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Oxford Nanopore MinION Sequencing and Genome Assembly

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Genomics, Proteomics & Bioinformatics 2016年第5期14卷 265-279页

作者： Hengyun Lu Francesca Giordano Zemin Ning National Centre of Gene Research Chinese Academy of Sciences The wellcome trust sanger institute Wellcome Genome Campus

The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies （ONT）. MiniON identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MiniON has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assem- bly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

关键词： Third-generation sequencing Oxford nanopore MiniON-device De novo assembly Structural variations Molecular clinical diagnostics

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Solar-powered miniature robot for on-site oil spill treatment under magnetic steering

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Science China Technological Sciences 2024年第7期67卷 2164-2175页

作者： WANG Ben CHEN YunRui WANG Yun JI FengTong LI HongYuan NIU ShiChao HAN ZhiWu ZHANG YaBin GUO ZhiGuang College of Chemistry and Environmental Engineering Shenzhen University wellcome trust/Cancer Research UK Gurdon institute University of Cambridge Department of Physiology Development and Neuroscience University of Cambridge State Key Laboratory for Turbulence and Complex Systems Department of Mechanics and Engineering Science Beijing Innovation Center for Engineering Science and Advanced Technology College of Engineering Peking University Key Laboratory for Bionic Engineering Ministry of Education Jilin University State Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite Structures Ministry of Education Key Laboratory of New Processing Technology for Nonferrous Metals and Materials and School of Resources Environment and Materials Guangxi University Hubei Collaborative Innovation Centre for Advanced Organic Chemical Materials Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials Hubei University

Walking on the water surface is an effective method for miniature robots to transport payloads with dramatically decreased interfacial drag. Current aquatic robots reported are generally actuated by a beam of focused light that can trigger asymmetrical deformation, enabling the directional movement through horizontal momentum transfer of photoinduced actuation force to the water. However, the operations are heavily dependent on manual manipulation of the focused light, making the long-term actuation and application of the aquatic robots in vast scenarios challenging. Herein, we developed a kind of water striderinspired robot that can autonomously manage the motion on the water surface under solar irradiation, with their direction steerable by a magnetic field. The motion of this bioinspired robot on the water surface was achieved by the use of a solar cell panel as a driving module to enable propulsive motion based on the conversion of light-electric-mechanical energies. The superhydrophobic design of its leg surfaces enables the aquatic robots with weight-bearing and drag-reducing abilities. With the assistance of magnetic navigation, the bioinspired robot can continuously and controllably locomote to the oily spill floating on the water body and collect them with high efficiency. For further demonstration, the treatment of oil spills in a campus pool with high efficiency has also been achieved. This on-site oil-spill treating strategy, taking advantage of a home-made bioinspired robot actuated by natural sunlight under magnetic steering, shows great potential applications in water-body remediation.

关键词： miniature robot superhydrophobic water strider interfacial friction magnetic actuation

Delineating nuclear reprogramming

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Protein & Cell 2012年第5期3卷 329-345页

作者： Jolene Ooi Pentao Liu wellcome trust sanger institute Hinxton CB101SAUnited Kingdom Agency for Science Technology and ResearchSingapore 138632Singapore

Nuclear reprogramming is described as a molecular switch,triggered by the conversion of one cell type to another.Several key experiments in the past century have provided insight into the field of nuclear repro-gramming.Previously deemed impossible,this re-search area is now brimming with new findings and developments.In this review,we aim to give a historical perspective on how the notion of nuclear reprogram-ming was established,describing main experiments that were performed,including(1)somatic cell nuclear transfer,(2)exposure to cell extracts and cell fusion,and(3)transcription factor induced lineage switch.Ultimately,we focus on(4)transcription factor induced pluripotency,as initiated by a landmark discovery in 2006,where the process of converting somatic cells to a pluripotent state was narrowed down to four tran-scription factors.The conception that somatic cells possess the capacity to revert to an immature status brings about huge clinical implications including per-sonalized therapy,drug screening and disease model-ing.Although this technology has potential to revolu-tionize the medical field,it is still impeded by technical and biological obstacles.This review describes the effervescent changes in this field,addresses bottle-necks hindering its advancement and in conclusion,applies the latest findings to overcome these issues.

