14 research outputs found
Skeletal dysplasia with bowing long bones: Proposed flowchart for prenatal diagnosis with case demonstration
Abstract Objective Skeletal dysplasia with bowing long bones is a rare group of multiple characterized congenital anomalies. Materials and Methods We introduce a simple, practical diagnostic flowchart that may be helpful in identifying the appropriate pathway of obstetrical management. Results Herein, we describe four fetal cases of bent bony dysplasia that focus on ultrasound findings, phenotype, molecular tests, distinctive X-ray features, and chondral growth plate histology. The first case was a typical campomelic dysplasia resulting from a de novo mutation in the SOX9 gene. The second fetus was affected by osteogenesis imperfecta Type II carrying a mutation in the COLA1 gene. The third case was a rare presentation of campomelic dysplasia, Cumming type, in which SOX9 examination was normal. Subsequently, a femoral hypoplasia unusual facies syndrome is also discussed. Conclusion Targeted molecular tests and genetic counseling are required for supplementing ultrasound imaging in order to diagnose the correct skeletal disorders
A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information
Abstract Background Human mitochondrial DNA has an important role in the cellular energy production through oxidative phosphorylation. Therefore, this process may be the cause and have an effect on mitochondrial DNA mutability, functional alteration, and disease onset related to a wide range of different clinical expressions and phenotypes. Although a large part of the observed variations is fixed in a population and hence expected to be benign, the estimation of the degree of the pathogenicity of any possible human mitochondrial DNA variant is clinically pivotal. Methods In this scenario, the establishment of standard criteria based on functional studies is required. In this context, a âdata and text miningâ pipeline is proposed here, developed using the programming language R, capable of extracting information regarding mitochondrial DNA functional studies and related clinical assessments from the literature, thus improving the annotation of human mitochondrial variants reported in the HmtVar database. Results The data mining pipeline has produced a list of 1,073 Pubmed IDs (PMIDs) from which the text mining pipeline has retrieved information on 932 human mitochondrial variants regarding experimental validation and clinical features. Conclusions The application of the pipeline will contribute to supporting the interpretation of pathogenicity of human mitochondrial variants by facilitating diagnosis to clinicians and researchers faced with this task
Battle through signaling between wheat and the fungal pathogen <em>Septoria tritici</em> revealed by proteomics and phosphoproteomics
The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheatâS. tritici interaction, we performed a time-course study of S. tritici infection in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger accumulation of signal molecules, including calcium, H(2)O(2), NO, and sugars, in the resistant than in the susceptible cultivar in response to the infection. Additionally, 31 proteins and 5 phosphoproteins from the pathogen were identified, including metabolic proteins and signaling proteins such as GTP-binding proteins, 14â3-3 proteins, and calcium-binding proteins. Quantitative PCR analysis showed the expression of fungal signaling genes and genes encoding a superoxide dismutase and cell-wall degrading enzymes. These results indicate roles of signaling, antioxidative stress mechanisms, and nutrient acquisition in facilitating the initial symptomless growth. Taken in its entirety, our dataset suggests interplay between the plant and S. tritici through complex signaling networks and downstream molecular events. Resistance is likely related to several rapidly and intensively triggered signal transduction cascades resulting in a multiple-level activation of transcription and translation processes of defense responses. Our sensitive approaches and model provide a comprehensive (phospho)proteomics resource for studying signaling from the point of view of both host and pathogen during a plantâpathogen interaction
1,5-Diaminonaphtalene is a Highly Performing Electron-Transfer Secondary-Reaction Matrix for Laser Desorption Ionization Mass Spectrometry of Indolenine-Based Croconaines
Croconaine dyes are appealing molecules synthesized via the condensation of croconic acid and reactive electron-donating aromatic or heterocyclic systems. Here, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) investigation of indolenine-based croconaines is presented for the first time. Archetype proton-transfer matrices, such as 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA), 9-aminoacridine (9AA) as the protonating/deprotonating matrix, and electron-transfer (ET) secondary-reaction matrices, such as 1,5-diaminonapthalene (DAN) and trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), were investigated. DHB, CHCA, and 9AA generate a mix of odd-electron molecular ions and protonated, sodiated, and potassiated adducts. Among the ET matrices, DAN was found to be capable of directing the ionization process toward the exclusive formation of odd-electron molecular ions M+⹠without fragmentation. MALDI tandem MS provides useful structural characterization of croconaine dyes, thus making identification very straightforward for all investigated compounds. Interestingly the fragmentation of bromo-containing croconaines revealed, for the first time, the gas-phase formation of a bromime cation [Br]+
Chemical Deamidation: A Common Pitfall in Large-Scale N-Linked Glycoproteomic Mass Spectrometry-Based Analyses
N-Linked glycoproteins are involved in several diseases
and are
important as potential diagnostic molecules for biomarker discovery.
