Integrating multi-attribute similarity networks for robust representation of the protein space

MOTIVATION: A global view of the protein space is essential for functional and evolutionary analysis of proteins. In order to achieve this, a similarity network can be built using pairwise relationships among proteins. However, existing similarity networks employ a single similarity measure and therefore their utility depends highly on the quality of the selected measure. A more robust representation of the protein space can be realized if multiple sources of information are used. RESULTS: We propose a novel approach for analyzing multi-attribute similarity networks by combining random walks on graphs with Bayesian theory. A multi-attribute network is created by combining sequence and structure based similarity measures. For each attribute of the similarity network, one can compute a measure of affinity from a given protein to every other protein in the network using random walks. This process makes use of the implicit clustering information of the similarity network, and we show that it is superior to naive, local ranking methods. We then combine the computed affinities using a Bayesian framework. In particular, when we train a Bayesian model for automated classification of a novel protein, we achieve high classification accuracy and outperform single attribute networks. In addition, we demonstrate the effectiveness of our technique by comparison with a competing kernel-based information integration approach.     

Surfactant protein A and D in the reproductive tract of stallion

The presence of surface-active material in the lung alveolus has been known for several decades as being essential for normal lung function. The host defense and controlling inflammatory processes of the lung are the major functions of SP-A and SP-D. SP-A and SP-D were originally demonstrated in alveolar type II cells, but recent studies have shown extrapulmonary expression of SP-A and SP-D indicating systemic roles of these proteins. Present study describes the presence of SP-A and SP-D in the stallion genital tract, prepuce, prostate, testis, and seminal vesicle using Western blotting and immunohistochemistry. This paper presents the first evidence for the existence of SP-A and SP-D glycoproteins in the stallion genital tract. We examined genital system organs and tissues from stallion and were able to show that surfactant protein A and D reactive with surfactant-specific antibodies were present in the stallion genital tract tissues and organs. On the basis of results, it can be postulated that surfactant proteins in the stallion reproductive tract contribute to the immune surveillance and to active barrier defense mechanism.     

Glucocorticoid alternative effects on proliferating and differentiated mammary epithelium are associated to opposite regulation of cell-cycle inhibitor expression

Glucocorticoids influence post-natal mammary gland development by sequentially controlling cell proliferation, differentiation, and apoptosis. In the mammary gland, it has been demonstrated that glucocorticoid treatment inhibits epithelial apoptosis in post-lactating glands. In this study, our first goal was to identify new glucocorticoid target genes that could be involved in generating this effect. Expression profiling, by microarray analysis, revealed that expression of several cell-cycle control genes was altered by dexamethasone (DEX) treatment after lactation. Importantly, it was determined that not only the exogenous synthetic hormone, but also the endogenous glucocorticoids regulated the expression of these genes. Particularly, we found that the expression of cell cycle inhibitors p21CIP1, p18INK4c, and Atm was differentially regulated by glucocorticoids through the successive stages of mammary gland development. In undifferentiated cells, DEX treatment induced their expression and reduced cell proliferation, while in differentiated cells this hormone repressed expression of those cell cycle inhibitors and promoted survival. Therefore, differentiation status determined the effect of glucocorticoids on mammary cell fate. Particularly, we have determined that p21CIP1 inhibition would mediate the activity of these hormones in differentiated mammary cells because over-expression of this protein blocked DEX-induced apoptosis protection. Together, our data suggest that the multiple roles played by glucocorticoids in mammary gland development and function might be at least partially due to the alternative roles that these hormones play on the expression of cell cycle regulators.     

