dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans

Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. Since certain types of retrotransposons, particularly members of the Alu, L1, and SVA families, are still active, their recent and ongoing propagation generates a unique and important class of human genomic diversity/polymorphism (for the presence and absence of an insertion) with some elements known to cause genetic diseases. So far, over 2,300, 500, and 80 Alu, L1, and SVA insertions, respectively, have been reported to be polymorphic and many more are yet to be discovered. We present here the Database of Retrotransposon Insertion Polymorphisms (dbRIP; http://falcon.roswellpark. org:9090), a highly integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). dbRIP currently contains a nonredundant list of 1,625, 407, and 63 polymorphic Alu, L1, and SVA elements, respectively, or a total of 2,095 RIPs. In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along with all other genome annotation information. Users can query the database by a variety of means and have access to the detailed information related to a RIP, including detailed insertion sequences and genotype data. dbRIP represents the first database providing comprehensive, integrative, and interactive compilation of RIP data, and it will be a useful resource for researchers working in the area of human genetics. © 2006 Wiley-Liss, Inc

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

Alu elements are the most active and predominant type of short interspersed elements (SINEs) in the human genome. Recently inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among different human populations, and they are useful genetic markers for population genetic studies. The objective of this study is to identify polymorphic Alu insertions through an in silico comparative genomics approach and to analyze their distribution pattern throughout the human genome. By computationally comparing the public and Celera sequence assemblies of the human genome, we identified a total of 800 polymorphic Alu elements. We used polymerase chain reaction-based assays to screen a randomly selected set of 16 of these 800 Alu insertion polymorphisms using a human diversity panel to demonstrate the efficiency of our approach. Based on sequence analysis of the 800 Alu polymorphisms, we report three new Alu subfamilies, Ya3, Ya4b, and Yb11, with Yb11 being the smallest known Alu subfamily. Analysis of retrotransposition activity revealed Yb11, Ya8, Ya5, Yb9, and Yb8 as the most active Alu subfamilies and the maintenance of a very low level of retrotransposition activity or recent gene conversion events involving S subfamilies. The 800 polymorphic Alu insertions are characterized by the presence of target site duplications (TSDs) and longer than average polyA-tail length. Their pre-integration sites largely follow an extended NT-AARA motif. Among chromosomes, the density of Alu insertion polymorphisms is positively correlated with the Alu-site availability and is inversely correlated with the densities of older Alu elements and genes. © 2005 Elsevier B.V. All rights reserved

CAG Repeat Variants in the POLG1 Gene Encoding mtDNA Polymerase-Gamma and Risk of Breast Cancer in African-American Women

The DNA polymerase-gamma (POLG) gene, which encodes the catalytic subunit of enzyme responsible for directing mitochondrial DNA replication in humans, contains a polyglutamine tract encoded by CAG repeats of varying length. The length of the CAG repeat has been associated with the risk of testicular cancer, and other genomic variants that impact mitochondrial function have been linked to breast cancer risk in African-American (AA) women. We evaluated the potential role of germline POLG-CAG repeat variants in breast cancer risk in a sample of AA women (100 cases and 100 age-matched controls) who participated in the Women's Circle of Health Study, an ongoing multi-institutional, case-control study of breast cancer. Genotyping was done by fragment analysis in a blinded manner. Results from this small study suggest the possibility of an increased risk of breast cancer in women with minor CAG repeat variants of POLG, but no statistically significant differences in CAG repeat length were observed between cases and controls (multivariate-adjusted odds ratio 1.74; 95% CI, 0.49–6.21). Our study suggests that POLG-CAG repeat length is a potential risk factor for breast cancer that needs to be explored in larger population-based studies

Reversible, interrelated mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts: functional and mechanistic implications