Therefore, it is important to provide sensitive and reliable analytical
methods to identify not only the glycoproteins but also the sites
of glycosylation. Recently, numerous strategies to identify N-linked
glycosylation sites have been described. These strategies have been
applied to cell lines and several tissues with the aim of identifying
many hundreds (or thousands) of glycosylation events. With high-throughput
strategies however, there is always the potential for false positives.
The confusion arises since the protein N-glycosidase F (PNGase F)
reaction used to separate N-glycans from formerly glycosylated peptides
catalyzes the cleavage and deamidates the asparagine residue. This
is typically viewed as beneficial since it acts to highlight the modification
site. We have evaluated this common large-scale N-linked glycoproteomic
strategy and proved potential pitfalls using <i>Escherichia coli</i> as a model organism, since it lacks the N-glycosylation machinery
found in mammalian systems and some pathogenic microbes. After isolation
and proteolytic digestion of <i>E. coli</i> membrane proteins,
we investigated the presence of deamidated asparagines. The results
show the presence of deamidated asparagines especially with close
proximity to a glycine residue or other small amino acid, as previously
described for spontaneous in vivo deamidation. Moreover, we have identified
deamidated peptides with incorporation of <sup>18</sup>O, showing
the pitfalls of glycosylation site assignment based on deamidation
of asparagine induced by PNGase F in <sup>18</sup>O-water in large-scale
analyses. These data experimentally prove the need for more caution
in assigning glycosylation sites and ânewâ N-linked
consensus sites based on common N-linked glycoproteomics strategies
without proper control experiments. Besides showing the spontaneous
deamidation, we provide alternative methods for validation that should
be used in such experiments
Chemical Deamidation: A Common Pitfall in Large-Scale N-Linked Glycoproteomic Mass Spectrometry-Based Analyses
N-Linked glycoproteins are involved in several diseases
and are
important as potential diagnostic molecules for biomarker discovery.
Therefore, it is important to provide sensitive and reliable analytical
methods to identify not only the glycoproteins but also the sites
of glycosylation. Recently, numerous strategies to identify N-linked
glycosylation sites have been described. These strategies have been
applied to cell lines and several tissues with the aim of identifying
many hundreds (or thousands) of glycosylation events. With high-throughput
strategies however, there is always the potential for false positives.
The confusion arises since the protein N-glycosidase F (PNGase F)
reaction used to separate N-glycans from formerly glycosylated peptides
catalyzes the cleavage and deamidates the asparagine residue. This
is typically viewed as beneficial since it acts to highlight the modification
site. We have evaluated this common large-scale N-linked glycoproteomic
strategy and proved potential pitfalls using <i>Escherichia coli</i> as a model organism, since it lacks the N-glycosylation machinery
found in mammalian systems and some pathogenic microbes. After isolation
and proteolytic digestion of <i>E. coli</i> membrane proteins,
we investigated the presence of deamidated asparagines. The results
show the presence of deamidated asparagines especially with close
proximity to a glycine residue or other small amino acid, as previously
described for spontaneous in vivo deamidation. Moreover, we have identified
deamidated peptides with incorporation of <sup>18</sup>O, showing
the pitfalls of glycosylation site assignment based on deamidation
of asparagine induced by PNGase F in <sup>18</sup>O-water in large-scale
analyses. These data experimentally prove the need for more caution
in assigning glycosylation sites and ânewâ N-linked
consensus sites based on common N-linked glycoproteomics strategies
without proper control experiments. Besides showing the spontaneous
deamidation, we provide alternative methods for validation that should
be used in such experiments
Chemical Deamidation: A Common Pitfall in Large-Scale N-Linked Glycoproteomic Mass Spectrometry-Based Analyses
N-Linked glycoproteins are involved in several diseases
and are
important as potential diagnostic molecules for biomarker discovery.
