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Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming,and long non-coding RNAs

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Science Bulletin 2015年第20期60卷 1722-1733页

作者： andrew paul hutchins Duanqing Pei Key Laboratory of Regenerative Biology South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences South China Institute for Stem Cell Biology and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

Transposable elements(TEs) are mobile genomic sequences of DNA capable of autonomous and nonautonomous duplication. TEs have been highly successful,and nearly half of the human genome now consists of various families of TEs. Originally thought to be non-functional,these elements have been co-opted by animal genomes to perform a variety of physiological functions ranging from TE-derived proteins acting directly in normal biological functions, to innovations in transcription factor logic and influence on epigenetic control of gene expression. During embryonic development, when the genome is epigenetically reprogrammed and DNA-demethylated, TEs are released from repression and show embryonic stage-specific expression, and in human and mouse embryos, intact TEderived endogenous viral particles can even be detected. Asimilar process occurs during the reprogramming of somatic cells to pluripotent cells: When the somatic DNA is demethylated, TEs are released from repression. In embryonic stem cells(ESCs), where DNA is hypomethylated, an elaborate system of epigenetic control is employed to suppress TEs, a system that often overlaps with normal epigenetic control of ESC gene expression. Finally, many long non-coding RNAs(lnc RNAs) involved in normal ESC function and those assisting or impairing reprogramming contain multiple TEs in their RNA. These TEs may act as regulatory units to recruit RNA-binding proteins and epigenetic modifiers. This review covers how TEs are interlinked with the epigenetic machinery and lnc RNAs, and how these links influence each other to modulate aspects of ESCs,embryogenesis, and somatic cell reprogramming.

关键词： Transposable elements Endogenousretroviruses Embryonic stem cells lncRNA Reprogramming Pluripotency

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glbase:a framework for combining,analyzing and displaying heterogeneous genomic and high-throughput sequencing data

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Cell Regeneration 2014年第1期3卷 1-20页

作者： andrew paul hutchins Ralf Jauch Mateusz Dyla Diego Miranda-Saavedra Key Laboratory of Regenerative Biology South China Institute for Stem Cell Biology and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Genome Regulation Laboratory South China Institute for Stem Cell Biology and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Laboratory for Structural Biochemistry Genome Institute of Singapore60 Biopolis StreetSingapore 138672Singapore Department of Molecular Biology and Genetics Aarhus UniversityAarhusDenmark Fibrosis Laboratories Institute of Cellular MedicineNewcastle University Medical SchoolFramlington PlaceNewcastle upon Tyne NE24HHUK

Genomic datasets and the tools to analyze them have proliferated at an astonishing ***,such tools are often poorly integrated with each other:each program typically produces its own custom output in a variety of non-standard file *** we present glbase,a framework that uses a flexible set of descriptors that can quickly parse non-binary data *** includes many functions to intersect two lists of data,including operations on genomic interval data and support for the efficient random access to huge genomic data *** glbase functions can produce graphical outputs,including scatter plots,heatmaps,boxplots and other common analytical displays of high-throughput data such as RNA-seq,ChIP-seq and microarray expression *** is designed to rapidly bring biological data into a Python-based analytical environment to facilitate analysis and data *** summary,glbase is a flexible and multifunctional toolkit that allows the combination and analysis of high-throughput data(especially next-generation sequencing and genome-wide data),and which has been instrumental in the analysis of complex data *** is freely available at http://***/oaxiom/glbase/.

关键词： ChIP-seq RNA-seq Genomics Microarray Motifs Transcription factor Bioinformatics

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The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting

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Protein & Cell 2023年第7期14卷 479-498页

作者： Yuhan Chen Jiansen Lu Yanwen Xu Yaping Huang Dazhuang Wang Peiling Liang Shaofang Ren Xuesong Hu Yewen Qin Wei Ke Ralf Jauch andrew paul hutchins Mei Wang Fuchou Tang Xiao-Yang Zhao State Key Laboratory of Organ Failure Research Department of Developmental BiologySchool of Basic Medical SciencesSouthem Medical UniversityGuangzhou 510515China Beijing Advanced Innovation Center for Genomics School of Life SciencesPeking UniversityBeijing 100871China Biomedical Pioneering Innovation Center Ministry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijing 100871China Departmentof Urology Nanfang HospitalSouthem Medical UniversityGuangzhou 510515China School of Biomedical Sciences Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina Department of Biology Southerm University of Science and TechnologyShenzhen 518055China Department of Neonatology Zhujiang HospitalSouthem Medical UniversityGuangzhou 510280China Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering Southem Medical UniversityGuangzhou 510515China Department of Gynecology Zhujiang HospitalSouthern Medical UniversityGuangzhou 510280China Key Laboratory of Mental Health of the Ministry of Education Guangzhou 510515China Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Guangzhou 510005China Department of Plastic Surgery Affliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhou 310006China