Connexin-dependent signaling in neuro-hormonal systems

The advent of multicellular organisms was accompanied by the development of short- and long-range chemical signalling systems, including those provided by the nervous and endocrine systems. In turn, the cells of these two systems have developed mechanisms for interacting with both adjacent and distant cells. With evolution, such mechanisms have diversified to become integrated in a complex regulatory network, whereby individual endocrine and neuro-endocrine cells sense the state of activity of their neighbors and, accordingly, regulate their own level of functioning. A consistent feature of this network is the expression of connexin-made channels between the (neuro)hormone-producing cells of all endocrine glands and secretory regions of the central nervous system so far investigated in vertebrates. This review summarizes the distribution of connexins in the mammalian (neuro)endocrine systems, and what we know about the participation of these proteins on hormone secretion, the life of the producing cells, and the action of (neuro)hormones on specific targets. The data gathered since the last reviews on the topic are summarized, with particular emphasis on the roles of Cx36 in the function of the insulin-producing beta cells of the endocrine pancreas, and of Cx40 in that of the renin-producing juxta-glomerular epithelioid cells of the kidney cortex. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics.     

Evaluation of the JAK2-V617F gene mutation in Turkish patients with essential thrombocythemia and polycythemia vera

An activating mutation of Janus kinase 2 (JAK2-V617F) was previously described in chronic myeloproliferative disorders (MPD). In previously published studies, the frequency of the JAK2-V617F mutation was determined to be 80-90 % for patients with polycythemia vera (PV) and 40-70 % for essential thrombocythemia (ET). In this study, we analyzed the relationship between the JAK2-V617F mutation and clinical-hematological parameters in Turkish patients with MPD and compared these findings with published studies from other geographic regions. A total of 148 patients were studied; of which, 70 were diagnosed with PV and 78 with ET. The mutation status of JAK2 was determined using a tetra-primer polymerase chain reaction. We found that 80 % of the PV group and 42 % of the ET group were positive for the JAK2-V617F mutation. When all patients were analyzed, the levels of white blood cells, hemoglobin and splenomegaly were significantly different in patients with the JAK2-V617F mutation (p < 0.05). To our knowledge, this study is the first to evaluate the relationship between MPD and JAK2-V617F in Turkish patients. The JAK2-V617F mutation is frequently detected in the Turkish patients with MPD, and especially in patients with PV. Hence, it would be useful to include JAK2 mutation screening in the initial evaluation of patients suspected to have MPD.     

Mutations in RIPK4 cause the autosomal-recessive form of popliteal pterygium syndrome

The autosomal-recessive form of popliteal pterygium syndrome, also known as Bartsocas-Papas syndrome, is a rare, but frequently lethal disorder characterized by marked popliteal pterygium associated with multiple congenital malformations. Using Affymetrix 250K SNP array genotyping and homozygosity mapping, we mapped this malformation syndrome to chromosomal region 21q22.3. Direct sequencing of RIPK4 (receptor-interacting serine/threonine kinase protein 4) showed a homozygous transversion (c.362T>A) that causes substitution of a conserved isoleucine with asparagine at amino acid position 121 (p.Ile121Asn) in the serine/threonine kinase domain of the protein. Additional pathogenic mutations-a homozygous transition (c.551C>T) that leads to a missense substitution (p.Thr184Ile) at a conserved position and a homozygous one base-pair insertion mutation (c.777_778insA) predicted to lead to a premature stop codon (p.Arg260ThrfsX14) within the kinase domain-were observed in two families. Molecular modeling of the kinase domain showed that both the Ile121 and Thr184 positions are critical for the protein's stability and kinase activity. Luciferase reporter assays also demonstrated that these mutations are critical for the catalytic activity of RIPK4. RIPK4 mediates activation of the nuclear factor-κB (NF-κB) signaling pathway and is required for keratinocyte differentiation and craniofacial and limb development. The phenotype of Ripk4(-/-) mice is consistent with the human phenotype presented herein. Additionally, the spectrum of malformations observed in the presented families is similar, but less severe than the conserved helix-loop-helix ubiquitous kinase (CHUK)-deficient human fetus phenotype; known as Cocoon syndrome; this similarity indicates that RIPK4 and CHUK might function via closely related pathways to promote keratinocyte differentiation and epithelial growth.     

