Giovanni Cardone

Giovanni Cardone
Max Planck Institute of Biochemistry | MPIB · Imaging Facillity

About

110
Publications
5,926
Reads
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2,535
Citations
Additional affiliations
January 2016 - present
Max Planck Institute of Biochemistry
Position
  • Image Analysis Specialist
October 2011 - December 2015
University of California, San Diego
Position
  • Researcher
March 2004 - October 2011
National Institutes of Health

Publications

Publications (110)
Article
Full-text available
Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here,...
Preprint
Background Mitochondria produce cellular energy in the form of ATP and are involved in various metabolic and signaling processes. However, the cellular requirements for mitochondria are different depending on cell type, cell state or organism. Information on the expression dynamics of genes with mitochondrial functions (mito-genes) is embedded in p...
Article
The co-self-assembly of proteins and nucleic acids (NAs) produces complex biomolecular machines (e.g., ribosomes and telomerases) that represent some of the most daunting targets for biomolecular design. Despite significant advances in protein and DNA or RNA nanotechnology, the construction of artificial nucleoprotein complexes has largely been lim...
Article
Full-text available
Microtubules are central elements of the eukaryotic cytoskeleton that often function as part of branched networks. Current models for branching include nucleation of new microtubules from severed microtubule seeds or from γ-tubulin recruited to the side of a pre-existing microtubule. Here, we found that microtubules can be directly remodelled into...
Article
Full-text available
Muscles organise pseudo-crystalline arrays of actin, myosin and titin filaments to build force-producing sarcomeres. To study sarcomerogenesis, we have generated a transcriptomics resource of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, most sarcomeric components group in two clusters, whi...
Data
This table includes the length measurements of the indirect flight muscle fibers at the indicated stage.
Data
This table includes the sarcomere length in wild type flight muscles measured at the indicated stage. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
This table includes the myofiber cross-sectional area measured in wild type flight muscle fibers or only fibers 3 and four at the indicated stage.
Data
This table includes the myofibril diameter measured in wild type flight muscles at the indicated stage.
Data
This table includes the length measurements of the indirect flight muscle fibers at the indicated stage for strn-mlck mutants and wild-type controls.
Data
This table includes the sarcomere length measured in strn-mlck mutant flight muscles at the indicated stage. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
This table includes calculation of the number of sarcomeres per myofibril in wild type flight muscles at the indicated stage.
Data
This table includes the muscle twitch events per Act88F >> salmIR fiber per 5 min and the respective controls recorded at the indicated stage.
Data
This table includes the sarcomere length measured in Act88F >> salmIR flight muscles and the respective controls at the indicated stage. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
This tables includes the sarcomere/myofibril width measured in Act88F >> salmIR flight muscles and the respective controls at the indicated stage. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
This table includes the sarcomere/myofibril width in wild type flight muscles measured at the indicated stage. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
This table includes the muscle twitch events per wild-type fiber per 5 min recorded at the indicated stage.
Data
This table includes the fiber divided by bead fluorescence intensity measurements for quantification of the indicated fosmid-GFP or UAS-GFP-Gma expression levels at the indicated stage.
Data
This table includes the calculated numbers of sarcomeres per myofibril at the indicated stage for strn-mlck mutants. Note that image analysis is limited by pixel size and thus can result in the same number.
Data
mRNA-Seq raw data The file includes multiple tabs containing the raw or input counts data from bioinformatics analysis, as well as a key to all original data provided in the supplementary tables. This table includes mRNA-Seq counts data, DESeq2 normalized counts data and standard normal counts data used for Mfuzz clustering for wild-type and salmIR...
Data
DESeq2 pairwise differential expression analysis This table contains multiple tabs containing the output data from DESeq2 differential expression analysis between sequential IFM development time points, from 30 to 72 hr APF as well as between WT and salmIR IFM.
Data
This table includes the number of myofibrils per myofiber calculated for either all wild type flight muscle fibers or only fibers 3 and four at the indicated stage.
Data
This table includes the fiber divided by bead fluorescence intensity measurements for various fosmid-GFPs in the Act88F >> salmIR or control Act88F-Gal4 x w- background at 90 hr APF.