Although somatic cells can be reprogrammed to pluripotent stem cells(PsCs)with pure chemicals,authentic pluripotency of chemically induced pluripotent stem celis(CipsCs)has never been achieved through tetraploid complementation *** reprogramming of spermatogonial stem cells(ssCs)was another non-transgenic way to obtain PsCs,but this process lacks mechanistic ***,we reconstructed the trajectory of mouse SsC reprogramming and developed a five-chemical combination,boosting the reprogramming effciency by nearly 80-to *** importantly,chemical induced germline-derived PsCs(5C-gPSCs),but not gpsCs and chemical induced pluripotent stem cells,had authentic pluripotency,as determined by tetraploid ***,ssCs traversed through an inverted pathway of in vivo germ ceil development,exhibiting the expression signatures and DNA methylation dynamics from spermatogonia to primordial germ cells and further to ***,ssC-specific imprinting control regions switched from biallelic methylated states to monoallelic methylated states by imprinting demethylation and then re-methylation on one of the two alleles in 5c-gPsCs,which was apparently distinct with the imprinting reprogramming in vivo as DNA methylation simultaneously occurred on both *** work sheds ight on the unique regulatory network underpinning SsC reprogramming,providing insights to understand generic mechanisms for cell-fate decision and epigenetic-relateddisorders in regenerative medicine.

关键词： reprogramming spermatogonial stem cell tetraploid complementation imprinting

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Can serious postoperative complications in patients with Crohn’s disease be predicted using machine learning?

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World Journal of Gastrointestinal Surgery 2024年第10期16卷 3358-3362页

作者： andrew paul Zbar Department of Neuroscience and Anatomy University of MelbourneMelbourne 3010VictoriaAustralia

The routine introduction of novel anti-inflammatory therapies into the mana-gement algorithms of patients with Crohn’s disease over the last 2 decades has not substantially changed the likelihood of ultimate *** it has delayed the operative need and altered the presentation *** prospect of complic-ations continues to remain high in this modern era but depending upon the cohort assessed,it remains difficult to make strict comparisons between individual spe-cialist *** patients who present rather late after their diagnosis with a septic complication like an intra-abdominal abscess and a penetrating/fistulizing pattern of disease are more likely to have a complicated course particularly if they have clinical features such as difficult percutaneous access to the collection or multilocularity both of which can make preoperative drainage ***-ually,those cases with extensive adhesions where an initial laparoscopic approach needs open conversion and where there is an extended operative time,unsur-prisingly will suffer more significant complications that impact their length of hospital *** need for a protective stoma also introduces its own derivative costs,utilizing a range of health resources as well as resulting in important alte-rations in quality of life *** established the parameters of the pro-blem can the statistical analysis of the available data identify high-risk cases,promote the notion of centralization of specialist services or improve the allo-cation of disease-specific health expenditure?

关键词： Crohn’s disease Postoperative complications Clavien-Dindo Machine learning Outcome

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Music alters heart rate and psychological responses but not muscle activation during light-intensity isometric exercise

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Sports Medicine and Health Science 2024年第4期6卷 394-401页

作者： andrew R.Moore Jasmin C.hutchinson Christa Winter paul C.Dalton Lori A.Bolgla Vincent J.Paolone Department of Kinesiology Augusta University112015th St.AugustaGA30912USA Department of Exercise Science&Athletic Training Springfield College263 Alden St.SpringfieldMA01109USA Department of Psychology Springfield College263 Alden St.SpringfieldMA01109USA Heart&Vascular Institute Penn State College of MedicinePenn State University500 HMC Crescent RoadNorth Lobby HersheyPA17033USA Department of Physical Therapy Augusta University112015th St.AugustaGA30912USA

