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Recent advances and perspectives in next generation sequencing application to the genetic research of type 2 diabetes

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World Journal of Diabetes 2019年第7期10卷 376-395页

作者： yulia A nasykhova Yury A Barbitoff Elena A Serebryakova Dmitry S Katserov Andrey S Glotov Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine St.Petersburg State UniversitySt.Petersburg 199034Russia Department of Genomic Medicine D.O.Ott Research Institute of ObstetricsGynaecology and ReproductologySt.Petersburg 199034Russia Bioinformatics Institute St.Petersburg 194021Russia Department of Genetics and Biotechnology St.Petersburg State UniversitySt.Petersburg 199034Russia Department of Genetics City Hospital No.40St.Petersburg 197706Russia Institute of Living Systems Immanuel Kant Baltic Federal UniversityKaliningrad 236016Russia

Type 2 diabetes(T2D)mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health ***-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of *** advances in the application of sequencing technologies to T2D research include,but are not limited to:(1)Fine mapping of causal rare and common genetic variants;(2)Identification of confident genelevel associations;(3)Identification of novel candidate genes by specific scoring approaches;(4)Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques;and(5)Investigation of microbial community alterations in patients with *** this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis,as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis,prevention,and treatment of the disease.

关键词： Type 2 diabetes next-generation sequencing Epigenetics Genome-wide association study Microbiome

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Alcoholic liver disease:Utility of animal models

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World Journal of Gastroenterology 2018年第45期24卷 5063-5075页

作者： Arantza Lamas-Paz Fengjie Hao Leonard J nelson Maria Teresa vázquez Santiago Canals Manuel Gómez del Moral Eduardo Martínez-naves yulia A nevzorova Francisco Javier Cubero Department of Immunology Ophthalmology and ORLComplutense University School of MedicineMadrid 28040Spain 12 de Octubre Health Research Institute(imas12) Madrid 28041Spain Institute for Bioengineering(IBioE) School of EngineeringFaraday BuildingThe University of EdinburghEdinburgh EH9 3 JLScotlandUnited Kingdom Department of Human Anatomy and Embryology Complutense University School of MedicineMadrid 28040Spain Instituto de neurociencias Consejo Superior de Investigaciones CientíficasUniversidad Miguel HernándezSan Juan de Alicante 03550Spain Department of Cell Biology Complutense University School of MedicineMadrid 28040Spain Department of Genetics Physiology and MicrobiologyFaculty of BiologyUniversidad ComplutenseMadrid 28040Spain Department of Internal Medicine Ⅲ University Hospital RWTH AachenAachen 52062Germany

Alcoholic liver disease(ALD) is a major cause of acute and chronic liver injury. Extensive evidence has been accumulated on the pathological process of ALD during the past decades. However, effective treatment options for ALD are very limited due to the lack of suitable in vivo models that recapitulate the full spectrum of ALD. Experimental animal models of ALD, particularly rodents, have been used extensively to mimic human ALD. An ideal animal model should recapitulate all aspects of the ALD process, including significant steatosis, hepatic neutrophil infiltration, and liver injury. A better strategy against ALD depends on clear diagnostic biomarkers, accurate predictor(s) of its progression and new therapeutic approaches to modulate stop or even reverse the disease. numerous models employing rodent animals have been established in the last decades to investigate the effects of acute and chronic alcohol exposure on the initiation and progression of ALD. Although significant progress has been made in gaining better knowledge on the mechanisms and pathology of ALD, many features of ALD are unknown, and require further investigation, ideally with improved animal models that more effectively mimic human ALD. Although differences in the degree and stages of alcoholic liver injury inevitably exist between animal models and human ALD, the acquisition and translational relevance will be greatly enhanced with the development of new and improved animal models of ALD.