Data
This table includes the numbers of sarcomeres calculated per strn-mlck mutant myofibril and the respective control at the indicated stage.
Data
GO-Elite analysis data. This table includes multiple tabs containing the GO-Elite analysis of enrichments in Mfuzz clusters as well as genes up- or down-regulated from 30–72 hr APF and between wild-type and salmIR IFM. It also contains a complete list of all genes included in the ‘User Defined’ gene sets.
Data
Statistical Data This table includes multiple tabs containing the statistical and calculation data for the different panels of Figures 1, 5, 6, 7 and 8.
Data
Summary of sarcomere and myofibril quantifications This table includes a numerical summary of quantification values reported graphically in Figures 5, 7 and 8. Quantifications of sarcomere length, myofibril width and myofibril diameter were performed with the MyofibrilJ script (see Materials and methods). Fiber length and cross-sectional area measu...
Article
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the...
Preprint
Full-text available
Muscles organise pseudo-crystalline arrays of actin, myosin and titin filaments to build force-producing sarcomeres. To study how sarcomeres are built, we performed transcriptome sequencing of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, two clusters are strongly enriched for sarcomeric co...
Article
Importance: The mechanism of AAV genome packaging is still poorly understood, particularly with respect to the capsid determinants of the required capsid-Rep interaction. Understanding this mechanism may aid in the improvement of AAV packaging efficiency, which is currently ∼1:10 (10%) genome packaged to empty capsid in vector preparations. This r...
Article
div class="title">Structural Rearrangements in R432A Variant of AAV2 Affect Genome Packaging - Volume 22 Issue S3 - Lauren M. Drouin, Bridget Lins, Mandy Janssen, Antonette Bennett, Paul R. Chipman, Robert McKenna, Weijun Chen, Nicholas Muzyczka, Giovanni Cardone, Timothy S. Baker, Mavis Agbandje-McKenna
Article
Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial cancers including cervical cancer. The HPV capsid is made up of 360 copies of major (L1) and 72 copies of minor (L2) capsid proteins. To date, limited high...
Article
Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties1, 2 that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge...
Article
Full-text available
Unlabelled: Giardia lamblia virus (GLV) is a small, nonenveloped, nonsegmented double-stranded RNA (dsRNA) virus infecting Giardia lamblia, the most common protozoan pathogen of the human intestine and a major agent of waterborne diarrheal disease worldwide. GLV (genus Giardiavirus) is a member of family Totiviridae, along with several other group...
Article
Full-text available
Unlabelled: As they mature, many capsids undergo massive conformational changes that transform their stability, reactivity, and capacity for DNA. In some cases, maturation proceeds via one or more intermediate states. These structures represent local minima in a rich energy landscape that combines contributions from subunit folding, association of...
Article
CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6...
Article
Full-text available
Papillomaviruses are a family of nonenveloped DNA viruses that infect the skin or mucosa of their vertebrate hosts. The viral life cycle is closely tied to the differentiation of infected keratinocytes. Papillomavirus virions are released into the environment through a process known as desquamation, in which keratinocytes lose structural integrity...
Article
Full-text available
In cryo-electron microscopy and single particle analysis, data acquisition and image processing are generally carried out in sequential steps and computation of a three-dimensional reconstruction only begins once all the micrographs have been acquired. We are developing an integrated system for processing images of icosahedral particles during micr...
Article
Despite being essential for successful infection, the molecular cues involved in host recognition and genome transfer of viruses are not completely understood. Bacterial outer membrane proteins A and C co-purify in lipid vesicles with bacteriophage Sf6, implicating both outer membrane proteins as potential host receptors. We determined that outer m...
Article
Full-text available
of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.
Article
Full-text available
Single particle analysis is a valuable tool in cryo-electron microscopy for determining the structure of biological complexes. However, the conformational state and the preparation of the sample are factors that play a critical role in the ultimate attainable resolution. In some cases extensive analysis at the microscope of a sample under different...
Data
MS/MS spectrum of the TVV1 CP/RdRp junctional peptide. The spectrum of the doubly charged tryptic peptide VGSLFLSK was observed at a mass/charge (m/z) ratio of 425.756 (double dagger) by reversed-phase microcapillary LC-MS/MS with a hybrid linear ion trap, Orbitrap mass spectrometer. The observed fragment ions b (derived from the N terminus) and y...
Data
