Targeted co-expression networks for the study of traits.

Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used approach for the generation of gene co-expression networks. However, networks generated with this tool usually create large modules with a large set of functional annotations hard to decipher. We have developed TGCN, a new method to create Targeted Gene Co-expression Networks.

Paired plasma lipidomics and proteomics analysis in the conversion from mild cognitive impairment to Alzheimer's disease.

Background: Alzheimer's disease (AD) is a neurodegenerative condition for which there is currently no available medication that can stop its progression. Previous studies suggest that mild cognitive impairment (MCI) is a phase that precedes the disease. Therefore, a better understanding of the molecular mechanisms behind MCI conversion to AD is needed.

Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications.

Primary familial brain calcification (PFBC) is characterized by calcium deposition in the brain, causing progressive movement disorders, psychiatric symptoms, and cognitive decline. PFBC is a heterogeneous disorder currently linked to variants in six different genes, but most patients remain genetically undiagnosed. Here, we identify biallelic NAA60 variants in ten individuals from seven families with autosomal recessive PFBC.

The locus controls glycogen aggregation in astrocytes of the aged hippocampus without impacting cognitive function.

In aged humans and mice, aggregates of hypobranched glycogen molecules called polyglucosan bodies (PGBs) accumulate in hippocampal astrocytes. PGBs are known to drive cognitive decline in neurological diseases but remain largely unstudied in the context of typical brain aging. Here, we show that PGBs arise in autophagy-dysregulated astrocytes of the aged C57BL/6J mouse hippocampus.

PhenoExam: gene set analyses through integration of different phenotype databases.

Background: Gene set enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) plays an important role in bioinformatics focused on diseases of genetic basis. To facilitate phenotype-oriented gene set analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases.

Results: PhenoExam generates sensitive and accurate phenotype enrichment analyses.

Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights.

Motivation: Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behavior for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.

Comparative study of the primary cilia in thyrocytes of adult mammals.

Since their discovery in different human tissues by Zimmermann in 1898, primary cilia have been found in the vast majority of cell types in vertebrates. Primary cilia are considered to be cellular antennae that occupy an ideal cellular location for the interpretation of information both from the environment and from other cells. To date, in mammalian thyroid gland, primary cilia have been found in the thyrocytes of humans and dogs (fetuses and adults) and in rat embryos.

Glomerular basement membrane selective permeability in short-term streptozotocin-induced diabetic rats.

In diabetes, the glomerular basement membrane undergoes thickening and structural alterations with loss of glomerular permselectivity properties. However, the onset of the alterations at early phases of diabetes is unclear. Aiming to determine the functional and structural alterations of the glomerular wall in the early stages of diabetes, we have studied the distribution of endogenous circulating albumin and type IV collagen in the glomerular basement membrane, using the immunocytochemical approach.

Apoptosis in breast carcinoma.

Apoptosis may play a major role in determining tumor growth and aggressiveness. The aim of this study was to examine the relationship between apoptosis, expression of bcl-2 and p53 proteins, proliferation index, and other clinicopathological features of breast carcinoma. Sixty-five formalin-fixed paraffin-embedded tissue sections from invasive ductal breast carcinomas were studied for the presence of apoptosis by the terminaldeoxynucleotidyl-transferase-mediated dUTP-FITC nick end-labeling (TUNEL) method.

Sarcomatoid carcinoma of the skin: report of a case.

We report the histological, immunohistochemical and ultrastructural findings of an exophytic cutaneous tumor composed of a mixture of typical basal cell carcinoma (BCC) and malignant fibrous histiocytoma. Nine previously reported carcinosarcomas of the skin are reviewed. We prefer the term "sarcomatoid carcinoma" for this rare neoplasm.

Mesenchymal chondrosarcoma of the retroperitoneum. Report of a case diagnosed by fine needle aspiration biopsy with immunohistochemical, electron microscopic demonstration of S-100 protein in undifferentiated cells.

Background: Mesenchymal chondrosarcoma (MC), first described in 1959 by Lichtenstein and Bernstein, is an uncommon tumor of the soft tissues and bone defined by the coexistence of nests of well-defined cartilaginous tissue within a proliferation of primitive mesenchymal cells.