[Background]: 4-Hydroxy-tamoxifen (4OHT) triggers Cre-mediated K-Ras removal in [H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert] fibroblasts, generating growth-arrested “Rasless” MEFs which are able to recover their proliferative ability after ectopic expression of Ras oncoproteins or constitutively active BRAF or MEK1. [Results]: Comparison of the transcriptional profiles of Rasless fibroblasts with those of MEFs lacking only H-Ras and N-Ras identified a series of differentially expressed mRNAs and microRNAs specifically linked to the disappearance of K-Ras from these cells. The rescue of cell cycle progression in Rasless cells by activated BRAF or MEK1 resulted in the reversal of most such transcriptional mRNA and microRNA alterations.Functional analysis of the differentially expressed mRNAs uncovered a significant enrichment in the components of pathways regulating cell division, DNA/RNA processing and response to DNA damage. Consistent with G1/S blockade, Rasless cells displayed repression of a series of cell cycle-related genes, including Cyclins, Cyclin-dependent kinases, Myc and E2F transcription targets, and upregulation of Cyclin-dependent kinase inhibitors. The profile of differentially expressed microRNAs included a specific set of oncomiR families and clusters (repressed miR-17 ~ 92, miR-106a ~ 363, miR-106b ~ 25, miR-212 ~ 132, miR-183 ~ 182, and upregulated miR-335) known for their ability to target a specific set of cellular regulators and checkpoint sensors (including Rb, E2F and Cdkns) able to modulate the interplay between the pro- and anti-proliferative or stress-response pathways that are reversibly altered in Rasless cells. [Conclusions]: Our data suggest that the reversible proliferation phenotype of Rasless cells is the pleiotropic result of interplay among distinct pro- and anti-proliferative, and stress-response pathways modulated by a regulatory circuitry constituted by a specific set of differentially expressed mRNAs and microRNAs and preferentially targeting two cross-talking signalling axes: Myc-Rb-E2F-dependent and Cdkns-p53-dependent pathways.Work in the lab of ES was supported by grants FIS Intrasalud PS09/01979 and the Red Tematica de Investigación Cooperativa en Cáncer (RTICC) (RD06/0020/0000 and RD12/0036/0001) from the Instituto de Salud Carlos III (ISCIII) Spain. Nuria Calzada is gratefully acknowledged for technical assistance.Peer Reviewe

Type II DNA topoisomerases in zebrafish development

DNA topoisomerases are vital enzymes for major cellular processes like replication, transcription, and chromosome segregation. They play an essential role in solving DNA topological problems by catalysing the passage of DNA strands through each other via introducing transient single or double strand breaks. Type IIA DNA topoisomerases members introduce double strand breaks via an ATP-dependent strand passage reaction. This study aimed to investigate the roles of topo Ila and topo Iip in zebrafish development.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

From Laboratory Processing to Continuous Processing of Cellulose Nanofibril (CNF) Sheets for Structural and Packaging Applications

First reported in the early 1980s, cellulose nanomaterials (CNMs) like cellulose nanofibrils (CNFs) have become a very attractive option to reinforce, replace, or reduce the need of oil-derived synthetic polymers. This is largely due to their inherent sustainability, abundance in nature, high crystalline contents, and ample surface chemistries possible (e.g., carboxylic acid, hydroxyls, esters, acetyls). Over the years, improved mechanical isolation processes (e.g., disk refining for isolation of the fibril-like CNFs) and acid hydrolysis processes (e.g., improved acid recovery for isolation of the rod-like cellulose nanocrystals (CNCs)) have increased industrial production capacity and allowed for CNMs to be readily accessible in both academic and industrial research settings. This, in turn, has accelerated research efforts regarding their processing into usable forms (e.g., films, fibers, coatings, etc.) which attain significantly higher properties when compared to synthetic polymer analogs. Although the reported CNM processing efforts are promising, further advances are still needed in order to galvanize the current polymer industry into processing CNMs and possibly ease their adoption in major markets like food packaging and construction. Out of the different CNM types, this work focuses specifically on CNFs and encompasses four main projects, each targeted at solving a different CNF processing related challenge or limitation. The first project addresses the challenge of processing thick CNF sheets (thickness \u3e 100 um) through the development of a wet-stacking lamination technique. The results showed that high-strength multi-layer CNF structures with a thickness of up to ~1.7 mm can be produced. The second project addresses the challenge of bulk continuous processing of CNF sheets through conventional single-screw extrusion. The results showed that near pure CNF sheets (comprised of ~91 wt.% CNFs and ≤ ~9 wt.% of a processing aid like carboxymethyl cellulose (CMC)) can be continuously extruded and calendered, and that traditional polymer compounders (e.g., Banbury mixer) can be used to prepare highly loaded CNF pastes (~25 wt.% solids) for extrusion. The third project addresses the susceptibility of CNFs to humid conditions through the use of different chemical treatments. The results showed that the redispersion and setting behavior of CNF with adsorbed CMC can be controlled and that new crosslinks were effectively formed due to the chemical treatment. Lastly, in hopes of further improving the mechanical performance and expand the possible end uses for CNFs and other CNMs, the fourth project presents preliminary research efforts into processing fiber reinforced CNF composites (FR-CNF)