关键词： Steatohepatitis Cirrhosis Hepatocellular carcinoma Alcoholic liver disease Reactive oxygen species

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Polysaccharide composition during cotton seed fibre development:temporal differences between species and in different seasons

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Journal of Cotton Research 2022年第4期5卷 12-24页

作者： PETTOLInO Filomena A. yulia Dina BACIC Antony LLEWELLYn Danny J. Commonwealth Scientific and Industrial Research Organisation(CSIRO) Agri-culture and FoodCanberraACT 2601Australia Department of Animal Plant&Soil SciencesLa Trobe Institute for Agriculture and FoodLa Trobe UniversityAgriBio BuildingBundooraVIC 3083Australia

Background:Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15-25 days until a secondary cell wall(SCW)begins to develop through a rapid increase in the deposition of microfibrillar cellulose between the plasma membrane and the primary cell wall that eventually terminates *** measurements of the different polysaccharide components in both wall types over time and how they influence fibre quality can direct studies involved in enhanc-ing fibre properties for yarn quality through cell wall manipulation or molecular ***:A detailed chemical analysis of cell wall composition by differential solvent fractionation was used to identify the range of polysaccharides present in mature cotton fibres and used to validate a simpler total cell wall monosaccharide linkage analysis protocol for wall compositional *** of fibres from 5 days post-anthesis through maturity for three cultivated species,Gossypium hirsutum,***,and ***,showed the dynamic nature of cell wall polysaccharide composition through fibre development and that it progressed differently for each *** grown in the glasshouse during either autumn to winter or spring to summer and within each species had fibre qualities and temporal aspects of cell wall development that were different for each ***,the timing of the deposition of the SCW was delayed in winter grown plants and appeared to influence key fibre qual-ity ***:These results suggest that the temporal aspects of cell wall polysaccharide biogenesis during fibre development influence final fibre quality,and this timing is determined by both genetic and environmental *** onset of SCW synthesis appears to be a critical factor coinciding with termination of fibre elongation and specify-ing the duration of wall thickening that then affects fibre le

关键词： Fibre development Gossypium hirsutum Gossypium barbadense Gossypium arboreum

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Intestinal microbiome changes in an infant with right atrial isomerism and recurrent necrotizing enterocolitis:A case report and review of literature

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World Journal of Clinical Cases 2022年第29期10卷 10583-10599页

作者： Aleksandra Kaplina Ekaterina Zaikova Artem Ivanov yulia volkova Tatiana Alkhova vladimir nikiforov Alexander Latypov Marina Khavkina Tatiana Fedoseeva Tatiana Pervunina yulia Skorobogatova Svetlana volkova vladimir Ulyantsev Olga Kalinina Stanislav Sitkin natalia Petrova Research Laboratory of Physiology and Diseases of newborns Almazov National Medical Research CentreSt.Petersburg 197341Russia Research Laboratory of Autoimmune and Autoinflammatory Diseases Almazov National Medical Research CentreSt.Petersburg 197341Russia vladimir Ulyantsev International Laboratory of Computer TechnologiesITMO UniversitySt.Petersburg 197101Russia Department of Cardiovascular Surgery for Children Almazov National Medical Research CentreSt.Petersburg 197341Russia Department of neonatal Physiology with an ICU Ward Almazov National Medical Research CentreSt.Petersburg 197341Russia Pediatric Cardiac Intensive Care Unit Almazov National Medical Research CentreSt.Petersburg 197341Russia neonatal and Preterm Special Care Unit(2nd Stage Care) Almazov National Medical Research CentreSt.Petersburg 197341Russia Institute of Perinatology and Pediatrics Almazov National Medical Research CentreSt.Petersburg 197341Russia Express Laboratory of Perinatal Centre Almazov National Medical Research CentreSt.Petersburg 197341Russia Clinical Diagnostic Laboratory Almazov National Medical Research CentreSt.Petersburg 197341Russia Epigenetics and Metagenomics Group Institute of Perinatology and PediatricsAlmazov National Medical Research CentreSt.Petersburg 197341Russia Department of Internal Diseases Gastroenterology and DieteticsNorth-Western State Medical University named after I.I.MechnikovSt.Petersburg 191015Russia

