3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition.


:Live cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories.


Sci Rep


Scientific reports


Gardini L,Capitanio M,Pavone FS




Has Abstract


2015-11-03 00:00:00










  • 18β-glycyrrhetyl-3-O-sulfate would be a causative agent of licorice-induced pseudoaldosteronism.

    abstract::Licorice-induced pseudoaldosteronism is a common adverse effect in traditional Japanese Kampo medicine, and 3-monoglucuronyl glycyrrhetinic acid (3MGA) was considered as a causative agent of it. Previously, we found 22α-hydroxy-18β-glycyrrhetyl-3-O-sulfate-30-glucuronide (1), one of the metabolites of glycyrrhizin (GL...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Ishiuchi K,Morinaga O,Ohkita T,Tian C,Hirasawa A,Mitamura M,Maki Y,Kondo T,Yasujima T,Yuasa H,Minamizawa K,Namiki T,Makino T

    更新日期:2019-02-07 00:00:00

  • A Network of SLC and ABC Transporter and DME Genes Involved in Remote Sensing and Signaling in the Gut-Liver-Kidney Axis.

    abstract::Genes central to drug absorption, distribution, metabolism and elimination (ADME) also regulate numerous endogenous molecules. The Remote Sensing and Signaling Hypothesis argues that an ADME gene-centered network-including SLC and ABC "drug" transporters, "drug" metabolizing enzymes (DMEs), and regulatory genes-is ess...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Rosenthal SB,Bush KT,Nigam SK

    更新日期:2019-08-15 00:00:00

  • Combination of Platelet expression of PKCepsilon and cardiac troponin-I for early diagnosis of chest pain patients in the emergency department.

    abstract::A rapid differential diagnosis of the clinical conditions underlying chest pain is a relevant clinical issue. Specifically, a fast rule-in or -out of acute myocardial infarction (AMI) is mandatory to improve diagnostic outcome and cost-effectiveness of patient management. We demonstrated that Protein Kinase C (PKC) ep...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Carubbi C,Masselli E,Pozzi G,Mattioli M,Martini S,Goldoni M,Aloe R,Cervellin G,Vitale M,Gobbi G

    更新日期:2019-02-14 00:00:00

  • Bioactive baculovirus nanohybrids for stent based rapid vascular re-endothelialization.

    abstract::Present study, for the first time, reports the development of a nanohybridized baculovirus based stent that can locally promote vascular re-endothelialization by efficient delivery of pro-angiogenic vascular endothelial growth factor (Vegf) genes. In vitro data demonstrated rapid expression of functionally active Vegf...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Paul A,Elias CB,Shum-Tim D,Prakash S

    更新日期:2013-01-01 00:00:00

  • Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.

    abstract::Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. W...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: De Wit P,Yamada K,Panova M,André C,Johannesson K

    更新日期:2018-11-14 00:00:00

  • The functional role of time compression.

    abstract::Multisensory integration provides continuous and stable perception from separate sensory inputs. Here, we investigated the functional role of temporal binding between the visual and the tactile senses. To this end we used the paradigm of compression that induces shifts in time when probe stimuli are degraded, e.g., by...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Zimmermann E,Derichs C,Fink GR

    更新日期:2016-05-16 00:00:00

  • The immune mediated role of extracellular HMGB1 in a heterotopic model of bladder cancer radioresistance.

    abstract::Radical cystectomy (RC) together with bilateral pelvic lymph node dissection remains the standard treatment for muscle invasive bladder cancer (MIBC). However, radiation-based treatments such as tri-modal therapy (TMT) involving maximally performed transurethral resection of bladder tumor (TURBT), radiotherapy (XRT), ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Ayoub M,Shinde-Jadhav S,Mansure JJ,Alvarez F,Connell T,Seuntjens J,Piccirillo CA,Kassouf W

    更新日期:2019-04-23 00:00:00

  • Triazophos (TAP) removal in horizontal subsurface flow constructed wetlands (HSCWs) and its accumulation in plants and substrates.