p57kip2 regulates glial fate decision in adult neural stem cells

Our recent studies revealed p57kip2 as an intrinsic regulator of late gliogenesis and demonstrated that in oligodendroglial precursor cells p57kip2 inhibition leads to accelerated maturation. Adult neural stem cells have been described as a source of glial progenitors; however, the underlying mechanisms of cell fate specification are still poorly understood. Here, we have investigated whether p57kip2 can influence early events of glial determination and differentiation. We found that Sox2/GFAP double-positive cells express p57kip2 in stem cell niches of the adult brain. Short-hairpin RNA-mediated suppression of p57kip2 in cultured adult neural stem cells was found to strongly reduce astroglial characteristics, while oligodendroglial precursor features were increased. Importantly, this anti-astrogenic effect of p57kip2 suppression dominated the bone morphogenetic protein-mediated promotion of astroglial differentiation. Moreover, we observed that in p57kip2 knockdown cells, the BMP antagonist chordin was induced. Finally, when p57kip2-suppressed stem cells were transplanted into the adult spinal cord, fewer GFAP-positive cells were generated and oligodendroglial markers were induced when compared with control cells, demonstrating an effect of in vivo relevance.     

Retroperitoneal masses mimicking adrenal tumors

ObjectiveTo report 10 cases of neoplasms that were initially thought to be primarily adrenal-derived masses but were later confirmed as tumors of a different origin.MethodsBetween 2000 and 2011, a total of 229 patients underwent adrenalectomy at our institution. Of this overall group, 10 patients had retroperitoneal pathologic conditions mimicking adrenal tumors. Using an institutional review board-approved database, we reviewed the clinical, biochemical, and radiologic characteristics of these 10 patients.ResultsThe study cohort consisted of 4 male and 6 female patients. The mean age of these 10 patients was 48 years. The pathologic conditions included schwannoma (n = 3), leiomyosarcoma (n = 2), and 1 each of metastatic angiosarcoma, metastatic granulosa cell tumor, retroperitoneal hematoma, perivascular epithelioid cell tumor, and bronchogenic cyst. The patient with angiosarcoma had elevated plasma and urine catecholamines and a positive metaiodobenzylguanidine scan, whereas the others had normal findings on biochemical work-up. A percutaneous biopsy was performed preoperatively in 2 patients.All patients, except the patient with hematoma, underwent abdominal exploration, which was laparoscopic in 5, open in 2, and robotic in 2. With exclusion of the patients with angiosarcoma and hematoma, resection was possible in all the remaining patients.ConclusionIn this report we describe our experience with retroperitoneal masses mimicking adrenal tumors. Increased awareness of these unusual pathologic conditions is important for appropriate clinical management of these tumors. The presentation of the patients and the surgical management of these individual pathologic entities are highlighted. (Endocr Pract. 2012;18:335-341)     

Retinal Neurodegeneration in Wilson’s Disease Revealed by Spectral Domain Optical Coherence Tomography

Background/Objective

In addition to cirrhosis of the liver, Wilson’s disease leads to copper accumulation and widespread degeneration of the nervous system. Delayed visual evoked potentials (VEPs) suggest changes to the visual system and potential structural changes of the retina.

Methods

We used the latest generation of spectral domain optical coherence tomography to assess the retinal morphology of 42 patients with Wilson’s disease and 76 age- and sex-matched controls. We measured peripapillary retinal nerve fiber layer (RNFL) thickness and total macular thickness and manually segmented all retinal layers in foveal scans of 42 patients with Wilson’s disease and 76 age- and sex-matched controls. The results were compared with VEPs and clinical parameters.

Results

The mean thickness of the RNFL, paramacular region, retinal ganglion cell/inner plexiform layer and inner nuclear layer was reduced in Wilson’s disease. VEPs were altered with delayed N75 and P100 latencies, but the N140 latency and amplitude was unchanged. An analysis of the laboratory parameters indicated that the serum concentrations of copper and caeruloplasmin positively correlated with the thickness of the outer plexiform layer and with N75 and P100 VEP latencies.

Conclusion

Neuronal degeneration in Wilson’s disease involves the retina and changes can be quantified by optical coherence tomography. While the VEPs and the thickness of the outer plexiform layer appear to reflect the current copper metabolism, the thicknesses of the RNFL, ganglion cell/inner plexiform layer, inner nuclear layer and the total paramacular thickness may be the best indicators of chronic neuronal degeneration.