Listening to music manipulates attention to be more externally focused,which has the potential to improve muscular *** study aimed to determine the effect of listening to music on muscle activation during an isometric exercise task,and compare this effect to those of other attentional focus *** healthy subjects(n=35;16 men/19 women)completed an isometric elbow flexion task for 1 min in three randomized and counterbalanced conditions:internal focus(INT),external focus with a simple distraction task(EXT),or listening to music(MUS).Muscle activation of the biceps and triceps brachii and heart rate(HR)were recorded throughout the exercise *** of perceived exertion(RPE),affective valence,and motivation were measured at the end of each *** was no difference in muscle activation measures among the three *** during MUS was lower than EXT at 15 s([89.4±11.8]beats/min vs.[93.1±12.9]beats/min;p=0.018)and 30 s([90.6±12.4]beats/min vs.[94.2±12.5]beats/min;p=0.026),and lower than INT at 60 s([93.3±13.3]beats/min vs.[96.7±12.0]beats/min;p=0.016).Overall RPE was higher for INT(13.4±2.2)than for MUS([12.6±2.0];p=0.020)and EXT([11.94±2.22];p<0.001).Affective valence was higher for MUS than for INT([2.7±1.4]vs.[2.1±1.5];p=0.011).Manipulating attentional focus did not alter muscle activation for a light-intensity isometric muscular endurance task,though MUS was reported as more positive and requiring less exertion to complete than *** music can therefore be recommended during light-intensity isometric exercise based on the psychological benefits observed.

关键词： Electromyography Attentional focus Rating of perceived exertion Elbow flexion

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Single cells and transposable element heterogeneity in stem cells and development

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Cell Regeneration 2021年第1期10卷 251-254页

作者： andrew P.hutchins Shenzhen Key Laboratory of Gene Regulation and Systems Biology Southern University of Science and TechnologyShenzhen 518055China Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

Recent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented ***,several cellular aspects are currently underutilized in single cell *** aspect is the expression and activity of transposable elements(TEs).TEs are selfish sequences of DNA that can replicate,and have been wildly successful in colonizing ***,most TEs are mutated,fragmentary and incapable of transposition,yet they are actively bound by multiple transcription factors,host complex patterns of chromatin modifications,and are expressed in mRNAs as part of the transcriptome in both normal and diseased *** contribution of TEs to development and cellular function remains unclear,and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells,development and human disease.

关键词： element utilized routine

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Integrated adsorption and absorption process for post-combustion CO_(2) capture

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Frontiers of Chemical Science and Engineering 2021年第3期15卷 483-492页

作者： Gongkui Xiao Penny Xiao andrew Hoadley paul Webley Department of Chemical Engineering The University of Western AustraliaPerth WA 6009Australia Department of Chemical Engineering University of MelbourneVictoria 3010Australia Department of Chemical Engineering Monash UniversityVictoria 3800Australia

This study explored the feasibility of integrating an adsorption and solvent scrubbing process for postcombustion CO_(2) capture from a coal-fired power *** integrated process has two stages:the first is a vacuum swing adsorption(VSA)process using activated carbon as the adsorbent,and the second stage is a solvent scrubber/stripper system using monoethanolamine (30 wt-%) as the *** results showed that the adsorption process could enrich CO_(2) in the flue gas from 12 to 50 mol-% with a CO_(2) recovery of >90%,and the concentrated CO_(2) stream fed to the solvent scrubber had a significantly lower volumetric *** increased CO_(2) concentration and reduced feed flow to the absorption section resulted in significant reduction in the diameter of the solvent absorber,bringing the size of the absorber from uneconomically large to readily achievable *** addition,the VSA process could also remove most of the oxygen initially existed in the feed gas,alleviating the downstream corrosion and degradation problems in the absorption *** findings in this work will reduce the technical risks associated with the state-of-the art solvent absorption technology for CO_(2) capture and thus accelerate the deployment of such technologies to reduce carbon emissions.