Therefore, it is important to provide sensitive and reliable analytical
methods to identify not only the glycoproteins but also the sites
of glycosylation. Recently, numerous strategies to identify N-linked
glycosylation sites have been described. These strategies have been
applied to cell lines and several tissues with the aim of identifying
many hundreds (or thousands) of glycosylation events. With high-throughput
strategies however, there is always the potential for false positives.
The confusion arises since the protein N-glycosidase F (PNGase F)
reaction used to separate N-glycans from formerly glycosylated peptides
catalyzes the cleavage and deamidates the asparagine residue. This
is typically viewed as beneficial since it acts to highlight the modification
site. We have evaluated this common large-scale N-linked glycoproteomic
strategy and proved potential pitfalls using <i>Escherichia coli</i> as a model organism, since it lacks the N-glycosylation machinery
found in mammalian systems and some pathogenic microbes. After isolation
and proteolytic digestion of <i>E. coli</i> membrane proteins,
we investigated the presence of deamidated asparagines. The results
show the presence of deamidated asparagines especially with close
proximity to a glycine residue or other small amino acid, as previously
described for spontaneous in vivo deamidation. Moreover, we have identified
deamidated peptides with incorporation of <sup>18</sup>O, showing
the pitfalls of glycosylation site assignment based on deamidation
of asparagine induced by PNGase F in <sup>18</sup>O-water in large-scale
analyses. These data experimentally prove the need for more caution
in assigning glycosylation sites and ânewâ N-linked
consensus sites based on common N-linked glycoproteomics strategies
without proper control experiments. Besides showing the spontaneous
deamidation, we provide alternative methods for validation that should
be used in such experiments
Phenotype to genotype characterization by array-comparative genomic hydridization (a-CGH) in case of fetal malformations: AÂ systematic review
The aim of the current review is to report a-CGH abnormalities identified in fetuses with prenatally diagnosed fetal malformations in whom a normal karyotype was diagnosed with conventional cytogenetic analysis.A systematic electronic search of databases (PubMed/Medline, EMBASE/SCOPUS) has been conducted from inception to May, 2017. Bibliographic analysis has been performed according to PRISMA statement for review. The following keywords were used: âarray-CGHâ and âfetal malformationsâ and âprenatal diagnosisâ; alternatively, âmicroarrayâ, âoligonucleotide arrayâ, âmolecular biologyâ, âantenatal diagnosticsâ, âfetal diagnosticsâ, âcongenital malformationsâ and âultrasoundâ were used to capture both âa-CGHâ and âprenatalâ.One-hundred and twelve fetuses with prenatally diagnosed fetal malformations with normal karyotyping and a-CGH abnormalities detected are described. Single or multiple microarray abnormalities diagnosed have been classified in relation to different organ/system affected. The most frequent a-CGH abnormalities were detected in cases of congenital heart diseases (CDHs), multiple malformations and central nervous system (CNS) malformations. Maternal or paternal carrier-state was seen in 19.64% (22/112), of cases while the number of reported de novo mutations accounted for 46.42% (52/112) of all CNVs microarray abnormalities. Array-comparative genomic hydridization (a-CGH) may become an integral and complemantary genetic testing when fetal malformations are detected prenatally in fetuses with normal cytogenetic karyotype. In addition, a-CGH enables the identification of CNVs and VOUS and improves the calculation of recurrent risk and the genetic counseling. Keywords: Array-CGH, Fetal malformations, Molecular genetics, Prenatal diagnosis, Ultrasoun