Phylogenetic relationships among members and tentative members of the family Totiviridae. A maximum-likelihood phylogram was derived from sequences encompassing the RdRp ORFs of all of the viruses analyzed. The following three steps were performed by using the “A la Carte” option at http://www.phylogeny.fr/, with default settings unless otherwise i...
Data
Comparison of TVV1 virion and empty capsid reconstructions. This animation alternates back and forth between the equatorial density sections (see Fig. S1) of the TVV1 virion and empty capsid 3D cryoreconstructions to highlight subtle differences between the two structures. The red box in later frames outlines one region in the capsid where some sig...
Data
Surface features of ScV-L-A and TVV1 virions viewed in closeup down an I5 axis of each. The images were generated as described in the legend to Fig. 7C, except that interior densities, below the lowermost radius of the capsid, were removed from the TVV1 cryo-TEM map to allow clearer perception of the capsid-spanning I5 channel. Scale bar, 20 Å. Dow...
Article
Author Summary Of the known dsRNA fungal viruses, the best characterized is Saccharomyces cerevisiae virus L-A (ScV-L-A), prototype of the genus Totivirus , family Totiviridae . Until the current study, there have been no subnanometer structures of dsRNA fungal viruses from the genus Victorivirus , which is the largest in family Totiviridae . The...
Data
Radial density plots. Radial density plots [64] calculated from the HvV190S virion, VLPC+, and VLPC cryo-reconstructions for radii between 10 and 255 Å. The dsRNA genome in virions is organized into five, roughly spherical shells that appear as distinct peaks in the radial density plot, centered at radii from a high of ∼143 Å (first shell) to a low...
Data
Effect of in vitro protease treatment on purified HvV190 virions. (A) Search for polypeptides 10 kDa or smaller generated by proteolytic processing of p88 of HvV190S, VLPc+, and VLPc after particle assembly. Purified preparation of HvV190S virions, VLPc+, and VLPc as well as total proteins were subjected to SDS-PAGE on a 15% polyacrylamide gel and...
Data
SDS-polyacrylamide gel electrophoresis of HvV190S virions and Western blot analysis. (A) SDS-polyacrylamide analysis of the 190S-1 and 190S-2 forms following two cycles of sucrose density gradient centrifugation; capsids of 190S-1 contain similar amounts of p83 and p88, whereas those of 190S-2 contain comparable amounts of p78 and p88. (B) Capsid c...
Data
Conformational differences between the HvV190S virion and VLPC+ capsid structures. Differences are highlighted by means of an animation produced with the Morph Map tool and default values in Chimera [63]. 3D density maps of the virion and VLPC+ cryo-reconstructions, each band-limited to 9.0-Å resolution and with the front-half removed (also genome...
Data
Segmented A-subunit of HvV190S virion and secondary-structure analysis. This animation, produced using Chimera [63] shows the result of a rigid-body fit of the ScV-L-A A-subunit atomic model, and the resulting locations of its α-helices are compared with the positions of the α-helices predicted from the HvV190S segmented density (see Materials and...
Data
Percent sequence identity between HvV190S CP conserved helical region (CHR) and the corresponding region in selected victoriviruses and related viruses in the family Totiviridae. The percent sequence identity was calculated for twelve totiviruses for the CHR and compared to that of HvV190S. Similar to what was found for the complete percent sequenc...
Data
Fourier Shell Correlation curves. The correlation curves calculated for the HvV190S virion, VLPC+, and VLPC intersect the threshold 0.5 (0.143) at 7.1 (6.8), 7.5 (7.1) and 7.6 (7.2) Å, respectively. See Table 1 for relevant reference citations for these calculations. (TIF)
Data
Sequence comparisons between the capsid protein of HvV190S and that of six other victoriviruses and six related viruses in the family Totiviridae. The predicted secondary structures of the capsid proteins of thirteen totiviruses suggest that they have a moderate level of sequence identity. BfTV1 is most closely related to HvV190S as their capsid pr...
Data
Pixel size calibration statistics for HvV190S virion 3D reconstruction. The pixel size and magnification for each micrograph recorded from the vitrified, mixed sample (HvV190S virions and HK97 prohead II particles) were determined by measuring the peak position of the radial density plot of each HK97 3D reconstruction and calibrating this against t...
Article
Full-text available
Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300-450 Å in diameter. Helminthosporium victoriae virus 190S (HvV190S), prototype of recently recognized genus Victorivirus, infects the filamentous fungus Hel...
Article
Full-text available
The flagellated protozoan Trichomonas vaginalis is an obligate human genitourinary parasite and the most frequent cause of sexually transmitted disease worldwide. Most clinical isolates of T. vaginalis are persistently infected with one or more double-stranded RNA (dsRNA) viruses from the genus Trichomonasvirus, family Totiviridae, which appear to...