关键词： vacuum swing adsorption monoethanolamine post-combustion CO_(2)capture integrated process

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Upsampling Monte Carlo neutron transport simulation tallies using a convolutional neural network

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Energy and AI 2023年第3期13卷 117-125页

作者： andrew Osborne Joffrey Dorville paul Romano Nuclear Science&Engineering The Colorado School of Mines101214th St.GoldenCO80401United States of America Department of Mechanical Engineering The Colorado School of Mines1610 Illinois St.GoldenCO80401United States of America Argonne National Laboratory LemontILUnited States of America

The physical quantities calculated by nuclear reactor Monte Carlo simulations are typically recorded on a grid of two or three spatial dimensions and one dimension of neutron *** of this,increasing the resolution of the calculated quantities can have a significant impact on the memory and CPU time required to run a *** neural networks have been shown to accurately upsample coarse-resolution photo-graphic images to resolutions multiple times finer than the *** we show that a convolutional neural network can accurately upsample flux tallies in a Monte Carlo neutron transport simulation by a factor of two along the spatial and energy *** flux tallies in pressurized water reactor assemblies were calculated using OpenMC at a 64×64 pixel spatial resolution and 8 neutron energy groups for input to the neural *** network upsamples the low-resolution neutron flux to 128×128 pixel spatial resolution and 16 neutron energy ***-resolution neutron flux tallies and their uncertainties were also calculated with OpenMC and compared with the network’s *** upsampled data and the high-resolution tally results agree to within the statistical uncertainty calculated by OpenMC.

关键词： OpenMC Convolutional neural network Residual network Neutron Monte Carlo

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The epidemiology of hyperferritinaemia

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World Journal of Gastroenterology 2006年第36期12卷 5866-5869页

作者： Sarah Hearnshaw Nick paul Thompson andrew McGill Department of Gastroenterology The Freeman Hospital Freeman Road High Heaton Newcastle Upon Tyne Tyne and Wear NE7 7DN United Kingdom Department of Biochemistry Newcastle General Hospital Westgate Road Newcastle upon Tyne Tyne and Wear United Kingdom

AIM： To discover the causes of markedly raised ferritin levels in patients seen at a teaching hospital in Newcastle Upon Tyne, United Kingdom. METHODS： Demographic and medical data were collected for all patients over 18 years who had a serum ferritin levels recorded as ≥ 1500 μg/L during the period January to September 2002. The cause or causes for their hyperferritinaemia were identified from their medical notes. Patients from a defined local population were identified. RESULTS： A total of 19 583 measurements were provided of which 406 from 199 patients were ≥ 1500 μg/L. An annual incidence for the local population was determined to be 0.44/1000. 150/199 medical notes were scrutinised and 81 patients were identified as having a single cause for their raised ferritin level. The most common single cause was alcoholic liver disease in the local population and renal failure was the most common single cause in the overall population. Confirmed hereditary haemochromatosis was the 10^th most common cause. Liver disease contributed to hyperferritinaemia in 44% of the patients. Weight loss may have contributed to hyperferritinaemia in up to 11%. CONCLUSION： Alcohol related liver disease, haematological disease, renal failure and neoplasia are much more common causes of marked hyperferritinaemia than haemochromatosis. The role of weight loss in hyperferritinaemia may warrant further investigation.

关键词： Ferritin Epidemiology Haemochromatosis

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The Dynamics of the Nucleation, Growth and Termination of Single-Walled Carbon Nanotubes from in situ Raman Spectroscopy During Chemical Vapor Deposition

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Nano Research 2009年第10期2卷 783-792页

作者： paul Finnie andrew Li-Pook-Than Jacques Lefebvre Institute for Microstructural Sciences National Research Council CanadaBuilding M-501200 Montreal RoadOttawaONK1A 0R6Canada Department of Physics University of Ottawa150 Louis PasteurOttawaON K1N 6N5Canada

The dynamics of the chemical vapor deposition(CVD)of single-walled carbon nanotubes(SWNTs)is extracted experimentally using in situ Raman *** are grown using a thinlm cobalt catalyst and an ethanol precursor in a miniature hot walled reactor with optical *** spectra at room temperature and at the growth temperature are compared for two growth *** evolution of the G-band,D-band,and radial breathing mode(RBM)is tracked at the growth temperature with time resolution of a few *** are three identifiable phases in the evolution of the Raman signal intensity:an initial exponential increasing phase,a linear growth phase,and a saturation *** situ optical spectroscopy thus enables the study of nucleation,steady growth,and deactivation processes to be investigated separately in real *** evolution curves for all bands(G,D,and RBM),when scaled,collapse onto the same curve,to within experimental uncertainty.

关键词： Single-walled carbon nanotube chemical vapor deposition Raman spectroscopy nucleation termination

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