BACKGROUnD necrotizing enterocolitis(nEC)is a multifactorial disease that predominantly affects premature *** dysbiosis plays a critical role in nEC pathogenesis in premature *** main risk factor for nEC in term infants is mesenteric hypoperfusion associated with ductaldependent congenital heart disease(CHD)that eventually leads to intestinal *** incidence of nEC in neonates with critical CHD is 6.8%-13%.However,the role of the intestinal microbiome in nEC pathogenesis in infants with ductal-dependent CHD remains *** SUMMARY A male term neonate with right atrial isomerism underwent modified Blalock-Taussig shunt placement on the 14^(th)day of life and had persistent mesenteric hypoperfusion after *** patient had episodes of nEC stageⅡA on the 1^(st)and 28^(th)days after cardiac *** microbial composition was analyzed before and after cardiac surgery by sequencing region v4 of the 16S rRnA *** surgery,species belonging to genera veillonella and Clostridia and class Gammaproteobacteria were detected,Bifidobacteriaceae showed a low *** first nEC episode was associated with postoperative hemodynamic instability,intestinal ischemiareperfusion injury during cardiopulmonary bypass,and a high abundance of Clostridium paraputrificum(Clostridium sensu stricto I)(56.1%).Antibacterial therapy after the first nEC episode resulted in increased abundance of Gammaproteobacteria,decreased abundance of Firmicutes,and low alpha *** changes in the microbial composition promoted the growth of Clostridium sensu strictoⅠ(72.0%)before the second nEC *** A high abundance of Clostridium sensu strictoⅠand mesenteric hypoperfusion may have contributed to nEC in the present case.

关键词： necrotizing enterocolitis Congenital heart disease Ivemark syndrome Heterotaxy Right atrial isomerism Intestinal microbiome Case report

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Evolution of clustered magnetic nulls in a turbulent-like reconnection region in the magnetotail

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Science Bulletin 2016年第24期61卷 1145-1150页

作者： Ruilong Guo Zuyin Pu Suiyan Fu Lun Xie Malcolm Dunlop yulia v. Bogdanova Jiansen He Xin Wang Zhonghua Yao School of Earth and Space Sciences Peking UniversityBeijing 100871 China PKU/UCLA Joint Research Institute in Science and Engineering Peking University Beijing 100871 China School of Astronautics Beihang University Beijing 100191China RAL Space Rutherford Appleton Laboratory STFCDidcot OXll 0QX UK UCL Mullard Space Science Laboratory Dorking RH5 6NT UK

t Magnetic null points and flux ropes play important roles in the three-dimensional process of magnetic reconnection. In this study, a cluster of null points are reconstructed in the reconnection region in the magnetotail by applying a fitting-reconstruction method to measurements from the Cluster mission. The number of recon- structed null points varies rapidly, presenting a turbulentlike evolution of the magnetic structure. The electron density and the flux of the accelerated electrons were enhanced in this turbulent-like region. During this unstable reconnection process, a B-As-B null structure was formed, showing flux rope features and resembling a secondary island in the observation.

关键词： Magnetic reconnection - Turbulent Magnetic null point Flux ropes Magnetotail

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Solution of Self-similar Equations of the k-ε Model in the Shear Turbulent Mixing Problem and Its numerical Simulation

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Journal of Physical Science and Application 2015年第6期5卷 377-395页

作者： vyacheslav P. Statsenko yulia v. Tret'yachenko Yury v. Yanilkin Russian Federal nuclear Centre VNIIEF Sarov 607200 Russia

The paper presents the k-ε model equations of turbulence with a single set of constants chosen by the authors, which is appropriate to simulate a wide range of turbulent flows. The model validation has been performed for a number of flows and its main results are given in the paper. The turbulent mixing of flow with shear in the tangential velocity component is discussed in details. An analytical solution to the system of ordinary differential equations of the k-ε model of turbulent mixing has been found for the self-similar regime of flow. The model coefficients were chosen using simulation results for some simplest turbulent flows. The solution can be used for the verification of codes. The numerical simulation of the problem has been performed by the 2D code EGAK using this model. A good agreement of the numerical simulation results with the self-similar solution, 3D DnS results and known experimental data has been achieved. This allows stating that the k-ε model constants chosen by the authors are acceptable for the considered flow.

