iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data

Many bioinformatics tools are available for the quantitative analysis of proteomics experiments. Most of these tools use a dedicated statistical model to derive absolute quantitative protein values from mass spectrometry (MS) data. Here, we present iSanXoT, a standalone application that processes relative abundances between MS signals and then integrates them sequentially to upper levels using the previously published Generic Integration Algorithm (GIA). iSanXoT offers unique capabilities that complement conventional quantitative software applications, including statistical weighting and independent modeling of error distributions in each integration, aggregation of technical or biological replicates, quantification of posttranslational modifications, and analysis of coordinated protein behavior. iSanXoT is a standalone, user-friendly application that accepts output from popular proteomics pipelines and enables unrestricted creation of quantification workflows and fully customizable reports that can be reused across projects or shared among users. Numerous publications attest the successful application of diverse integrative workflows constructed using the GIA for the analysis of high-throughput quantitative proteomics experiments. iSanXoT has been tested with the main operating systems. Download links for the corresponding distributions are available at https://github.com/CNIC-Proteomics/iSanXoT/releases.

Non-invasive electromechanical assessment during atrial fibrillation identifies underlying atrial myopathy alterations with early prognostic value

Electromechanical characterization during atrial fibrillation (AF) remains a significant gap in the understanding of AF-related atrial myopathy. This study reports mechanistic insights into the electromechanical remodeling process associated with AF progression and further demonstrates its prognostic value in the clinic. In pigs, sequential electromechanical assessment during AF progression shows a progressive decrease in mechanical activity and early dissociation from its electrical counterpart. Atrial tissue samples from animals with AF reveal an abnormal increase in cardiomyocytes death and alterations in calcium handling proteins. High-throughput quantitative proteomics and immunoblotting analyses at different stages of AF progression identify downregulation of contractile proteins and progressive increase in atrial fibrosis. Moreover, advanced optical mapping techniques, applied to whole heart preparations during AF, demonstrate that AF-related remodeling decreases the frequency threshold for dissociation between transmembrane voltage signals and intracellular calcium transients compared to healthy controls. Single cell simulations of human atrial cardiomyocytes also confirm the experimental results. In patients, non-invasive assessment of the atrial electromechanical relationship further demonstrate that atrial electromechanical dissociation is an early prognostic indicator for acute and long-term rhythm control.

Heteroplasmy of Wild Type Mitochondrial DNA Variants in Mice Causes Metabolic Heart Disease With Pulmonary Hypertension and Frailty

Background: In most eukaryotic cells, the mitochondrial DNA (mtDNA) is uniparentally transmitted and present in multiple copies derived from the clonal expansion of maternally inherited mtDNA. All copies are therefore near-identical, or homoplasmic. The presence of more than one mtDNA variant in the same cytoplasm can arise naturally or result from new medical technologies aimed at preventing mitochondrial genetic diseases and improving fertility. The latter is called divergent non-pathological mtDNAs heteroplasmy (DNPH). We hypothesized that DNPH is maladaptive and usually prevented by the cell. Methods: We engineered and characterized DNPH mice throughout their lifespan using transcriptomic, metabolomic, biochemical, physiological and phenotyping techniques. We focused on in vivo imaging techniques for non-invasive assessment of cardiac and pulmonary energy metabolism. Results: We show that DNPH impairs mitochondrial function, with profound consequences in critical tissues that cannot resolve heteroplasmy, particularly cardiac and skeletal muscle. Progressive metabolic stress in these tissues leads to severe pathology in adulthood, including pulmonary hypertension and heart failure, skeletal muscle wasting, frailty, and premature death. Symptom severity is strongly modulated by the nuclear context. Conclusions: Medical interventions that may generate DNPH should address potential incompatibilities between donor and recipient mtDNA.

Transcriptome and proteome mapping in the sheep atria reveal molecular featurets of atrial fibrillation progression

AIMS

Atrial fibrillation (AF) is a progressive cardiac arrhythmia that increases the risk of hospitalization and adverse cardiovascular events. There is a clear demand for more inclusive and large-scale approaches to understand the molecular drivers responsible for AF, as well as the fundamental mechanisms governing the transition from paroxysmal to persistent and permanent forms. In this study, we aimed to create a molecular map of AF and find the distinct molecular programmes underlying cell type-specific atrial remodelling and AF progression.

