Widespread Hypomethylation Occurs Early and Synergizes with Gene Amplification during Esophageal Carcinogenesis

Although a combination of genomic and epigenetic alterations are implicated in the multistep transformation of normal squamous esophageal epithelium to Barrett esophagus, dysplasia, and adenocarcinoma, the combinatorial effect of these changes is unknown. By integrating genome-wide DNA methylation, copy number, and transcriptomic datasets obtained from endoscopic biopsies of neoplastic progression within the same individual, we are uniquely able to define the molecular events associated progression of Barrett esophagus. We find that the previously reported global hypomethylation phenomenon in cancer has its origins at the earliest stages of epithelial carcinogenesis. Promoter hypomethylation synergizes with gene amplification and leads to significant upregulation of a chr4q21 chemokine cluster and other transcripts during Barrett neoplasia. In contrast, gene-specific hypermethylation is observed at a restricted number of loci and, in combination with hemi-allelic deletions, leads to downregulatation of selected transcripts during multistep progression. We also observe that epigenetic regulation during epithelial carcinogenesis is not restricted to traditionally defined “CpG islands,” but may also occur through a mechanism of differential methylation outside of these regions. Finally, validation of novel upregulated targets (CXCL1 and 3, GATA6, and DMBT1) in a larger independent panel of samples confirms the utility of integrative analysis in cancer biomarker discovery

CYTOGENETIC STUDIES OF THE HORSE, EQUUS CABALLUS (L.), THE DONKEY, EQUUS ASINUS (L.) (PERISSODACTYLA: EQUIDAE) AND THE MULE

Comparative cytogenetic studies using conventional stains, as well as different banding techniques, have been performed on three diploid fibroblast cell lines derived from horse (Equus caballus, 2n = 64), donkey (Equus asinus, 2n = 62) and mule (2n = 63). Conventional staining and banding techniques were utilized to morphologically identify and characterize individual chromosomes of horse, donkey and mule in metaphase chromosome preparations. Studies performed on horse metaphases yielded results similar to those obtained in previously published reports. Similar studies performed on donkey metaphase preparations have clearly established that out of 31 chromosome pairs, 19 pairs of autosomes were metacentric or submetacentric, and 11 paris of autosomes were acrocentric with the donkey X chromosome classified as the fourth largest submetacentric chromosome pair in the donkey diploid complement. The cytogenetic studies performed on horse and donkey chromosome preparations facilitated the ultimate identification of the horse- and donkey-derived chromosomes in the mule diploid chromosome complement. A system of nomenclature has now been established as a result of this study to clearly identify individual mule chromosomes. Within the mule diploid chromosome complement 32 chromosomes have been identified as being derived from the female horse parent, while 31 mule chromosomes have been identified as being derived from the male donkey parent. The mule diploid chromosome complement displayed a great deal of conservatism with respect to the comparative banding patterns of horse and donkey. This may indicate a similarity to horse and donkey in the arrangement of gene sequences on the mule chromosomes. These gene sequences in mule are probably transcribed differently than in the horse and donkey. Some differences could be observed in mule chromosomes banding patterns when compared to donkey and horse banding patterns. However these variations could be due to chromosome condensation differences that naturally arise in different metaphase spreads of all three cell lines. Heterogeneity was observed between homologous horse and donkey chromosomes with respect to the degree of heterochromatic staining obtained by the C banding technique. This phenomenon has been observed in many different organisms and it may be involved in the karyotypic evolution of some organisms by initiating karyotypic changes before gross phenotypic changes are observed. Ag-As staining of NOR\u27s which codes specifically for rRNA was performed on all three cell lines. In horse, an average of 8 chromosomes exhibited telomeric NOR\u27s along with 58-60 chromosomes which exhibited centromeric NOR\u27s. In donkey an average of 8 chromosomes in each metaphase exhibited telomeric NOR\u27s, and a range of 3-26 chromosomes exhibited some centromeric NOR\u27s. In mule, however, only 4 chromosomes exhibited telomeric NOR\u27s which was substantially lower than expected based on the number of NOR\u27s observed in the horse and donkey. This low number of observable NOR\u27s in the interspecific mule hybrid indicates some type of suppression mechanism is operating in the mule. The precise nature of this suppression mechanism is unknown, but may be operating at the level of transcription of one parent species rDNA

SEISMIC ASSESSMENT OF THE HISTORICAL MIXED MASONRY-REINFORCED CONCRETE GOVERNMENT PALACE IN LA SPEZIA

Government Palace in La Spezia is a six-story mixed masonry-reinforced concrete construction, built in 1926 and today seat of the Prefecture of La Spezia city (Italy). In the paper, after the description of the case study, the attention is focused on the evaluation of the seismic performance of the building. The seismic assessment is performed by means of a numerical hybrid approach: the reinforced concrete frame is modelled according to a concentrated plasticity beam-column element, while the masonry infill is simulated by a plane macro-element which interacts with the surrounding frame, by means of discrete distribution of nonlinear links. The 3D-model has been implemented in the computer code 3DMacro that allows the modelling of both unreinforced masonry and mixed reinforced concrete-masonry structures. According to the performed numerical simulation the building, although not designed to resist to seismic actions, does not possess a high vulnerability with reference to the expected earthquake in the construction site