    abstract::Triazophos (TAP) is a widely used phosphorus pesticide in China that possesses a potential risk for water pollution. We have studied the removal efficiency of TAP using pilot-scale horizontal subsurface flow constructed wetlands (HSCWs) as well as the contribution of plants, substrates and other pathways to its remova...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Wu J,Li Z,Wu L,Zhong F,Cui N,Dai Y,Cheng S

    更新日期:2017-07-14 00:00:00

  • Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals.

    abstract::Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical eviden...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Clarke CL,Edwards ME,Gielly L,Ehrich D,Hughes PDM,Morozova LM,Haflidason H,Mangerud J,Svendsen JI,Alsos IG

    更新日期:2019-12-23 00:00:00

  • p66Shc: A novel biomarker of tubular oxidative injury in patients with diabetic nephropathy.

    abstract::Increased p66Shc expression has been associated with diabetic nephropathy (DN). However, whether p66Shc can serve as a potential biomarker for tubular oxidative injury in DN is unknown. We measured the expression of p66Shc in peripheral blood monocytes (PBMs) and renal biopsy tissues from DN patients and then analysed...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Xu X,Zhu X,Ma M,Han Y,Hu C,Yuan S,Yang Y,Xiao L,Liu F,Kanwar YS,Sun L

    更新日期:2016-07-05 00:00:00

  • Effectiveness of Traditional Chinese Medicineas as an Adjunct Therapy for Refractory Schizophrenia: A Systematic Review and Meta Analysis.

    abstract::Although recent studies focused on traditional Chinese medicine (TCM) for the treatment of refractory schizophrenia have reported that it may be beneficial, there is still lack of convincing evidence and critical meta-analytic work regarding its effectiveness as an adjunctive therapy. Therefore, we performed a meta-an...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析


    authors: Wei YY,Lin WF,Zhang TH,Tang YX,Wang JJ,Zhong MF

    更新日期:2018-04-18 00:00:00

  • Contribution of DNA methylation to the expression of FCGRT in human liver and myocardium.

    abstract::FcRn mediates recycling and transcytosis of IgG and albumin in various cell types. The MHC-class-I-like protein of the FcRn heterodimer is encoded by FCGRT. Few determinants of variable FCGRT expression in humans have been identified so far. In this study, we investigated the presence of DNA methylation in regulatory ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Cejas RB,Ferguson DC,Quiñones-Lombraña A,Bard JE,Blanco JG

    更新日期:2019-06-17 00:00:00

  • The 2020 coronavirus lockdown and seismic monitoring of anthropic activities in Northern Italy.

    abstract::In March/April 2020 the Italian government drastically reduced vehicle traffic and interrupted all non-essential industrial activities over the entire national territory. Italy thus became the first country in the world, with the exception of Hubei, to enact lockdown measures as a consequence of the COVID-19 outbreak ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Poli P,Boaga J,Molinari I,Cascone V,Boschi L

    更新日期:2020-06-10 00:00:00

  • Evaluation of reference genes for real-time quantitative PCR analysis in southern corn rootworm, Diabrotica undecimpunctata howardi (Barber).

    abstract::Quantitative reverse transcription PCR (RT-qPCR) is one of the most efficient, reliable and widely used techniques to quantify gene expression. In this study, we evaluated the performance of six southern corn rootworm, Diabrotica undecimpunctata howardi (Barber), housekeeping genes (HKG), β-actin (Actin), β-tubulin (T...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Basu S,Pereira AE,Pinheiro DH,Wang H,Valencia-Jiménez A,Siegfried BD,Louis J,Zhou X',Vélez AM

    更新日期:2019-07-24 00:00:00

  • Author Correction: Role of extrinsic mechanical force in the development of the RA-I tactile mechanoreceptor.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误


    authors: Pham TQ,Kawaue T,Hoshi T,Tanaka Y,Miyata T,Sano A

    更新日期:2018-09-07 00:00:00

  • Pulsed electromagnetic fields increase osteogenetic commitment of MSCs via the mTOR pathway in TNF-α mediated inflammatory conditions: an in-vitro study.

