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Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes

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Horticulture Research 2023年第5期10卷 193-206页

作者： Upuli Nakandala Ardashir Kharabian Masouleh Malcolm WSmith Agnelo Furtado Patrick Mason lena Constantin Robert j.Henry Queensland Alliance for Agriculture and Food Innovation University of QueenslandBrisbane 4072Australia ARC Centre of Excellence for Plant Success in Nature and Agriculture University of QueenslandBrisbane 4072Australia Department of Agriculture and Fisheries Bundaberg Research StationBundabergQueensland 4670Australia

Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for *** few genomes have been anchored at the chromosome level and/or are haplotype phased,with the available genomes of varying accuracy and *** now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime)using highly accurate PacBio HiFi long reads,complemented with Hi-C *** with Hi-C integrated assembly resulted in a 331 Mb genome of *** with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness(BUSCO).Repeat analysis showed that more than 50% of the genome contained interspersed *** them,LTR elements were the predominant type(21.0%),of which LTR Gypsy(9.8%)and LTR copia(7.7%)elements were the most abundant repeats.A total of 29464 genes and 32009 transcripts were identified in the *** these,28222 CDS(25753 genes)had BLAST hits and 21401 CDS(75.8%)were annotated with at least one GO *** specific genes for antimicrobial peptides,defense,volatile compounds and acidity regulation were *** synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2,4,7 and *** chromosome scale,and haplotype resolved *** genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.

关键词： citrus Citrus breeding

Beyond cardiomyocytes:Cellular diversity in the heart's response to exercise

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运动与健康科学(英文) 2023年第4期12卷 423-437,F0003页

作者： lena E.Trager Margaret Lyons Alexandra Kuznetsov Cedric Sheffield Kangsan Roh Rebecca Freeman james Rhee j.Sawalla Guseh Haobo Li Anthony Rosenzweig Corrigan Minehan Heart Center Division of CardiologyCardiovascular Research CenterDepartment of MedicineMassachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA University of Minnesota Medical School MinneapolisMI 55455USA Department of Anesthesiology and Critical Care Massachusetts General HospitalHarvard Medical SchoolBostonMA 02115USA Institute for Heart and Brain Health University of Michigan Medical CenterAnn ArborMI 48109USA

Cardiomyocytes comprise~70%to 85%of the total volume of the adult mammalian heart but only about 25%to 35%of its total number of *** in single cell and single nuclei RNA sequencing have greatly facilitated investigation into and increased appreciation of the potential functions of non-cardiomyocytes in the *** much of this work has focused on the relationship between non-cardiomyocytes,disease,and the heart's response to pathological stress,it will also be important to understand the roles that these cells play in the healthy heart,cardiac homeostasis,and the response to physiological stress such as *** present review summarizes recent research highlighting dynamic changes in non-cardiomyocytes in response to the physiological stress of *** particular interest are changes in fibrotic pathways,the cardiac vasculature,and immune or inflammatory *** many instances,limited data are available about how specific lineages change in response to exercise or whether the changes observed are functionally important,underscoring the need for further research.

关键词： Angiogenesis Cardiac fibrosis Cardioprotection Hypertrophy Non-cardiomyocytes Proliferation

Acute liver failure secondary to acute antibody mediated rejection after compatible liver transplant: A case report

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World journal of Hepatology 2022年第1期14卷 287-294页

作者： Todd j Robinson james B Hendele Idoia Gimferrer Nicolae Leca Scott W Biggins jorge D Reyes lena Sibulesky Department of Surgery Virginia MasonSeattleWA 98101United States Department of Surgery University of Washington Medical CenterSeattleWA 98195United States Bloodworks Northwest SeattleWA 98104United States Department of Nephrology University of Washington Medical CenterSeattleWA 98195United States Department of Gastroenterology and Hepatology University of Washington Medical CenterSeattleWA 98195United States

BACKGROUND The liver has traditionally been regarded as resistant to antibody-mediated rejection(AMR).AMR in liver transplants is a field in its infancy compared to kidney and lung *** our case we present a patient with alpha-1-antitrypsin disease who underwent ABO compatible liver transplant complicated by acute liver failure(ALF)with evidence of antibody mediated rejection on allograft biopsy and elevated serum donor-specific antibodies(DSA).This case highlights the need for further investigations and heightened awareness for timely *** SUMMARY A 56 year-old woman with alpha-1-antitrypsin disease underwent ABO compatible liver transplant from a deceased *** recipient MELD at the time of transplant was *** flow cytometric crossmatches were noted to be positive for T and B *** patient had an uneventful recovery *** on postoperative day 5 the patient developed fevers,elevated liver function tests,distributive shock,renal failure,and hepatic *** went into ALF with evidence of antibody mediated rejection with portal inflammation,bile duct injury,endothelitis,and extensive centrizonal necrosis,and C4d staining on allograft biopsy and elevated *** various interventions including plasmapheresis and immunomodulating therapy,she continued to *** was relisted and successfully underwent liver *** This very rare case highlights AMR as the cause of ALF following liver transplant requiring retransplantation.