关键词： nuclear reprogramming naïve pluripotency

COVID-19-2021:A New,Less Predictable Phase of the Pandemic

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China CDC weekly 2021年第7期3卷 125-127页

作者： Jeremy Farrar wellcome trust

It is just over a year ago that what we now know as coronavirus disease 2019(COVID-19)first emerged in Wuhan,China(1).In twelve short months every village,every city in every continent has been affected.Hundreds of millions of people have been infected and recovered and over two million of people have tragically died from COVID-19.In reality,many more have lost loved ones.Yet we may still be closer to the start of this pandemic than to the end.

关键词： closer COV Wuhan

Risk factors for hepatocellular carcinoma associated with hepatitis C genotype 3 infection:A systematic review

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World Journal of Gastrointestinal Oncology 2024年第4期16卷 1596-1612页

作者： Hamzah Z Farooq Michael James Jane Abbott Patrick Oyibo Pip Divall Naheed Choudhry Graham R Foster Blizard institute Queen Mary University of LondonLondon E12ATUnited Kingdom School of Health and Psychological Sciences University of LondonLondon EC1V 0HBUnited Kingdom University Hospitals of Leicester Library University Hospitals of Leicester NHS TrustLeicester LE39QPUnited Kingdom

BACKGROUND Hepatitis C virus(HCV)is a blood-borne virus which globally affects around 79 million people and is associated with high morbidity and mortality.Chronic infection leads to cirrhosis in a large proportion of patients and often causes hepatocellular carcinoma(HCC)in people with cirrhosis.Of the 6 HCV genotypes(G1-G6),genotype-3 accounts for 17.9%of infections.HCV genotype-3 responds least well to directly-acting antivirals and patients with genotype-3 infection are at increased risk of HCC even if they do not have cirrhosis.AIM To systematically review and critically appraise all risk factors for HCC secondary to HCV-G3 in all settings.Consequently,we studied possible risk factors for HCC due to HCV-G3 in the literature from 1946 to 2023.METHODS This systematic review aimed to synthesise existing and published studies of risk factors for HCC secondary to HCV genotype-3 and evaluate their strengths and limitations.We searched Web of Science,Medline,EMBASE,and CENTRAL for publications reporting risk factors for HCC due to HCV genotype-3 in all settings,1946-2023.RESULTS Four thousand one hundred and forty-four records were identified from the four databases with 260 records removed as duplicates.Three thousand eight hundred and eighty-four records were screened with 3514 excluded.Three hundred and seventy-one full-texts were assessed for eligibility with seven studies included for analysis.Of the seven studies,three studies were retrospective case-control trials,two retrospective cohort studies,one a prospective cohort study and one a cross-sectional study design.All were based in hospital settings with four in Pakistan,two in South Korea and one in the United States.The total number of participants were 9621 of which 167 developed HCC(1.7%).All seven studies found cirrhosis to be a risk factor for HCC secondary to HCV genotype-3 followed by higher age(five-studies),with two studies each showing male sex,high alpha feto-protein,directly-acting antivirals treatment and achievement of sustained virologic res

关键词： Hepatocellular carcinoma Hepatitis C Genotype 3 Systematic review Blood-borne viruses Liver cancer

Self-replicating digital data storage with synthetic chromosomes

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National Science Review 2021年第7期8卷 66-67页

作者： Xinyu Lu Tom Ellis Imperial College Centre for Synthetic Biology Imperial College London Department of Bioengineering Imperial College London wellcome trust sanger institute

With the rapid development of the Internet and computational technologies, the exponential growth of digital data is beginning to overwhelm existing storage device capacities, driving an unprecedented demand for new data storage media. DNA, a natural genetic information storage system, has been proposed as a promising alternative[1]. Compared with traditional siliconbased storage, DNA-based storage hasmany advantages—incredible density,

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Pluripotency and its layers of complexity

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Cell Regeneration 2012年第1期1卷 47-56页

作者： Jolene Ooi Pentao Liu wellcome trust sanger institute Hinxton CB101SAUK Technology and Research Agency for Science1 Fusionopolis Way#20-10Connexis North Tower 138632Singapore.