Case: A 27-year-old, white female consulted a physician for a left lumbar mass associated with sciatica-type pain, asthenia, anorexia and weight loss. Abdominal computed tomography showed a 20-cm, retroperitoneal neoplasm that occupied the lower half of the left abdominal flank.

Immunocytochemical investigation of the in vivo endocytosis by renal tubular epithelial cells.

The internalization and degradation of glomerular filtered serum proteins by the proximal tubular epithelium has been extensively studied by microperfusion methods. By using a cationic probe that easily traverses the glomerular wall into the urinary space, we have performed a morpho-cytochemical and quantitative study of the in vivo endocytotic activity of the proximal tubular epithelial cell. Bovine serum albumin (BSA) was tagged with dinitrophenol (DNP) and cationized to pI over 8.

Fine needle aspiration cytology of primary soft tissue tumors. Morphologic analysis of the most frequent types.

We reviewed 98 cases of fine needle aspiration of soft tissue tumors with histologic confirmation performed during an eight-year period and propose a working morphologic classification based on the most prominent cytologic features. Six main tumor groups are recognized: myxoid, round cells, spindle cells, pleomorphic cells, polygonal cells and well differentiated. We believe that this classification allows recognition of the most common soft tissue tumors while helping with the differential diagnosis of other neoplasia, primary or secondary, with similar morphology and a similar presentation.

Fine needle aspiration of peripheral neuroepithelioma of soft tissues.

Peripheral neuroepithelioma of soft tissue is a malignant primitive neuroectodermal tumor that appears both in children and adults and usually has a poor outcome. Fine needle aspiration on two patients with tumors in the lower limbs showed small round cells with unipolar processes and a tendency to form Homer-Wright rosettes. The cells had a round to oval nucleus with fine chromatin, up to four small, conspicuous nucleoli and vacuolated, periodic acid-Schiff-positive cytoplasm.

Nucleolar organizer regions in pigmented skin lesions. Value in the differential diagnosis of Spitz nevi.

Forty-one cases of typical melanocytic skin lesions (15 intradermal nevi, 14 Spitz nevi and 12 malignant melanomas) were used to investigate the value of staining of nucleolar organizer regions (NORs) in the differential diagnosis of such pigmented lesions. Histologic sections were stained by the silver colloid (Ag) method, with and without the prior use of a melanin blocking agent. There were statistically significant differences in the mean numbers of AgNORs per nucleus between the groups of lesions studied (1.

Neuroendocrine (NE) cells in rat neonatal lungs. A histochemical and immunocytochemical study.

A study has been carried out to determine the presence of NE cells in the newborn rat lung. The localization of these cell was achieved by an argyrophil method. Both single NE and NEB, were found.

Cytologic diagnosis of a case of recurrent adamantinoma.

The cytologic features of a case of recurrent adamantinoma of the tibia diagnosed by fine needle aspiration (FNA) in a 31-year-old patient are described. The FNA smears contained single-lying cells and cells arranged in small clusters and Indian files, with some nuclear molding. Three cell types were present: (1) large polygonal cells with chromatin clearing, (2) smaller cells with poorly defined cytoplasm and dense chromatin and (3) fusiform cells.

Demonstration of sugar residues in the ultimobranchial tubule and thyroid C-cells of the rat using peroxidase labelled lectins.

The distribution of various sugars, that contribute to the composition of the carbohydrate components of the glycoprotein in the ultimobranchial tubule and the thyroid C-cells has been studied, using eight peroxidase-labelled lectins (Dolichos biblorus, Glycine max, Bauhinia purpurea, Helix pomatia, Arachis hipogaea, Ulex europaeus I, Limax flavus and Sophora japonica). The results obtained seem to show that there are receptors for Dolichos biflorus, Glycine max, Bauhinia purpurea, Helix pomatia, Arachis hipogaea, Ulex europaeus I and Limax flavus in the ultimobranchial tubule, suggesting the existence of N-acetylgalactosamine, galactose, L-fucose and sialic acid. However, the C-cells show only a positive reaction with Ulex europaeus I indicating the existence of fucosyl residues in those cells.