关键词： Liver transplant Acute antibody mediated rejection Acute liver failure Donor specific antibody Liver rejection Case report

Characterizing the patient experience during neoadjuvant therapy for pancreatic ductal adenocarcinoma:A qualitative study

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World journal of Gastrointestinal Oncology 2022年第6期14卷 1175-1186页

作者： lena Stevens Zachary j Brown Ryan Zeh Christina Monsour Sharla Wells-Di Gregorio Heena Santry Aslam M Ejaz Timothy Michael Pawlik jordan M Cloyd Department of Surgery The Ohio State University Wexner Medical CenterColumbusOH 43210United States Department of General Surgery University of Pittsburgh Medical CenterPittsburghPA 15213United States Department of Psychiatry Center for Palliative CareThe Ohio State University Wexner Medical CenterColumbusOH 43210United States

BACKGROUND Neoadjuvant therapy(NT)has increasingly been utilized for patients with localized pancreatic ductal adenocarcinoma(PDAC).It is the recommended approach for borderline resectable(BR)and locally advanced(LA)cancers and an increasingly utilized option for potentially resectable(PR)*** its increased use,little research has focused on patient-centered metrics among patients undergoing NT,including patient experiences,preferences,and recommendations.A better understanding of all aspects of the patient experience during NT may identify opportunities to design interventions aimed at improving quality of life;it may also facilitate the completion of NT and receipt of surgery,ultimately optimizing long-term *** To understand the experience of patients initiating and receiving NT to identify opportunities to improve neoadjuvant cancer care *** Semi-structured interviews of patients with localized PDAC during NT were conducted to explore their experience initiating and receiving *** took place between August 2020 and October *** to the descriptive nature of the research,questions were open *** were conducted over the phone,audio recorded and then *** interviews were coded by two independent researchers using NVivo 12,iteratively identifying themes until thematic saturation was *** integrative approach to qualitative analysis was used,utilizing both inductive and deductive *** A total of 12 patients with localized PDAC were *** with BR(n=7),PR(n=2),and LA(n=3)cancers participated in the *** patients indicated that choosing NT was the doctor’s recommendation,while most reported not being familiar with the concept of NT(n=11)and that NT was presented as the only option(n=8).Five themes describing the patient experience emerged:physical symptoms,emotional symptoms,coping mechanisms,access to care,and life *** most commonly cited recommendation for

关键词： Pancreatic ductal adenocarcinoma Neoadjuvant therapy Patient experience Patient-centered care Quality of life Qualitative research

Senescence-specific Alteration of Hydrogen Peroxide Levels in Arabidopsis thaliana and Oilseed Rape Spring Variety Brassica napus ***

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journal of Integrative Plant Biology 2012年第8期54卷 540-554页

作者： Stefan Bieker lena Riester Mark Stahl jürgen Franzaring Ulrike Zentgraf ZMBP (Center for Plant Molecular Biology) University of TübingenAuf der Morgenstelle 2872076 Tübingen Germany Institute for Landscape and Plant Ecology kologiezentrum 2August-von-Hartmann-Str.370599 StuttgartGermany

In order to analyze the signaling function of hydrogen peroxide （H202） production in senescence in more detail, we manipulated intracellular H202 levels in Arabidopsis thaliala （L.） Heynh by using the hydrogen- peroxide-sensitive part of the Escherichia coil transcription regulator OxyR, which was directed to the cytoplasm as well as into the peroxisomes. H202 levels were lowered and senescence was delayed in both transgenic lines, but OxyR was found to be more effective in the cytoplasm. To transfer this knowledge to crop plants, we analyzed oilseed rape plants Brassica napus L. cv. Mozart for H20~ and its scavenging enzymes catalase （CAT） and ascorbate peroxidase （APX） during leaf and plant development. H202 levels were found to increase during bolting and flowering time, but no increase could be observed in the very late stages of senescence. With increasing H202 levels, CAT and APX activities declined, so it is likely that similar mechanisms are used in oilseed rape and Arabidopsis to control H202 levels. Under elevated CO2 conditions, oilseed rape senescence was accelerated and coincided with an earlier increase in H202 levels, indicating that H202 may be one of the signals to inducing senescence in a broader range of Brassicaceae.

关键词： Arabidopsis thaliana Brassica napus E. coil Oxy-RD intracellular hydrogen peroxide senescence phenotype catalase ascorbatePeroxidase elevated CO2.