    abstract::Pulsed electromagnetic fields (PEMFs) have been considered a potential treatment modality for fracture healing, however, the mechanism of their action remains unclear. Mammalian target of rapamycin (mTOR) signaling may affect osteoblast proliferation and differentiation. This study aimed to assess the osteogenic diffe...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Ferroni L,Gardin C,Dolkart O,Salai M,Barak S,Piattelli A,Amir-Barak H,Zavan B

    更新日期:2018-03-23 00:00:00

  • Magnocellular Based Visual Motion Training Improves Reading in Persian.

    abstract::The visual magnocellular system is thought to play a crucial role in learning to read. Here therefore, we examined whether magnocellular based training could improve reading in children with visual reading problems. The participants were 24 male primary school students aged between 9-11 (Mean = 9.76, SD = 0.59) with s...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Ebrahimi L,Pouretemad H,Khatibi A,Stein J

    更新日期:2019-02-04 00:00:00

  • Amygdala-centred functional connectivity affects daily cortisol concentrations: a putative link with anxiety.

    abstract::The amygdala plays a critical role in emotion. Its functional coupling with the hippocampus and ventromedial prefrontal cortex extending to a portion of the anterior cingulate cortex (ACC) is implicated in anxiogenesis and hypothalamic-pituitary-adrenal (HPA) system regulation. However, it remains unclear how amygdala...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Hakamata Y,Komi S,Moriguchi Y,Izawa S,Motomura Y,Sato E,Mizukami S,Kim Y,Hanakawa T,Inoue Y,Tagaya H

    更新日期:2017-08-16 00:00:00

  • Amorphous solid dispersions of enzalutamide and novel polysaccharide derivatives: investigation of relationships between polymer structure and performance.

    abstract::Amorphous solid dispersion (ASD) is a widely employed formulation technique for drugs with poor aqueous solubility. Polymers are integral components of ASDs, but mechanisms by which polymers lead to the generation and maintenance of supersaturated solutions, which enhance oral absorption in vivo, are poorly understood...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Wilson VR,Lou X,Osterling DJ,Stolarik DF,Jenkins GJ,Nichols BLB,Dong Y,Edgar KJ,Zhang GGZ,Taylor LS

    更新日期:2020-10-28 00:00:00

  • Genome-Wide Identification of Mitogen-activated Protein Kinase Cascade Genes and Transcriptional Profiling Analysis during Organ Development in Eucommia ulmoides.

    abstract::The mitogen-activated protein kinase (MAPK) cascades, which play crucial roles in plant development processes, are universal modules of signal transduction in eukaryotes and consist of a core module of three sequentially phosphorylated kinases: MAPK, MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK). This is the first re...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Jing T,Wang L,Liu H,Wuyun TN,Du H

    更新日期:2017-12-18 00:00:00

  • A prospective, randomized, double-blind, placebo-controlled trial of acute postoperative pain treatment using opioid analgesics with intravenous ibuprofen after radical cervical cancer surgery.

    abstract::This study assessed the efficacy and tolerability of intravenous ibuprofen in the improvement of post-operative pain control and the reduction of opioid usage. Patients were randomly divided into placebo, ibuprofen 400 mg and ibuprofen 800 mg groups. All patients received patient-controlled intravenous morphine analge...

    journal_title:Scientific reports

    pub_type: 杂志文章,随机对照试验


    authors: Liu X,Wang X,Zhao W,Wei L,Zhang P,Han F

    更新日期:2018-07-05 00:00:00

  • Thin films of formamidinium lead iodide (FAPI) deposited using aerosol assisted chemical vapour deposition (AACVD).

    abstract::Formamidinium lead iodide (CH(NH2)2PbI3, FAPI) thin films have been deposited on glass substrates at 150 °C using ambient pressure aerosol assisted chemical vapour deposition (AACVD). The films have been analysed by a range of techniques including powder X-ray diffraction (pXRD), scanning electron microscopy (SEM), en...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Alam F,Lewis DJ

    更新日期:2020-12-17 00:00:00

  • Platelet activation determines the severity of thrombocytopenia in dengue infection.

