Challenges in quantitative single molecule localization microscopy.

Abstract:

:Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Shivanandan A,Deschout H,Scarselli M,Radenovic A

doi

10.1016/j.febslet.2014.06.014

subject

Has Abstract

pub_date

2014-10-01 00:00:00

pages

3595-602

issue

19

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(14)00472-4

journal_volume

588

pub_type

杂志文章,评审
  • Retinal dehydrogenase gene expression in stomach and small intestine of rats during postnatal development and in vitamin A deficiency.

    abstract::Retinal dehydrogenase (RALDH) catalyzes the oxidation of retinal to all-trans and 9-cis retinoic acid, which function as ligands controlling RAR and RXR nuclear receptor-signaling pathways. We have recently shown the expression of RALDH transcript in the stomach and small intestine by reverse transcription polymerase ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)00355-x

    authors: Bhat PV

    更新日期:1998-04-17 00:00:00

  • Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence.

    abstract::A novel gene for advanced red-shifted protein with an emission maximum at 593 nm was cloned from Discosoma coral. The protein, named dsFP593, is highly homologous to the recently described GFP-like protein drFP583 with an emission maximum at 583 nm. Using the remarkable similarity of the drFP583 and dsFP593 genes, we ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)01895-0

    authors: Fradkov AF,Chen Y,Ding L,Barsova EV,Matz MV,Lukyanov SA

    更新日期:2000-08-18 00:00:00

  • IκBL, a novel member of the nuclear IκB family, inhibits inflammatory cytokine expression.

    abstract::We previously reported that IκBL prevents experimental autoimmune arthritis. The molecular mechanism, however, still remains unclear. In contrast to four splicing-isoforms of IκBL in human, two isoforms were identified in mouse. The major isoform IκBL-α(S) suppressed LPS-induced NF-κB activation and transcription of T...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2011.10.024

    authors: Chiba T,Miyashita K,Sugoh T,Warita T,Inoko H,Kimura M,Sato T

    更新日期:2011-11-16 00:00:00

  • The integrin alphaVbeta6 binds and activates latent TGFbeta3.

    abstract::Transforming growth factors-beta (TGFbeta1, 2 and 3) are secreted in a complex with their propeptides (latency-associated peptide 1 (LAP1), 2 and 3). TGFbeta signaling requires the dissociation of LAP and TGFbeta, a process termed latent TGFbeta activation. This process is a critical but incompletely understood step i...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(01)03280-x

    authors: Annes JP,Rifkin DB,Munger JS

    更新日期:2002-01-30 00:00:00

  • Antibodies to a C-terminal peptide of the rat brain glutamate receptor subunit, GluR-A, recognize a subpopulation of AMPA binding sites but not kainate sites.

    abstract::Antibodies were made to a thirteen amino acid synthetic peptide corresponding to the C-terminal portion of the glutamate (glu) receptor, GluR-A. The immunoprecipitation of kainic acid (KA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) binding sites by the anti-peptide antibodies was studied using...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(90)80529-r

    authors: Wenthold RJ,Hunter C,Wada K,Dechesne CJ

    更新日期:1990-12-10 00:00:00

  • Capsular polysaccharide production and serum survival of Vibrio vulnificus are dependent on antitermination control by RfaH.

    abstract::The human pathogen Vibrio vulnificus undergoes phase variation among colonial morphotypes, including a virulent opaque form which produces capsular polysaccharide (CPS) and a translucent phenotype that produces little or no CPS and is attenuated. Here, we found that a V. vulnificus mutant defective for RfaH antitermin...

    journal_title:FEBS letters

    pub_type: 信件

    doi:10.1002/1873-3468.12490

    authors: Garrett SB,Garrison-Schilling KL,Cooke JT,Pettis GS

    更新日期:2016-12-01 00:00:00

  • Original involvement of antimicrobial peptides in mussel innate immunity.

    abstract::Recently, the existence and extended diversity of antimicrobial peptides has been revealed in two mussel species. These molecules are classified into four groups according to common features of their primary structure: defensins, mytilins, myticins and mytimycin. In Mytilus galloprovincialis, gene structure reveals sy...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/s0014-5793(00)02192-x

    authors: Mitta G,Vandenbulcke F,Roch P

    更新日期:2000-12-15 00:00:00

  • The dipyridyls paraquat and diquat attenuate the interaction of G-actin with thymosin beta4.

