879
DOI	10.1002/bmc.3404
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