    abstract::Thrombocytopenia is common in patients with dengue virus (DENV) infections. With a focus on understanding the possible mechanism of thrombocytopenia in DENV infections we described a direct correlation between activation and depletion of platelets in patients. Our data showed a sharp decrease in platelet counts at day...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Ojha A,Nandi D,Batra H,Singhal R,Annarapu GK,Bhattacharyya S,Seth T,Dar L,Medigeshi GR,Vrati S,Vikram NK,Guchhait P

    更新日期:2017-01-31 00:00:00

  • Frequent occurrence of Mungbean yellow mosaic India virus in tomato leaf curl disease affected tomato in Oman.

    abstract::Next generation sequencing (NGS) of DNAs amplified by rolling circle amplification from 6 tomato (Solanum lycopersicum) plants with leaf curl symptoms identified a number of monopartite begomoviruses, including Tomato yellow leaf curl virus (TYLCV), and a betasatellite (Tomato leaf curl betasatellite [ToLCB]). Both TY...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Shahid MS,Shafiq M,Ilyas M,Raza A,Al-Sadrani MN,Al-Sadi AM,Briddon RW

    更新日期:2019-11-12 00:00:00

  • The evolution of interdisciplinarity in physics research.

    abstract::Science, being a social enterprise, is subject to fragmentation into groups that focus on specialized areas or topics. Often new advances occur through cross-fertilization of ideas between sub-fields that otherwise have little overlap as they study dissimilar phenomena using different techniques. Thus to explore the n...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Pan RK,Sinha S,Kaski K,Saramäki J

    更新日期:2012-01-01 00:00:00

  • Studying the role of axon fasciculation during development in a computational model of the Xenopus tadpole spinal cord.

    abstract::During nervous system development growing axons can interact with each other, for example by adhering together in order to produce bundles (fasciculation). How does such axon-axon interaction affect the resulting axonal trajectories, and what are the possible benefits of this process in terms of network function? In t...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Davis O,Merrison-Hort R,Soffe SR,Borisyuk R

    更新日期:2017-10-19 00:00:00

  • Functional dichotomy of Vδ2 γδ T cells in chronic hepatitis C virus infections: role in cytotoxicity but not for IFN-γ production.

    abstract::Vδ2 γδ (Vδ2) T cells, a major human γδ T cell subset, exhibit broad anti-tumor and anti-infective activity; however, their precise role in chronic hepatitis C virus (HCV) infections remains unclear. In this study, we analyzed the phenotype and function of Vδ2 T cells in 43 HCV-infected patients compared to 39 healthy ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Yin W,Tong S,Zhang Q,Shao J,Liu Q,Peng H,Hu H,Peng M,Hu P,Ren H,Tian Z,Zhang D

    更新日期:2016-05-19 00:00:00

  • A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association.

    abstract::Human KHDRBS1/Sam68 is an oncogenic splicing factor involved in signal transduction and pre-mRNA splicing. We explored the molecular mechanism of KHDRBS1 to be a prognostic marker in four different cancers. Within specific cancer, including kidney renal papillary cell carcinoma (KIRP), lung adenocarcinoma (LUAD), acut...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Sumithra B,Saxena U,Das AB

    更新日期:2019-07-31 00:00:00

  • Seasonal flow dynamics exacerbate overlap between artisanal fisheries and imperiled Ganges River dolphins.

    abstract::Here we quantify the effects of artisanal fisheries on the ecology of a small cetacean, the Ganges River dolphin (Platanista gangetica gangetica, GRD), in a large river system of Nepal. We examine the size-classes of fisheries' catches, behavioural changes in GRD in response to fishing activities, and diel overlap bet...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Paudel S,Koprowski JL,Cove MV

    更新日期:2020-11-02 00:00:00

  • Assessment of different techniques for 3D superimposition of serial digital maxillary dental casts on palatal structures.

    abstract::Serial 3-dimensional dental model superimposition provides a risk-free, detailed evaluation of morphological alterations on a patient's mouth. Here, we evaluated accuracy and precision of five palatal areas, used for superimposition of maxillary 3D digital dental casts. Sixteen pre- and post-orthodontic treatment dent...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Vasilakos G,Schilling R,Halazonetis D,Gkantidis N

    更新日期:2017-07-19 00:00:00