    abstract::Beta-thymosins sequester G-actin and preserve a pool of monomers of actin which constitute an important prerequisite for cellular function of the microfilament system. To study the influence of paraquat binding to G-actin on the interaction of G-actin with thymosin beta4 we determined the apparent dissociation constan...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)00295-6

    authors: Huff T,Cappelletti G,Hannappel E

    更新日期:1998-04-03 00:00:00

  • Vibrio vulnificus glycogen branching enzyme preferentially transfers very short chains: N1 domain determines the chain length transferred.

    abstract::The glycogen branching enzyme from Vibrio vulnificus (VvGBE) transfers short side chains (DP 3-5) significantly greater than any other bacterial glycogen branching enzyme (GBE). To elucidate the role of the N-domain of VvGBE in the unique branching pattern, domain-truncated (N1 and N) and N1-domain-swapped (with VvGBE...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2015.03.011

    authors: Jo HJ,Park S,Jeong HG,Kim JW,Park JT

    更新日期:2015-04-28 00:00:00

  • Commitment of Annexin A2 in recruitment of microRNAs into extracellular vesicles.

    abstract::Extracellular vesicles (EVs) contain microRNAs (miRNAs). However, the exact molecular mechanisms of the recruitment of miRNAs in EVs are not well characterized. Based on proteomic analysis, we identified that silencing of Annexin A2 (ANXA2) significantly decreased the amount of miRNAs in EVs. In addition, microarray a...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2015.11.036

    authors: Hagiwara K,Katsuda T,Gailhouste L,Kosaka N,Ochiya T

    更新日期:2015-12-21 00:00:00

  • Nuclear functions in space and time: gene expression in a dynamic, constrained environment.

    abstract::All eukaryotic cells enclose their genome within a dedicated, membrane-bound organelle termed the nucleus, which functions to partition gene transcription from sites of protein translation in the cytoplasm. Despite a great deal of research effort, basic questions about chromosome structure and gene expression mechanis...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2008.04.029

    authors: Trinkle-Mulcahy L,Lamond AI

    更新日期:2008-06-18 00:00:00

  • The chlorophyll-binding protein IsiA is inducible by high light and protects the cyanobacterium Synechocystis PCC6803 from photooxidative stress.

    abstract::The products of the isiAB operon are a chlorophyll antenna protein (IsiA) and flavodoxin (IsiB), which accumulate in cyanobacteria grown under iron starvation conditions. Here we show that strong light triggers de-repression of isiAB transcription and leads to IsiA and flavodoxin accumulation under iron replete condit...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2005.03.021

    authors: Havaux M,Guedeney G,Hagemann M,Yeremenko N,Matthijs HC,Jeanjean R

    更新日期:2005-04-25 00:00:00

  • Hepoxilins raise circulating insulin levels in vivo.

    abstract::We have demonstrated over a decade ago that hepoxilins cause the release of insulin from isolated pancreatic islets of Langerhans in vitro. However, no studies are available so far to indicate whether these compounds are active in vivo. The present study is the first to our knowledge which demonstrates that hepoxilins...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)01460-x

    authors: Pace-Asciak CR,Demin PM,Estrada M,Liu G

    更新日期:1999-11-19 00:00:00

  • Phosphorylation and changes in the distribution of nucleolin promote tumor metastasis via the PI3K/Akt pathway in colorectal carcinoma.

    abstract::Here, we investigated the molecular mechanism underlying the changes in the distribution of nucleolin. Our study identified PI3K/Akt signaling as an essential pathway regulating the distribution of nucleolin. Furthermore, nucleolin can interact with phospho-PI3K-p55, and changes in the distribution of nucleolin were r...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2014.03.047

    authors: Wu DM,Zhang P,Liu RY,Sang YX,Zhou C,Xu GC,Yang JL,Tong AP,Wang CT

    更新日期:2014-05-21 00:00:00

  • Substrate-induced structural alterations of Mycobacterial mycothione reductase and critical residues involved.

    abstract::Redox homeostasis is a prerequisite for survival of the pathogen Mycobacterium tuberculosis (Mtb) which employs the low molecular weight thiol mycothiol (MSH). The Mycobacterial NADPH-dependent mycothione reductase (MtMtr), composed of an NADPH-, FAD-, and a dimerization-domain connected by linkers, regulates the bala...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1002/1873-3468.12984

    authors: Kumar A,Subramanian Manimekalai MS,Grüber G

    更新日期:2018-02-01 00:00:00

  • Molecular and cellular activities of Helicobacter pylori pathogenic factors.

