Targeted Analysis of Lysosomal Directed Proteins and Their Sites of Mannose-6-phosphate Modification

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Highlights

• •Fe³⁺-IMAC enables co-enrichment of mannose-6-phosphate (M6P) modified glycopeptides.
• •Detailed characterization of intact M6P modified glycopeptides from HeLa and CHO cell lines.
• •EThcD results in a cleavage between 2 core GlcNAc residues enabling unambiguous glycoform identification.
• •Double knock out of the phosphatases Acp2/5 results in a 20-fold increase in abundance of M6P modified glycopeptides.

     

Deciphering key genes in cardio-renal syndrome using network analysis

Cardio-renal syndrome (CRS) is a rapidly recognized clinical entity which refers to the inextricably connection between heart and renal impairment, whereby abnormality to one organ directly promotes deterioration of the other one. Biological markers help to gain insight into the pathological processes for early diagnosis with higher accuracy of CRS using known clinical findings. Therefore, it is of interest to identify target genes in associated pathways implicated linked to CRS. Hence, 119 CRS genes were extracted from the literature to construct the PPIN network. We used the MCODE tool to generate modules from network so as to select the top 10 modules from 23 available modules. The modules were further analyzed to identify 12 essential genes in the network. These biomarkers are potential emerging tools for understanding the pathophysiologic mechanisms for the early diagnosis of CRS. Ontological analysis shows that they are rich in MF protease binding and endo-peptidase inhibitor activity. Thus, this data help increase our knowledge on CRS to improve clinical management of the disease.     

Optimal design of feedback control by inhibition

Summary A recently developed, nonlinear method of systems analysis has been used to compare alternative patterns of control by feedback inhibition in otherwise equivalent unbranched biosynthetic pathways. The steady state performance of the simple case with end-product inhibition at the first physiologically important step is optimal with respect to the following criteria: the ability to (i) meet an increased demand for the end-product, (ii) meet this increased demand with limited accumulation of the intermediates, (iii) respond to an increased supply of the initial substrate, and (iv) limit the accumulation of the intermediates while responding to the increased availability of the initial substrate. The importance of these properties for the selection of feedback patterns in biosynthetic pathways is discussed.     

The clustering on thePseudomonas putida chromosome of genes specifying dissimilatory functions

Summary Two previously demonstrated linkage groups containing genes with catabolic function inPseudomonas putida have been shown to cotransduce with a third cluster of catabolic genes, namely those specifying enzymes of nicotinic acid dissimilation. Thus enzymes of the following dissimilatory pathways are coded by genes clustered in one small (10-15% of the chromosome) genetic region:p-hydroxy-benzoic, quinic, shikimic, benzoic, mandelic, phenylacetic, and nicotinic acids; and histidine, tyrosine and phenylalanine. We propose that this clustering is a consequence of the selection, in natural populations of bacteria, of gene arrangements which permit simultaneous transfer of the genetic determinants of a variety of dissimilatory pathways.     

Growth and plasmid-encoded naphthalene catabolism of Pseudomonas putida in batch culture

Abstract The growth characteristics of Pseudomonas putida plasmid-harbouring strains which catabolize naphthalene via various pathways in batch culture with naphthalene as the sole source of carbon and energy have been investigated. The strains under study were constructed using the host strain P. putida BS394 which contained various naphthalene degradation plasmids. The highest specific growth rate was ensured by the plasmids that control naphthalene catabolism through the meta-pathway of catechol oxidation. The strains metabolizing catechol via the ortho -pathway grew at a lower rate. The lowest growth rate was observed with strain BS291 harbouring plasmid pBS4 which controls naphthalene catabolism via the gentisic acid pathway. Various pathways of naphthalene catabolism appear to allow these strains to grow at various rates which should be taken into account when constructing efficient degraders of polycyclic aromatic compounds.     

Neural differentiation from embryonic stem cells in vitro: An overview of the signaling pathways

Neurons derived from embryonic stem cells (ESCs) have gained great merit in both basic research and regenerative medicine. Here we review and summarize the signaling pathways that have been reported to be involved in the neuronal differentiation of ESCs, particularly those associated with in vitro differentiation. The inducers and pathways explored include retinoic acid, Wnt/β-catenin, transforming growth factor/bone morphogenetic protein, Notch, fibroblast growth factor, cytokine, Hedgehog, c-Jun N-terminal kinase/mitogen-activated protein kinase and others. Some other miscellaneous molecular factors that have been reported in the literature are also summarized and discussed. These include calcium, calcium receptor, calcineurin, estrogen receptor, Hox protein, ceramide, glycosaminioglycan, ginsenoside Rg1, opioids, two pore channel 2, nitric oxide, chemically defined medium, cell-cell interactions, and physical stimuli. The interaction or crosstalk between these signaling pathways and factors will be explored. Elucidating these signals in detail should make a significant contribution to future progress in stem cell biology and allow, for example, better comparisons to be made between differentiation in vivo and in vitro. Of equal importance, a comprehensive understanding of the pathways that are involved in the development of neurons from ESCs in vitro will also accelerate their application as part of translational medicine.     