METHODS AND RESULTS

We used a sheep model of long-standing, tachypacing-induced AF, sampled right and left atrial tissue, and isolated cardiomyocytes (CMs) from control, intermediate (transition), and late time points during AF progression, and performed transcriptomic and proteome profiling. We have merged all these layers of information into a meaningful three-component space in which we explored the genes and proteins detected and their common patterns of expression. Our data-driven analysis points at extracellular matrix remodelling, inflammation, ion channel, myofibril structure, mitochondrial complexes, chromatin remodelling, and genes related to neural function, as well as critical regulators of cell proliferation as hallmarks of AF progression. Most important, we prove that these changes occur at early transitional stages of the disease, but not at later stages, and that the left atrium undergoes significantly more profound changes than the right atrium in its expression programme. The pattern of dynamic changes in gene and protein expression replicate the electrical and structural remodelling demonstrated previously in the sheep and in humans, and uncover novel mechanisms potentially relevant for disease treatment.

CONCLUSIONS

Transcriptomic and proteomic analysis of AF progression in a large animal model shows that significant changes occur at early stages, and that among others involve previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.

Scaf1 promotes respiratory supercomplexes and metabolic efficiency in zebrafish

The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here, we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2  + IV2 , I + IV, and I + III2  + IV2 . To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (scaf1). scaf1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complexes III and IV. scaf1-/- fish were smaller in size and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by Scaf1 modulates OXPHOS efficiency and allows the optimization of metabolic resources.

The development of episodic future thinking in middle childhood

The ability to imagine future events (episodic future thinking-EFT) emerges in preschoolers and further improves during middle childhood and adolescence. In the present study, we focused on the possible cognitive factors that affect EFT and its development. We assessed the ability to mentally project forward in time of a large cohort of 135 6- to 11-year-old children through a task with minimal narrative demands (the Picture Book Trip task adapted from Atance and Meltzoff in Cogn Dev 20(3):341-361. doi:10.1016/j.cogdev.2005.05.001, 2005) in order to avoid potential linguistic effects on children's performance. The results showed that this task can be used to assess the development of EFT at least until the age of 8. Furthermore, EFT scores correlated with measures of phonological short-term and verbal working memory. These results support the possibility that cognitive factors such as working memory play a key role in EFT.

Brief Report: Self-Based and Mechanical-Based Future Thinking in Children with Autism Spectrum Disorder

This brief report is a partial replication of the study by Jackson and Atance (J Dev Disabil 14:40-45, 2008) assessing nonverbal Self-based and Mechanical-based future thinking (FT) in children with Autism Spectrum Disorder (ASD). In a first step, these tasks were administered to 30 children with ASD. The two Self-based tasks were then modified as a verbal component could not be completely ruled out. Consequently, 77 children with ASD and 77 children with typical development received the modified Self-based FT tasks and the Mechanical-based FT tasks. We partially replicated the previous findings. Participants with ASD had impaired FT in both kinds of tasks and both groups performed better on tasks assessing Mechanical-based FT than Self-based FT. These results suggest that impairments of FT in ASD are not limited to Self-Projection.

Electro-oculographic abnormality in eyes with uveal melanoma

PURPOSE

To seek out correlations between preoperative electro-oculogram (EOG) recordings with different types of uveal melanomas, after surgery.

METHODS

We analysed the EOG recordings of 120 patients with uveal melanomas, histologically verified, 100 in the choroid and 20 in the iris and ciliary body. The EOG data were correlated with the site, size and histological type of the tumor.

RESULTS

In 100 eyes with choroidal melanoma the Arden Index (AI) was less than in fellow eyes (mean 126.6, SD +/- 23.8 and 202.9, SD +/- 47.0; p=0.01). The EOG values were not different with respect to the histological type, site and size of tumor. In cases with iris and ciliary body melanomas the AI were not significantly different from the fellow eyes (mean 180.6, SD +/- 23.6 and 203.2, SD +/- 38.7; p=0.07).

