The organization of bacterial genomes: towards understanding the interplay between structure and function

Genomes are arranged in a confined space in the cell, the nucleoid or nucleus. This arrangement is hierarchical and dynamic, and follows DNA/chromatin-based transactions or environmental conditions. Describing the interplay between local genome structure and gene activity is a long-standing quest in biology. Here, we focus on systematic studies correlating bacterial genome folding and function. Parallels on organizational similarities with eukaryotes are drawn. The biological relevance of hierarchical units in bacterial genome folding and the causal relationship between genome folding and its activity is unclear. We discuss recent quantitative approaches to tackle these questions. Moreover, we sketch a perspective of experiments necessary to iteratively and systematically build, test and improve structure–function models of bacterial chromatin.Macromolecular Biochemistr

Renal Replacement Lipomatosis Presenting in the Setting of Ureteral Stricture with Absence of Renal Calculus Disease

Renal replacement lipomatosis of the kidney is a rare, benign entity in which extensive fibrofatty proliferation of the renal sinus is associated with marked atrophy of the renal parenchyma. It is often associated with calculi or long-standing inflammation. This entity may be confused with a fatty neoplasm of the kidney. A 51-year-old woman with a past medical history of pancreas transplant for type 1 diabetes subsequently developed ureteral stricture. This was initially managed by a nephrostomy tube and nephroureterostomy stenting with periodic exchanges to help restore urine flow; however, the renal function of the kidney progressively declined with recurrent and complicated urinary tract infections. She presented for kidney transplant with right native nephrectomy. Gross examination of the right kidney revealed a 12.8 cm renal sinus lipomatous mass replacing much of the kidney. Microscopically, the mass consisted of mature adipose tissue with fibrous septae and occasional thick-walled vessels with prominent smooth muscle bundles. A rare atypical stromal cell was present, otherwise no significant cytologic atypia or lipoblasts were identified. After excluding fat-predominant angiomyolipoma and well-differentiated liposarcoma, a diagnosis of renal replacement lipomatosis was made. Renal replacement lipomatosis is a benign condition typically associated with a nonfunctioning or poorly functioning kidney often linked to renal calculus disease or chronic renal infection. The presentation in our case was atypical given an absence of associated renal calculus disease. This case is intended to increase awareness of this less commonly encountered entity as it may be confused with a fatty neoplasm of the kidney, some with malignant potential

HI-NESS:a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.Genome Instability and Cance

Handmade clay bricks: chemical, physical and mechanical properties

The clay brick masonry that is much used in historical structures often is in a rather poor state of conservation. In order to intervene correctly in these buildings, it is convenient to characterize the old material. For this purpose, a large sample of clay brick specimens from the 12th to 19th century were collected from six Portuguese monasteries, and were characterized chemically, physically and mechanically. A large variability of the properties was found. Additionally, a sample of handmade new bricks, which are commonly used as replacing material, was also analysed. The results were compared to the old bricks and could be possibly adequate as substitution bricks. Still, significant differences were found in chemical composition, and in water absorption and porosity, which are much lower in modern handmade bricks. With respect to mechanical properties, the range of values found in old bricks was rather high and the degree of deterioration exhibited a large scatter, meaning that a conclusion is hardly possible.The authors gratefully acknowledge the Instituto de Gestao do Patrimonio Arquitectonico e Arqueologico (IGESPAR) for providing the old clay bricks used in the present work. The first author acknowledges the partial funding of this work by the FCT through the following scholarships POCTI SFRH/BD/6409/2001 and POCTI SFRH/BPD/26706/2005

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.Animal science