Observation of a single protein by ultrafast X-ray diffraction

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Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova johan Bielecki Rebecca Boll Benedikt j.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr jannik Lübke Adrian P.Mancuso Tommaso Mazza Carl Nettelblad Yevheniy Ovcharenko Daniel E.Rivas Max Rose Amit K.Samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko Daniel Westphal Tamme Wollweber lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.Chapman jonas A.Sellberg Carolin Seuring Ivan A.Vartanyants jochen Küpper Michael Meyer Filipe R.N.C.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly Center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS CR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User CryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical Center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg Center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific Computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

Current Injection Provokes Rapid Expansion of the Guard Cell Cytosolic Volume and Triggers Ca^2＋ Signals

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Molecular Plant 2016年第3期9卷 471-480页

作者： lena j. Voss Rainer Hedrich M. Rob G. Roelfsema Molecular Plant Physiology and Biophysics Julius-von-Sachs Institute for Biosciences Biocenter Werzburg University Julius-von-Sachs-Platz 2 97082 Werzburg Germany

High-resolution microscopy opens the door for detailed single-cell studies with fluorescent reporter dyes and proteins. We used a confocal spinning disc microscope to monitor fluorescent dyes and the fluorescent protein Venus in tobacco and Arabidopsis guard cells. Multi-barreled microelectrodes were used to inject dyes and apply voltage pulses, which provoke transient rises in the cytosolic Ca^2＋ level. Voltage pulses also caused changes in the distribution of Lucifer Yellow and Venus, which pointed to a reversible increase of guard cell cytosolic volume. The dynamic cytosolic volume changes turned out to be provoked by current injection of ions. A reduction of the clamp current, by blocking K^＋ uptake channels with Cs^＋, strongly suppressed the cytosolic volume changes. Cs^＋ not only inhibited the expansion of the cytosol, but also inhibited hyperpolarization-induced elevations of the cytosolic Ca^2＋ concentration. A complete loss of voltage-induced Ca^2＋ signals occurred when Ca^2＋-permeable plasma membrane channels were simultaneously blocked with La^3＋. This shows that two mechanisms cause hyperpolarization-induced elevation of the cytosolic Ca^2＋-concentration：（i） activation of voltage-dependent Ca^2＋-permeable channels, （ii） osmotically induced expansion of the cytosol, which leads to a release of Ca^2＋ from intracellular stores.

关键词： guard cell cytosolic Ca^2+ cytosolic volume voltage clamp current injection ion channel

Methods for measuring pre-,intra-,and postoperative skin thickness for cochlear implants

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journal of Otology 2022年第2期17卷 72-77页

作者： lena Zaubitzer Elena Schaefer Elisabeth Wallhaeuser-Franke johannes Burkart Katrin Herrmann Beatrice Walter Angela Schell Claudia Scherl jerome Servais Daniel Haeussler Department of Otorhinolaryngology Head and Neck Surgery University Hospital MannheimMedical Faculty MannheimRuprecht-Karls-Universitat HeidelbergGermany Department of Neuroradiology University Hospital MannheimMedical Faculty MannheimRuprecht-Karls-Universitat HeidelbergGermany

Objective:This study was conducted to determine whether there is a reliable method for measuring the thickness of the retroauricular skin before,during,and after cochlear implantation,which allows the assessment of the optimal force of the external magnet of the cochlear implant(CI).Methods:The retroauricular skin thickness of 83 patients who received a CI was measured using three different *** thickness was measured on pre-and postoperative CT images,as well as *** magnet category chosen by the surgeon was recorded when the implant was switched on and during the first follow-up *** analyses were performed on the different skin thickness measurements and between the skin thickness and magnet strength ***:Only six patients required an exchange of the magnet until the *** the median absolute thickness differed significantly between the three measures(p<0.0001),their thickness values showed highly significant correlations(Pearson’s r=0.457-0.585;p<0.01).In addition,magnet strength,was significantly correlated with the flap thickness determined pre-,post-,and during *** lowest correlation with magnet strength was found in the intraoperative needle ***:All three measurements methods provided a suitable base for determining the ideal magnetic ***,of particular interest were the pre-and postoperative CT *** first enabled the early assessment of the required magnetic strength and thus a timely postoperative supply,whereas the latter helped to estimate the need for magnetic strength reduction during follow-up care and the feasibility of an early swith-on.

关键词： Cochlear implant Headpiece Magnet strength Flap thickness

Live and Let Die： The Core Circadian Oscillator Coordinates Plant Life History and Pilots Leaf Senescence

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Molecular Plant 2018年第3期11卷 351-353页

作者： Ulrike Zentgraf jasmin Doll lena Riester Centre of Molecular Biology of Plants (ZMBP) University of Tübingen Auf der Morgenstelle 32 72076 Tübingen Germany

For a long time, many scientists were keen on discovering ＂the master regulator＂ of plant senescence. However, in the last two decades, it became very clear that this ＂master regulator＂ does not exist, but an extremely complex regulatory network controls all aspects and phases of senescence. Temporal transcript profiling of a defined leaf of Arabidopsis with high resolution, which covered 22 time points during onset and progression of leaf senescence, revealed expression changes of more than 6500 genes and disclosed a distinct chronology of events （Breeze et al., 2011）. Besides autophagy and transport,

关键词： ARABIDOPSIS