A New Criterion for Fluoroquinolone-Associated Disability Diagnosis: Functional Gastrointestinal Disorders

Background and Objectives: Fluoroquinolones (FQs) are a broad-spectrum class of antibiotics routinely prescribed for common bacterial infections despite recent recommendations to use them only for life-threatening cases. In addition to their antimicrobial properties, FQs act in the central nervous system as GABAA receptor inhibitors, which could potentially affect functionality of the vagus nerve at the forefront of gastrointestinal (GI) tract function. Alterations in neural control of digestion have been shown to be linked to Functional Gastrointestinal Disorders (FGIDs), which are usually diagnosed based on self-reported symptoms. The aim of this study was to assess the incidence of FGIDs following FQ use. Materials and Methods: Self-reports from the FDA Adverse Event Reporting System were analyzed together with ~300 survey responses from a social network derived sample to the Bowel Disease Questionnaire. Results: The results of this study suggested that six different FQs are associated with a wide range of GI symptoms not currently reported in the drugs’ labels. The responses from the survey suggested that ~70% of FQ users scored positive for FGID, with no positive correlation between drug type, duration of administration, dosage and frequency of administration. Conclusions: This study showed that GI disorders other than nausea, vomiting and diarrhea are more common than currently reported on the drug labels, and that FGIDs are possibly a common consequence of FQ use even after single use

Chromosome locations of genes encoding human signal transduction adapter proteins, Nck (NCK), Shc (SHC1), and Grb2 (GRB2).

Abnormalities due to chromosomal aberration or point mutation in gene products of growth factor receptors or in ras gene products, which lie on the same signaling pathway, can cause disease in animals and humans. Thus, it can be important to determine chromosomal map positions of genes encoding "adapter" proteins, which are involved in transducing signals from receptor tyrosine kinases to downstream signal recipients such as ras, because adaptor protein genes could also, logically, serve as targets of mutation, rearrangement, or other aberration in disease. Therefore, DNAs from panels of rodent-human hybrids carrying defined complements of human chromosomes were assayed for the presence of the cognate genes for NCK, SHC, and GRB2, three SH2 or SH2/SH3 (Src homology 2 and 3) domain-containing adapter proteins. Additionally, NCK and SHC genes were more narrowly localized by chromosomal in situ hybridization. The NCK locus is at chromosome region 3q21, a region involved in neoplasia-associated changes; the SHC cognate locus, SHC1, is at 1q21, and the GRB2 locus is at 17q22-qter telomeric to the HOXB and NGFR loci. Both SHC1 and GRB2 are in chromosome regions that may be duplicated in some tumor types

A human histone H2B.1 variant gene, located on chromosome 1, utilizes alternative 3\u27 end processing

A variant human H2B histone gene (GL105), previously shown to encode a 2300 nt replication independent mRNA, has been cloned. We demonstrate this gene expresses alternative mRNAs regulated differentially during the HeLa S3 cell cycle. The H2B-Gl105 gene encodes both a 500 nt cell cycle dependent mRNA and a 2300 nt constitutively expressed mRNA. The 3\u27 end of the cell cycle regulated mRNA terminates immediately following the region of hyphenated dyad symmetry typical of most histone mRNAs, whereas the constitutively expressed mRNA has a 1798 nt non-translated trailer that contains the same region of hyphenated dyad symmetry but is polyadenylated. The cap site for the H2B-GL105 mRNAs is located 42 nt upstream of the protein coding region. The H2B-GL105 histone gene was localized to chromosome region 1q21-1q23 by chromosomal in situ hybridization and by analysis of rodent-human somatic cell hybrids using an H2B-GL105 specific probe. The H2B-GL105 gene is paired with a functional H2A histone gene and this H2A/H2B gene pair is separated by a bidirectionally transcribed intergenic promoter region containing consensus TATA and CCAAT boxes and an OTF-1 element. These results demonstrate that cell cycle regulated and constitutively expressed histone mRNAs can be encoded by the same gene, and indicate that alternative 3\u27 end processing may be an important mechanism for regulation of histone mRNA. Such control further increases the versatility by which cells can modulate the synthesis of replication-dependent as well as variant histone proteins during the cell cycle and at the onset of differentiation

Role of the HLA class II: HCV-related disorders

The paper highlights the role of different HLA class II molecules in hepatic and lymphoproliferative HCV-related disorders. HLA molecules have been reviewed, according to an in silico cluster classification, based on the sequence, the biochemical structure of the pockets, and the functional characteristics of the HLA II molecules. Thus, by reducing the complexity of HLA II polymorphism, charateristics that unite different HLA molecules with specific HCV-associated pathologies may be recognized with greater case. Results show that HLA clusters associated with better dlimination of the virus are protective against HCC development, while the same clusters are associated with a higher risk of developing cryoglobulinemic syndrome and the concomitant NHL. These data added further acknowledgements on pathogenetic mechanisms associated with HCV infection. Results also highlight differences of NHL occurring in HCV-positive subjects, with or without a concomitant type II autoimmune cryoglobulinemic syndrome, suggesting that cryoglobulinemic background associated with NHL should be considered in the evaluation of the effectiveness of new therapies in the course of HCV-associated NHLs