    abstract::Stomach infection with pathogenic strains of Helicobacter pylori causes in some patients severe gastroduodenal diseases. These bacteria produce various virulence factors and, here, we review the recent acquisition on the biochemical mode of action of three major factors. We discuss the role of urease both as buffer of...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/s0014-5793(99)00652-3

    authors: Montecucco C,Papini E,de Bernard M,Zoratti M

    更新日期:1999-06-04 00:00:00

  • Replicable and recombinogenic RNAs.

    abstract::This paper summarizes results of the 40-year studies on replication and recombination of RNA molecules in the cell-free amplification system of bacteriophage Q. Special attention is paid to the molecular colony technique that has provided for the discovery of the nature of "spontaneous" RNA synthesis by Q replicase an...

    journal_title:FEBS letters

    pub_type: 杂志文章,评审

    doi:10.1016/j.febslet.2004.03.066

    authors: Chetverin AB

    更新日期:2004-06-01 00:00:00

  • SABP2, a methyl salicylate esterase is required for the systemic acquired resistance induced by acibenzolar-S-methyl in plants.

    abstract::Tobacco SABP2, a 29kDa protein catalyzes the conversion of methyl salicylic acid (MeSA) into salicylic acid (SA) to induce SAR. Pretreatment of plants with acibenzolar-S-methyl (ASM), a functional analog of salicylic acid induces systemic acquired resistance (SAR). Data presented in this paper suggest that SABP2 catal...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2010.06.046

    authors: Tripathi D,Jiang YL,Kumar D

    更新日期:2010-08-04 00:00:00

  • Triphenyltin chloride inhibits superoxide production by human neutrophils stimulated with a surface active agent.

    abstract::Treatment of human neutrophils with triphenyltin chloride (TPTCl)-inhibited superoxide (O-2) production stimulated with phorbol myristate acetate (PMA). TPTCl was more potent as inhibitor of O-2 production than other phenyltin compounds. The O-2 production by the xanthine oxidase-acetaldehyde system was not inhibited ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(83)80296-8

    authors: Matsui H,Wada O,Ushijima Y,Akuzawa T

    更新日期:1983-12-12 00:00:00

  • Protein Phosphatase 1 dephosphorylates TDP-43 and suppresses its function in tau exon 10 inclusion.

    abstract::Transactive response DNA-binding protein of 43 kDa (TDP-43) regulates RNA processing, including alternative splicing of tau exon 10. Pathological TDP-43 is hyperphosphorylated. However, how do the protein phosphatase(s) (PP) regulate TDP-43 phosphorylation is unclear. Here, we found that both PP1 and PP2A were coimmun...

    journal_title:FEBS letters

    pub_type: 信件

    doi:10.1002/1873-3468.12976

    authors: Gu J,Wang W,Miao S,Chen F,Wu F,Hu W,Iqbal K,Gong CX,Liu F

    更新日期:2018-02-01 00:00:00

  • Effect of lysophosphatidic acid on the preimplantation development of mouse embryos.

    abstract::The effect of lysophosphatidic acid (LPA) on the preimplantation development of mouse embryos was examined. The blastocyst rates from 2-cell and 4-cell stage embryos were significantly higher in the presence of LPA at the pronuclear stage. However, the blastocyst rate from 4-cell stage embryos was significantly lower ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)00815-9

    authors: Kobayashi T,Yamano S,Murayama S,Ishikawa H,Tokumura A,Aono T

    更新日期:1994-08-29 00:00:00

  • The hinge region of chicken annexin I contains no site for tyrosine phosphorylation.

    abstract::Annexin I (AnxI) is a calcium-dependent membrane binding protein which has been implicated in various physiological activities. The region of the chicken anxI cDNA encoding the first 130 amino terminal residues was cloned by reverse transcription PCR in order to determine the relationship of its variable amino-termina...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(93)80241-l

    authors: Sidis Y,Horseman ND

    更新日期:1993-08-30 00:00:00

  • Phosphoinositide-dependent kinase l (PDK1) haplo-insufficiency inhibits production of alpha/beta (alpha/beta) but not gamma delta (gamma/delta) T lymphocytes.