CONCLUSIONS

Since the EOG is abnormal in eyes with choroidal melanoma, it can be considered a powerful auxiliary for diagnosing these tumors.

Unilateral retinitis pigmentosa: clinical and electrophysiological report of four cases

Unilateral retinitis pigmentosa (URP) is a rare tapetoretinal dystrophy affecting only one eye. The François and Verriest criteria are necessary to make a correct diagnosis of URP: exclude all infective etiologies, check that the clinical signs of retinitis are present in the affected eye and ensure the total absence of any signs or symptoms of retinitis pigmentosa in the fellow eye. The standard electroretinogram and standard electro-oculogram are very useful for the correct diagnosis. Other pigmentary retinopathies simulating retinitis pigmentosa have to be excluded, such as previous retinal inflammatory diseases like syphilis, rubeola, other viral diseases and onchocerciasis. In this paper, 4 cases of URP are reported.

Electronystagmographic investigation in X-linked ocular albinism

Albinism represents the most frequent cause of nystagmus induced by visual sensory disorders. We studied five patients aged between three and five years with ocular albinism with the aim of identifying the characteristics of nystagmic oscillations. The patients underwent complete ophthalmological examination and electronystagmography (ENG). ENG revealed either pendular or jerk waveforms (or both) with the same complex effects of fixation seen in those with idiopathic congenital nystagmus. Three children presented face turn due to reduced severity of nystagmus in lateroversion. Latent nystagmus was not observed.

Effect of myopic excimer laser photorefractive keratectomy on the electrophysiologic function of the retina and optic nerve

PURPOSE

To assess by electrophysiologic testing the effect of photorefractive keratectomy (PRK) on the retina and optic nerve.

SETTING

Eye Clinic, S. Salvatore Hospital, L'Aquila University, Italy.

METHODS

Standard pattern electroretinograms (P-ERGs) and standard pattern visual evoked potentials (P-VEPs) were done in 25 eyes of 25 patients who had myopic PRK for an attempted correction between 5.00 and 15.00 diopters (D) (mean 8.00 D). Testing was done preoperatively and 3, 6, 12, and 18 months postoperatively. The contralateral eyes served as controls. During the follow-up, 3 patients (12%) developed steroid-induced elevated intraocular pressure (IOP) that resolved after corticosteroid therapy was discontinued.

RESULTS

No statistically significant differences were seen between treated and control eyes nor between treated eyes preoperatively and postoperatively.

CONCLUSION

Myopic excimer laser PRK did not seem to affect the posterior segment. The transient steroid-induced IOP rise did not seem to cause functional impairment.

Homonymous Bilateral Hemianopsia: Electrophysiological Study of a Case

Described is a case of bilateral homonymous hemianopsia with macular sparing, resulting from head trauma. The case presented lesions of the occipital visual areas which involved entirely the left hemisphere and only partially the right hemisphere. VEP were obtainable only from electrodes placed on the right hemisphere with both right eye and left eye stimulation. VEP mapping showed that each eye projects macular fibres towards functional areas of the right occipital hemisphere.

Electrophysiological examination confirmed objectively and for the first time in man the theory of “double cortical macular representation”.

Clinical implications of this finding are discussed.

Assessment of visual contrast sensitivity in hyperbaric oxygen

Hyperbaric oxygen therapy is used in ophthalmology in ischemic pathologies of the anterior and posterior segments. Our experiment was done on a healthy group of volunteers aged between 10 and 50 yr. We examined the subject's vision before and after acute HBO exposure (60 min at 2.5 atm abs with pure oxygen) to verify whether vasoconstriction induced by hyperoxemia can influence eyesight. We measured the psychophysical determination of the threshold contrast according to Maione-Maffei's zebra test. The results demonstrated that contrast sensitivity is significantly improved for almost all the studied frequencies in normal subjects after acute HBO exposure. We hypothesize that the visual system has a reserve which is activated by an improvement of retinal oxygenation.