Controlled Dispersion and Setting of Cellulose Nanofibril (CNF) - Carboxymethyl Cellulose (CMC) Pastes

Abstract This work investigated the redispersion and setting behavior of highly loaded (~18 wt.% solids in water) pastes of cellulose nanofibrils (CNFs) with carboxymethyl cellulose (CMC). A single-screw extruder was used to continuously process CNF+CMC pastes into cord. The adsorption of CMC onto the CNF fibrils was assessed through zeta potential and titration which revealed a surface charge change of ~61 % from -36.8 mV and 0.094 mmol/g COOH for pure CNF to -58.1 mV and 0.166 mmol/g COOH for CNF+CMC with a CMC degree of substitution of 0.9. Dried CNF with adsorbed CMC was found to be fully redispersible in water and re-extruded back into a cord without any difficulties. On the other hand, chemical treatment with hydrochloric acid, a carbodiimide crosslinker, or two wet strength enhancers (polyamide epichlorohydrin and polyamine epichlorohydrin) completely suppressed the dispersibility previously observed for dried-untreated CNF+CMC. Turbidity was used to quantify the level of redispersion or setting achieved by the untreated and chemically treated CNF+CMC in both water and a strong alkaline solution (0.1 M NaOH). Depending on the chemical treatment used, FTIR analysis revealed the presence of ester, N-acyl urea, and anhydride absorption bands which were attributed to newly formed linkages between CNF fibrils, possibly explaining the suppressed redispersion behavior. Water uptake of the differently treated and dried CNF+CMC materials agreed with both turbidity and FTIR results.</jats:p

Wet-Stacking Lamination of Multilayer Mechanically Fibrillated Cellulose Nanofibril (CNF) Sheets with Increased Mechanical Performance for Use in High-Strength and Lightweight Structural and Packaging Applications

Mechanically fibrillated cellulose nanofibril (CNF) sheets of varying thicknesses were fabricated by using a wet stacking lamination technique without the use of solvents other than water or binders. The use of this technique allowed for the creation of multilayer structures with a working area of 117 mm by 117 mm and thickness of up to 0.547 ± 0.03 mm in under 2 h, which represents the shortest total processing time reported for such thickness of CNF sheets. To highlight the capabilities of utilizing wet stacking, the thickest reported 100% pure multilayer CNF sheet with a thickness of 1.65 ± 0.02 mm was produced. To gauge the effect of processing parameters on the mechanical performance of the produced sheets, thickness (85–547 μm thick), pressing time (35 min, 1 h, and 2 h), pressing pressure (0–5.17 MPa), and loading rate (4 min, 2 min, and 20 s) were varied. Tensile testing results show that the ultimate strength increased as the thickness increased and subsequently reached a plateau at a value of 207 ± 2.51 MPa at a critical thickness between 85 ± 2 and 153 ± 4 μm. A slight decrease in ultimate strength to a value of 184 ± 10.9 MPa was seen for the thicker 547 μm (0.547 mm) specimens. The specific strength was comparable to 2024 aluminum (T3 tempered) due to the relatively low density of CNF. The apparent toughness (work of failure) of the sheets was found to be on average 3.53 ± 0.36 MJ/m3, which is about 6 times greater than the reported value for poly­(styrene). Because of their improved mechanical properties, these sheets could serve in high-strength and low-density structural applications where aluminum alloys (2024 and 6061) and packing materials/containers where commodity polymers like poly­(styrene) are currently used