Most transcription factor binding sites are in a few mosaic classes of the human genome

Background: Many algorithms for finding transcription factor binding sites have concentrated on the characterisation of the binding site itself: and these algorithms lead to a large number of false positive sites. The DNA sequence which does not bind has been modeled only to the extent necessary to complement this formulation. Results We find that the human genome may be described by 19 pairs of mosaic classes, each defined by its base frequencies, (or more precisely by the frequencies of doublets), so that typically a run of 10 to 100 bases belongs to the same class. Most experimentally verified binding sites are in the same four pairs of classes. In our sample of seventeen transcription factors — taken from different families of transcription factors — the average proportion of sites in this subset of classes was 75%, with values for individual factors ranging from 48% to 98%. By contrast these same classes contain only 26% of the bases of the genome and only 31% of occurrences of the motifs of these factors — that is places where one might expect the factors to bind. These results are not a consequence of the class composition in promoter regions. Conclusions:This method of analysis will help to find transcription factor binding sites and assist with the problem of false positives. These results also imply a profound difference between the mosaic classes

Marketing Kentucky Hay — A Reality

As I write this in early December, Kentucky does not yet have a system for marketing hay. The above title reflects an attitude which positively expects a marketing system to be in place by the 1989 season. Many details of such a system have been discussed, some decisions have already been made and more will be made by the time you read this. