Polymorphism and divergence at the 5' flanking region of the sex- determining locus, Sry, in mice

We have investigated patterns of evolution in the nonrecombining portion of the Y chromosome in mice by comparing levels of polymorphism within Mus domesticus with levels of divergence between M. domesticus and M. spretus. A 1,277-bp fragment of noncoding sequence flanking the sex determining locus (Sry) was PCR amplified, and 1,063 bases were sequenced and compared among 20 M. domesticus and 1 M. spretus. Two polymorphic base substitutions and two polymorphic insertion/deletion sites were identified within M. domesticus; nucleotide diversity was estimated to be 0.1%. Divergence between M. domesticus and M. spretus for this region (1.9%) was slightly lower than the average divergence of single-copy nuclear DNA for these species. Comparison of levels of polymorphism and divergence at Sry with levels of polymorphism and divergence in the mitochondrial DNA control region provided no evidence of a departure from the expectations of neutral molecular evolution. These findings are consistent with the presumed lack of function for much of the Y chromosome.      

Protein refolding in reversed micelles: Interactions of the protein with micelle components

A novel process has been developed to improve the refolding yield of denatured proteins. It uses reversed micelles to isolate denatured protein molecules from each other and thus, upon refolding, reduces the intermolecular interactions which lead to aggregation. The feasibility of this process was first demonstrated with Ribonuclease A as a model protein. In the present work, we expanded the scope of this study to better understand both the general mechanisms of protein refolding in reversed micelles and the biotechnological applicability of the process. First, we investigated the interactions between the individual components of the reversed micellar system (the protein molecule, the denaturant guanidine hydrochloride (GuHCl), and the surfactant (AOT)) during the refolding process. We then extended our studies to a more hydrophobic protein, gamma-interferon, which aggregates upon refolding in aqueous solution. However, it was also found to aggregate in our reversed micelle process during the extraction step. Since gamma-interferon is a much more hydrophobic protein than RNase, we hypothesize that interactions between hydrophobic amino acids and the surfactant layer may interfere with refolding. This hypothesis was tested by studying the refolding of chemically modified RNase. The substitution of 55% of the surface lysine residues with hydrophobic caproyl groups caused a significant decrease in the refolding yield of RNase in the reversed micellar system without affecting aqueous solution renaturation. In addition, the extraction efficiency of the enzyme from reversed micelles back into aqueous solution was severely reduced and resulted in aggregation. These experiments indicate that unfolded hydrophobic Proteinsinteract with the Surfactant molecules, which limits their ability to refold in reversed micelles.     

Differences in methylation profiles between HPV-positive and HPV-negative oropharynx squamous cell carcinoma: A systematic review

Oropharyngeal squamous cell carcinoma (OPSCC) is associated with human papillomavirus (HPV). HPV-positive OPSCC is considered a distinct molecular entity with a better prognosis than HPV-negative cases of OPSCC. However, the exact pathogenic mechanisms underlying the differences in clinical and molecular behavior between HPV-positive and HPV-negative OPSCC remain poorly understood. Epigenetic events play an important role in the development of cancer. Hypermethylation of DNA in promoter regions and global hypomethylation are 2 epigenetic changes that have been frequently observed in human cancers. It is suggested that heterogeneous epigenetic changes play a role in the clinical and biological differences between HPV-positive and HPV-negative tumors. Unraveling the differences in methylation profiles of HPV-associated OPSCC may provide for promising clinical applications and may pave the road for personalized cancer treatment. This systematic review aims to assess the current state of knowledge regarding differences in promoter hypermethylation and global methylation between HPV-positive and HPV-negative OPSCC.     

Epigenetic reprogramming in the porcine germ line

Background  

Epigenetic reprogramming is critical for genome regulation during germ line development. Genome-wide demethylation in mouse primordial germ cells (PGC) is a unique reprogramming event essential for erasing epigenetic memory and preventing the transmission of epimutations to the next generation. In addition to DNA demethylation, PGC are subject to a major reprogramming of histone marks, and many of these changes are concurrent with a cell cycle arrest in the G2 phase. There is limited information on how well conserved these events are in mammals. Here we report on the dynamic reprogramming of DNA methylation at CpGs of imprinted loci and DNA repeats, and the global changes in H3K27me3 and H3K9me2 in the developing germ line of the domestic pig.     

Reversed micelles recognize an active protein

Summary The extraction behavior of native and heated-denatured -chymotrypsin has been investigated with two different reversed micellar systems. A large difference in the degree of extraction was observed for the native relative to the denatured -chymotrypsin. In particular, mixed reversed micelles formulated with DOLPA (dioleyl phosphoric acid) and AOT show a high selectivity for the active -chymotrypsin.     

Early seral trends in plant community diversity on a recontoured surface mine

The initial floristic composition and structure of vegetation on a recontoured surface mine in southwestern Wyoming was experimentally manipulated to test ideas concerning successional convergence. Experimental treatments involving the planting pattern and density of shrubs and the storage of topsoil were evaluated on the basis of their ability to divert the successional trajectories of the redeveloping vegetation and to increase species diversity. The change in compositional similarity along a topographic gradient was also monitored.The influence of initial composition and soil storage generally declined with time; successional convergence among treatments over the four years of the study was largely monotonic. The planting of shrubs and the storage of topsoil did, however, influence the rate of plant succession. There were no persistent differences in alpha diversity among the experimental treatments. Compositional dissimilarity along the topographic gradient, as expressed by beta diversity, increased with time.     

Vegetation, landscape and human activity in Midland Ireland: mire and lake records from the Lough Kinale-Derragh Lough area, Central Ireland

A high-resolution pollen record for the Holocene has been obtained from Derragh Bog, a small raised mire located on a peninsula in Lough Kinale-Derragh Lough, in Central Ireland as part of the Discovery Programme (Ireland) Lake Settlements Project. The data are compared with two lower resolution diagrams, one obtained from Derragh Lough and one from adjacent to a crannog in Lough Kinale. The general trends of vegetation change are similar and indicate that landscape-scale clearance did not occur until the Medieval period (ca. a.d. 800–900). There are, however, significant differences between the diagrams due primarily to core location and taphonomy, including pollen source area. Only the pollen profile from Derragh Bog reveals an unusually well represented multi-phase primary decline in Ulmus ca. 3500–3100 b.c. (4800–4750¹⁴C b.p.) which is associated with the first arable farming in the area. The pollen diagram indicates a rapid, and almost complete, clearance of a stand of Ulmus with some Quercus on the Derragh peninsula, arable cultivation in the clearing and then abandonment by mobile/shifting late Neolithic farmers. Subsequently there are a number of clearance phases which allow the colonisation of the area by Fraxinus and are probably associated with pastoral activity. The pollen sequence from adjacent to a crannog in Lough Kinale shows clear evidence of the construction and use of the crannog for the storage of crops (Hordeum and Avena) whereas the Derragh Bog diagram and the diagram from Derragh Lough reflect the growth of the mire. This study reveals that in this landscape the record from a small mire shows changes in prehistoric vegetation caused by human agriculture that are not detectable in the lake sequences. Although in part this is due to the higher temporal resolution and more consistent and complete chronology for the mire, the most important factor is the closer proximity of the raised mire sequence to the dry land. However, the pollen sequence from adjacent to a crannog does provide detailed evidence of the construction and function of the site. It is concluded that in order to ascertain a complete picture of vegetation changes in a lowland shallow lake-dominated landscape, cores from both the lake and surrounding small mires should be analysed.