关键词： The k-ε model of turbulent mixing shear turbulent mixing self-similar equations numerical simulation.

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SuperDARn CUTLASS Finland radar observations of high-latitude magnetic reconnections under northward interplanetary magnetic field (IMF) conditions

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Science China(Technological Sciences) 2012年第5期55卷 1207-1216页

作者： ZHAnG QingHe LIU RuiYuan YAnG HuiGen HU HongQiao ZHAnG BeiChen DUnLOP Malcolm LESTER Mark BOGDAnOvA yulia WALSH Andrew SOA Key Laboratoryfor Polar Science Polar Research Institute of ChinaShanghai 200136China Space Science Department Rutherford-Appleton LaboratoryChiltonDidcotUK Department of Physics and Astronomy University of LeicesterLeicesterUK Mullard Space Science Laboratory University College LondonDorkingSurreyUK

A number of backscatter power enhancement events with ＂equatorward-moving radar auroral forms＂ in the high-latitude ionosphere were observed by SuperDARn CUTLASS Finland radar when the IMF was northward during 09：00 -10：00 UT on 26 March 2004. These events were also associated with sunward flow enhancements at each location in the northern Hemisphere which were shown in ionospheric convections measured by the SuperDARn radars. These are typical features of high-latitude （lobe） magnetic reconnections. The durations of the velocity enhancements imply that the evolution time of the lobe reconnec- tions is about 8-16 rain from their origin at the reconnection site to their addition to the magnetotall lobe again. In additional, the Double Star TC-1 spacecraft was moving from magnetosheath into magnetosphere, and crossing the magnetopause near the subsolar region during this interval, and observed typical low-latitude magnetic reconnection signatures. This infers that the dayside high- and low-latitude reconnections may occur simultaneously.

关键词： high-latitude magnetic reconnection equatorward-moving radar auroral form evolution time of the lobe reconnections

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Functional and Pathological Influence of Hypothermia on Spike Activity of Cortical neurons

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Journal of Behavioral and Brain Science 2021年第5期11卷 107-130页

作者： yulia S. Mednikova nadezhda M. Zakharova natalia v. Pasikova Institute of Higher nervous Activity and neurophysiology of RAS Moscow Russia ICB RAS Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences Pushchino Russia

In sensorimotor cortical slices of guinea pig using local iontophoretic application of glutamate to the soma and dendrites it was found that a decrease of temperature of incubating fluid from 34 to 21°C - 22°C changes the somatic responses to the local injection of glutamate to the dendritic loci, while the responses to iontophoretic application of glutamate to the soma remain unchanged. Hypothermic changes in reactivity to dendritic stimulation start below 30°C and coincide with changes in the spontaneous activity of neurons, both in the direction of increasing and decreasing the frequency of firing in different nerve cells. On hypothermic decrease of spontaneous activity, the latencies of evoked dendritic responses on the soma became more longer, while on hypothermic increase of firing level, somatic spike responses to iontophoretic application of glutamate to dendritic loci appeared with shorter latencies. Hypothermic changes in the physiological parameters of neurons were accompanied by a drop in spike amplitude at the same temperature and with its further decrease. At the same time, there was a decrease of spike reaction to iontophoretic application of acetylcholine below 30°. It is proposed that the reason for hypothermic changes of neuronal activity is decreasing rate of M-cholinergic process at 27°C - 29°C which leads to opening K+ channels of neuronal membranes and hence to attenuation of conductive function of dendrites and to imbalance of K+ ion homeostasis. Peculiarities of hypothermic regulation of neuronal spike activity depend on individual functional properties of cortical neurons.