Pluripotency is depicted by a self-renewing state that can competently differentiate to form the three germ layers.Different stages of early murine development can be captured on a petri dish,delineating a spectrum of pluripotent states,ranging from embryonic stem cells,embryonic germ cells to epiblast stem cells.Anomalous cell populations displaying signs of pluripotency have also been uncovered,from the isolation of embryonic carcinoma cells to the derivation of induced pluripotent stem cells.Gaining insight into the molecular circuitry within these cell types enlightens us about the significance and contribution of each stage,hence deepening our understanding of vertebrate development.In this review,we aim to describe experimental milestones that led to the understanding of embryonic development and the conception of pluripotency.We also discuss attempts at exploring the realm of pluripotency with the identification of pluripotent stem cells within mouse teratocarcinomas and embryos,and the generation of pluripotent cells through nuclear reprogramming.In conclusion,we illustrate pluripotent cells derived from other organisms,including human derivatives,and describe current paradigms in the comprehension of human pluripotency.

关键词： Naïve pluripotency Primed pluripotency Embryonic stem cells Induced pluripotent stem cells Epiblast stem cells

Neurocognitive Dysfunction After Treatment for Pediatric Brain Tumors:Subtype-Specific Findings and Proposal for Brain Network-Informed Evaluations

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Neuroscience Bulletin 2023年第12期39卷 1873-1886页

作者： Charlotte Sleurs Paul Fletcher Conor Mallucci Shivaram Avula Thankamma Ajithkumar Department of Cognitive Neuropsychology Tilburg University5037 ABTilburgThe Netherlands Department of Oncology KU Leuven3000LeuvenBelgium Department of Psychiatry University of CambridgeAddenbrookes HospitalCambridgeCB20QQUK wellcome trust MRC institute of Metabolic Science University of CambridgeCambridge Biomedical CampusCambridgeCB20QQUK Department of Neurosurgery Alder Hey Children’s NHS Foundation TrustLiverpoolL145ABUK Department of Radiology Alder Hey Children’s NHS Foundation TrustLiverpoolL145ABUK Department of Oncology Cambridge University Hospital NHS TrustCambridgeCB20QQUK

The increasing number of long-term survivors of pediatric brain tumors requires us to incorporate the most recent knowledge derived from cognitive neuroscience into their oncological treatment.As the lesion itself,as well as each treatment,can cause specific neural damage,the long-term neurocognitive outcomes are highly complex and challenging to assess.The number of neurocognitive studies in this population grows exponentially worldwide,motivating modern neuroscience to provide guidance in follow-up before,during and after treatment.In this review,we provide an overview of structural and functional brain connectomes and their role in the neuropsychological outcomes of specific brain tumor types.Based on this information,we propose a theoretical neuroscientific framework to apply appropriate neuropsychological and imaging follow-up for future clinical care and rehabilitation trials.

关键词： Connectome Pediatric brain tumor Neuroimaging Neurocognition-Neuropsychological assessment

How Often Does Human DNA Mutate?

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Science Foundation in China 2009年第1期17卷 37-39页

作者： Yali Xue The wellcome trust sanger institute Hinxton Cambridge CBIO 1SA UK

The human mutation rate—how often new changes appear in the DNA—is fundamental to understanding many aspects of medical genetics and human evolutionary genetics.But it is low,and has therefore been difficult to measure.In the past,scientists could only estimate it approximately, either by observing how often mutant phenotypes appeared,or by comparison of humans and closely related species,such as chimpanzee, where many mutations could accumulate but the time period was uncertain.Now,a new study supported by the NSFC in China and The Royal Society in the UK reports the first direct measurement of the human mutation rate at the individual letters(nucleotides or bases) of DNA.This was possible because new(next)-generation sequencing technology is much more powerful than the methods available previously.The work was published in the leading journal Current Biology on 15th September 2009.The results were reported in the news by Nature, Science and the BBC,as well as in more than 20 Chinese newspapers and radio stations after the work first appeared online on 27th August.It was also one of the research highlights in Nature on 3rd September,which commented'This direct measurement of the human mutation rate should help researchers to refine evolutionary dating and better understand the source of genetic disease'.From the work,researchers could estimate that everyone has around 200 new mutations in their genome;as the authors said,'we are all mutants'.The ability to reliably measure rates of DNA mutation means we can begin to ask how mutation rates vary between different regions of the genome and perhaps also between different individuals.

关键词：人类基因变异国家自然科学基金英国广播公司进化遗传学突变率直接测量研究人员

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