Single-sweep analysis using an autoregressive with exogenous input (ARX) model

Single-sweep visual evoked potential analysis would be useful in clinical electrophysiology practice because it would make possible the evaluation of transient phenomena, but recording single-sweep visual evoked potentials is difficult because of the low signal-noise ratio. To increase this ratio we used a filter based on an autoregressive with exogenous input model. We studied a group of 12 diabetic patients matched with a control group of 14 normal subjects. The model, in most cases, allowed us to extrapolate the P100 component from each single sweep of visual evoked potential. The visual evoked potential values obtained by means of averaging were not significantly different in the groups studied, but single-sweep analysis showed different distribution of the P100 component amplitude. The preliminary results of our study evidenced differences in the amplitude and latency distribution of normal and diabetic subjects, thus confirming the power of this new technique and its ability to obtain some information that is masked by the averaging method.

Electroretinographic findings in congenital oculomotor apraxia (Cogan's syndrome)

We performed visual evoked potential testing and electroretinography in five patients with Cogan's oculomotor apraxia. The visual evoked potentials were normal, confirming previously reported data. Electroretinograms were abnormal in two of the five patients examined. A previous study showed normal electroretinogram responses bilaterally in one patient. Our findings suggest the existence of two variants of the syndrome; the one with electroretinogram anomalies has a worse visual prognosis.

Best's multiple vitelliform degeneration

Best's disease with multifocal lesions is rare. The authors describe four cases of multifocal vitelliform disease. The fluorescein angiographic features of macular and extramacular lesions are considered. Different stages of evolution may be present between central and extramacular lesions.

Corneal endothelial anomalies in the fetal alcohol syndrome

The fetal alcohol syndrome involves various neural crest-derived structures thus causing systemic and ocular malformations. This study investigated anomalies of the corneal endothelium, a neural crest-derived tissue, in eight children affected by fetal alcohol syndrome without known anterior segment anomalies. We performed specular biomicroscopy on the central corneal endothelium. The data were then compared with those from 80 age-matched healthy children, applying the same methods. Significant differences were found between patients with fetal alcohol syndrome and healthy subjects for mean cell density (P = .032), polymegethism (P = .000), and percentage of hexagonal cells (P = .000). We also found a close correlation between endothelial anomalies and auditory dysfunction in the patients with fetal alcohol syndrome. These alterations may be a consequence of alcohol-induced toxic effects on neural crest cells destined to form both the corneal endothelium and the organ of Corti in the same embryogenic period.

Microphthalmos with colobomatous orbital cyst in trisomy 13

The authors describe a case of trisomy 13 with microphthalmos and colobomatous cyst of the optic nerve and of the chorioretina with orbital extension, in a six-month-old female patient. The colobomatous cyst has been studied by means of computerized axial tomography and ultrasonography in order to follow its evolution. The orbital cyst has not increased in size.

Carotid occlusive disease: an electrophysiological macular investigation

Thirteen patients with carotid stenosis were studied by the authors by the measuring the Visual Evoked Potentials (VEPs) before and after thromboendarterectomy. This test of retinal function measures the recovery time of the amplitude of the major positive peak (P100) after photostress. When compared to that we observed in controls, we found, a significant increase of the P100 recovery time in patients suffering from carotid disease with severe stenosis. The method proved suitable for the functional evaluation of the vascular reconstruction of the carotid area, since four weeks after surgery a physiological recovery of the amplitude of VEP was observed. This method is proposed by the authors for the long-term functional evaluation of patients subjected to carotid thromboendarterectomy for tight stenosis of the carotid bifurcation.

VEP pattern after photostress: an index of macular function

Eighty-seven subjects were examined by means of visual evoked potentials (VEPs) to evaluate the recovery time of the amplitude of the pattern VEP after photostress. Twenty-eight subjects were normal and 59 patients were affected by carotid occlusive disease, vascular retinopathies with and without macular involvement, and connective tissue diseases treated with antimalarial drugs. This examination method emphasizes visual dysfunction in a stage where ophthalmological changes are absent or minimal and therefore may be a useful test for the investigation of macular function.