关键词： Cortical Slices Spike Activity Acetylcholine Glutamate Hypothermia Dendro-Somatic Propagation

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咖啡酸代谢物的抗肾炎活性分析

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生物工程学报 2008年第12期24卷 2140-2141页

作者： yulia v. Inyushkina Konstantin v. Kiselev victor P. Bulgakov Biotechnology Department Institute of Biology and Soil Science Far East Branch of Russian Academy of Sciences Vladivostok 690022 Russia

在研究治疗肾功能紊乱植物的细胞培养时,建立了一个Eritrichium sericeum的E-4愈伤组织株系,发现此株系可产生大量的咖啡酸代谢物、(–)-rabdosiin(1.8%干重)和迷迭香酸(4.6%干重),通过诱导(–)-rabdosiin的含量提高至4.1%(干重)。将E-... 详细信息

在研究治疗肾功能紊乱植物的细胞培养时,建立了一个Eritrichium sericeum的E-4愈伤组织株系,发现此株系可产生大量的咖啡酸代谢物、(–)-rabdosiin(1.8%干重)和迷迭香酸(4.6%干重),通过诱导(–)-rabdosiin的含量提高至4.1%(干重)。将E-4愈伤组织喂服Masugi肾炎大鼠,结果发现,与对照组(未喂服E-4愈伤组织的Masugi肾炎大鼠)相比,处理组(喂服E-4愈伤组织)中的大鼠出现如下症状:尿多、排泄物中肌氨酸酐降低、尿蛋白水平降低;当对照组中所有大鼠都出现疼痛症状时,处理组中仍有约/4的大鼠表现出健康状况良好。以上结果表明,E-4株系具有缓解肾炎症状的潜在功能。此外,利用富含多酚的rolC转基因的细胞株系,研究了愈伤组织中咖啡酸代谢物的诱导合成机制。结果发现,在rloC转基因的***愈伤组织中,咖啡酸代谢物的高产与迷迭香酸生物合成中的关键基因CYP98A3的高表达有关。

关键词：咖啡酸代谢物细胞培养血管球性肾炎 CYP98

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MicroRnA Regulation in Extreme Environments: Differential Expression of MicroRnAs in the Intertidal Snail Littorina littorea During Extended Periods of Freezing and Anoxia

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Genomics, Proteomics & Bioinformatics 2012年第5期10卷 302-309页

作者： Kyle K.Biggar Samantha F.Kornfeld yulia Maistrovski Kenneth B.Storey Institute of Biochemistry&Department of Biology Carleton University

Several recent studies of vertebrate adaptation to environmental stress have suggested roles for microRnAs （miRnAs） in regulating glo- bal suppression of protein synthesis and/or restructuring protein expression patterns. The present study is the first to characterize stress- responsive alterations in the expression of miRnAs during natural freezing or anoxia exposures in an invertebrate species, the intertidal gastropod Littorina littorea. These snails are exposed to anoxia and freezing conditions as their environment constantly fluctuates on both a tidal and seasonal basis. The expression of selected miRnAs that are known to influence the cell cycle, cellular signaling pathways, carbohydrate metabolism and apoptosis was evaluated using RT-PCR. Compared to controls, significant changes in expression were observed for miR-la-1, miR-34a and miR-29b in hepatopancreas and for miR-la-1, miR-34a, miR-133a, miR-125b, miR-29b and miR-2a in foot muscle after freezing exposure at -6 ~C for 24 h （P 〈 0.05）. In addition, in response to anoxia stress for 24 h, significant changes in expression were also observed for miR-la-1, miR-210 and miR-29b in hepatopancreas and for miR-1 a-1, miR-34a, miR-133a, miR-29b and miR-2a in foot muscle （P 〈 0.05）. Moreover, protein expression of Dicer, an enzyme responsible for mature microRnA processing, was increased in foot muscle during freezing and anoxia and in hepatopancreas during freezing. Alterations in expression of these miRnAs in L. littorea tissues may contribute to organismal survival under freezing and anoxia.

关键词： Freeze tolerance Anaerobiosis Metabolic rate depression Periwinkle Marine mollusk

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