Unusual cause of cardiomyopathy in a young woman

Dual atrioventricular nodal nonreentrant tachycardia (DAVNNT) is a rare form of supraventricular tachycardia. In some patients, the presence of a dual pathway physiology results in two paths in the atrioventricular (AV) node with different conduction velocities. An atrial impulse arriving at the AV node may unfold and travel along these two pathways simultaneously, causing two ventricular activations. Thus, the ventricular rate will be twice the atrial rate. DAVNNT is less common than AVNRT, but its frequency may be underestimated.The ECG is crucial to suspect the diagnosis. At first glance it looks like an irregular tachycardia, but a more careful look shows a rhythmic pattern. A sinus P wave followed by two QRS complexes (narrow or wide) should raise suspicion of this arrhythmia.It is often unnoticed by the patient, and ventricular dysfunction due to tachycardiomyopathy is not uncommon. The response of DAVNNT to medication, including beta-blockers, flecainide, and amiodarone is very poor or absent, so the treatment of choice is slow pathway ablation. We report a Case of cardiomyopathy caused by this entity.     

Contribution à l'étude infrastructurale du système neurosécréteur rétrocérébral chez Locusta migratoria migratorioides (R. et F.)

Résumé L'étude infrastructurale des nerfs cardiaques afférents et des nerfs allato-cardiaques qui entrent dans la constitution du système neurosécréteur rétrocérébral de Locusta migratoria migratorioides (R. et F.) révèle l'existence des trois types de fibres neurosécrétrices définis dans les corpora cardiaca. Une quatrième catégorie de fibres caractérisées par la présence de vésicules claires existe dans les nerfs allato-cardiaques et dans les corpora allata. L'origine des fibres et l'évolution des grains de neurosécrétion au cours de leur transit sont envisagées.

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Ultrastructural study of the retrocerebral neurosecretory system in Locusta migratoria migratorioides (R. et F.)II. Neurosecretory pathways

Summary An ultrastructural study of the nervi corporis cardiaci and nervi corporis allati, which are part of the retrocerebral neurosecretory system of Locusta migratoria migratorioides, reveals the existence of three neurosecretory fiber types. A fourth neurosecretory fibertype with electron lucent vesicles is also present in the nervi corporis allati and in the corpora allata. The fibers are characterized by differences in the size and electron opacity of the neurosecretory granules. The origin of the various neurosecretory fiber types and the evolution of the neurosecretory granules are discussed.

     

Mitochondrial Superoxide Radical Formation is Controlled by Electron Bifurcation to the High and Low Potential Pathways

The generation of oxygen radicals in biological systems and their sites of intracellular release have been subject of numerous studies in the last decades. Based on these studies mitochondria are considered to be the major source of intracellular oxygen radicals. Although this finding is more or less accepted, the mechanism of univalent oxygen reduction in mitochondria is still obscure. One of the most critical electron transfer steps in the respiratory chain is the electron bifurcation at the cytochrome bc 1 complex. Recent studies with genetically mutated mitochondria have made it clear that electron bifurcation from ubiquinol to the cytochrome bc 1 complex requires the free mobility of the head domain of the Rieske iron-sulfur protein. On the other hand, it has been long known that inhibition of electron bifurcation by antimycin A causes leakage of single electrons to dioxygen, which results in the release of superoxide radicals. These findings lead us to study whether hindrance of the interaction of ubiquinol with the cytochrome bc 1 complex is the regulator of single electron diversion to oxygen. Hindrance of electron bifurcation was observed following alterations of the physical state of membrane phospholipids in which the cytochrome bc 1 complex is inserted. Irrespective of whether the fluidity of the membrane lipids was elevated or decreased, electron flow rates to the Rieske iron-sulfur protein were drastically reduced. Concomitantly superoxide radicals were released from these mitochondria, strongly suggesting an effect on the mobility of the head domain of the Rieske iron-sulfur protein. This revealed the involvement of the ubiquinol cytochrome bc 1 redox couple in mitochondrial superoxide formation. The regulator, which controls leakage of electrons to oxygen, appears to be the electron-branching activity of the cytochrome bc 1 complex.