    abstract::In the present study, we have explored the impact of deleting a single allele of PDK1 in T cell progenitors on alpha/beta and gamma/delta T cell development. The data show that deleting a single allele of PDK1 allows differentiation of alpha/beta T cells but prevents their proliferative expansion in the thymus. Accord...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.03.022

    authors: Kelly AP,Hinton HJ,Clarke RG,Cantrell DA

    更新日期:2006-04-03 00:00:00

  • MiR-449c targets c-Myc and inhibits NSCLC cell progression.

    abstract::MicroRNAs (miRNA) play an important role in tumorigenesis, proliferation, and differentiation. Altered miRNA expression in cancer indicates that miRNAs can function as tumor suppressors or oncogenes. MiR-449c downregulation in non-small cell lung cancer (NSCLC) compared with normal lung tissues was investigated in thi...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2013.03.006

    authors: Miao LJ,Huang SF,Sun ZT,Gao ZY,Zhang RX,Liu Y,Wang J

    更新日期:2013-05-02 00:00:00

  • Protective effect of L-carnitine on hyperammonemia.

    abstract::Inborn errors of the urea cycle, liver malfunction and drug-induced hepatotoxicity are causes of life-threatening encephalopathies arising from hyperammonemia. L-Carnitine prevented entirely ammonia toxicity in mice when injected intraperitoneally 30 min before a lethal dose of ammonium acetate. Survival depends on th...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(84)80106-4

    authors: O'Connor JE,Costell M,Grisolía S

    更新日期:1984-01-30 00:00:00

  • Purification and crystallization of the ternary complex of elongation factor Tu:GTP and Phe-tRNA(Phe).

    abstract::Elongation factor Tu (EF-Tu) is the most abundant protein in prokaryotic cells. Its general function in protein biosynthesis is well established. It is a member of the large family of G-proteins, all of which bind guanosine phosphates (GDP or GTP) as cofactors. In its active GTP bound state EF-Tu binds aminoacylated t...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(94)01254-7

    authors: Nissen P,Reshetnikova L,Siboska G,Polekhina G,Thirup S,Kjeldgaard M,Clark BF,Nyborg J

    更新日期:1994-12-19 00:00:00

  • TNF-alpha enhances intracellular glucocorticoid availability.

    abstract::For understanding the mechanism(s) relating inflammation to corticosteroid action, the effect of tumour necrosis factor-alpha (TNF-alpha) on 11beta-hydroxysteroid dehydrogenase type 2 (11beta-HSD2), the enzyme regulating access of 11beta-hydroxycorticosteroids to receptors, was studied in LLC-PK(1) cells. We observed ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(01)03004-6

    authors: Heiniger CD,Rochat MK,Frey FJ,Frey BM

    更新日期:2001-11-02 00:00:00

  • Interaction between calmodulin and microtubule-associated proteins prepared at different stages of brain development.

    abstract::Rat brain microtubules were prepared at the adult stage and from immature (i.e., 4-day-old) animals. At an early stage of development, the composition of microtubule-associated proteins is qualitatively different from that found at the adult stage [(1982) Eur. J. Biochem. 129, 465-471]. The influence of calmodulin on ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(84)81148-5

    authors: Erneux C,Passareiro H,Nunez J

    更新日期:1984-07-09 00:00:00

  • Identification of a troponin-I like protein in platelet preparations as histone H2B.

    abstract::A tropomyosin-binding protein (app. Mr 17000) was detected in equine platelet preparations by a gel overlay technique. Its isolation, amino acid and partial sequence analyses have shown it to be histone H2B. As with a similar protein from pig platelet preparations [der Terrossian et al. (1983) FEBS Lett. 152, 202-206]...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(83)81130-2

    authors: Stewart DI,Golosinska K,Smillie LB

    更新日期:1983-06-27 00:00:00

  • Function and structure of GH13_31 α-glucosidase with high α-(1→4)-glucosidic linkage specificity and transglucosylation activity.

    abstract::α-Glucosidase hydrolyzes α-glucosides and transfers α-glucosyl residues to an acceptor through transglucosylation. In this study, GH13_31 α-glucosidase BspAG13_31A with high transglucosylation activity is reported in Bacillus sp. AHU2216 and biochemically and structurally characterized. This enzyme is specific to α-(1...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1002/1873-3468.13126

    authors: Auiewiriyanukul W,Saburi W,Kato K,Yao M,Mori H

    更新日期:2018-07-01 00:00:00