The Iowa Homemaker vol.3, no.12

Table of Contents A Greeting to Iowa Homemakers by Dr. Louise Stanley, page 3 A New Book on “Meal Planning and Table Service” by Florence E. Busse, page 4 A Bill of Rights for the Child by Lulu R. Lancaster, page 4 Shrubs as a Garden Background by Juanita Beard, page 5 ‘Tis Egg Time Again by Beth Bailey McLean, page 6 The New Domestic System by Claude L. Benner, page 7 A Time Budget for the Homemaker by Ruth M. Lindquist, page 8 Figures That Do Not Lie by Mae L. Kelley, page 9 The Cooking of Meats by P. Mabel Nelson, page 10 The Psychology of Clothing by Eveleth Pedersen, page 11 Iowa State Women in Rural Schools by W. H. Lancelot, page 12 A Yarn about Yarns by Irene Christian, page 13 Tea Room Accounting by George M. Fuller, page 14 Who’s There and Where by Dryden Quist, page 15 Editorial, page 16 Homemaker as Citizen, page 17 The Eternal Question, page 18 Mrs. Purchaser Chooses Upholstery by Lucile Barta, page 1

The Iowa Homemaker vol.3, no.2

Table of Contents It Is Not Always May by Maybelle A. Payton, page 1 The Why of a Home Economics Course by Florence Busse, page 2 Why I Came to Iowa State compiled by Clara Jordan, page 2 Picnic Ingredients by Grata Thorn, page 3 Iowa State Women Attend Voters’ Convention by Eleanor Murray and Jeanette Beyer, page 4 A Modern Version of the Hope Box by N. Beth Bailey, page 5 A Summer Living Room by Mildred Boyt, page 7 Canning Early Fruits and Vegetables by Helen G. Lamb, page 8 Hazards of Bird Life by J. E. Guthrie, page 9 Nile Styles by Harriett Schleiter, page 10 Shall Mother Have a Vacation? by Eda Lord Murphy, page 10 The Fallacy of An Expensive Standard of Living by Claude L. Benner, page 11 What Shall We Take? by Lucille Barta, page 12 Who’s There and Where by Helen Reidy, page 1

Mining protein loops using a structural alphabet and statistical exceptionality

<p>Abstract</p> <p>Background</p> <p>Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied.</p> <p>Results</p> <p>We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints.</p> <p>Conclusions</p> <p>We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at <url>http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/</url>.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genetic variants in the regulatory T cell related pathway and colorectal cancer prognosis.

Background: High numbers of lymphocytes in tumor tissue, including T regulatory cells (Treg), have been associated with better colorectal cancer survival. Tregs, a subset of CD4(+) T lymphocytes, are mediators of immunosuppression in cancer, and therefore variants in genes related to Treg differentiation and function could be associated with colorectal cancer prognosis.Methods: In a prospective German cohort of 3,593 colorectal cancer patients, we assessed the association of 771 single-nucleotide polymorphisms (SNP) in 58 Treg-related genes with overall and colorectal cancer-specific survival using Cox regression models. Effect modification by microsatellite instability (MSI) status was also investigated because tumors with MSI show greater lymphocytic infiltration and have been associated with better prognosis. Replication of significant results was attempted in 2,047 colorectal cancer patients of the International Survival Analysis in Colorectal Cancer Consortium (ISACC).Results: A significant association of the TGFBR3 SNP rs7524066 with more favorable colorectal cancer-specific survival [hazard ratio (HR) per minor allele: 0.83; 95% confidence interval (CI), 0.74-0.94; P value: 0.0033] was replicated in ISACC (HR: 0.82; 95% CI, 0.68-0.98; P value: 0.03). Suggestive evidence for association was found with two IL7 SNPs, rs16906568 and rs7845577. Thirteen SNPs with differential associations with overall survival according to MSI in the discovery analysis were not confirmed.Conclusions: Common genetic variation in the Treg pathway implicating genes such as TGFBR3 and IL7 was shown to be associated with prognosis of colorectal cancer patients. Impact: The implicated genes warrant further investigation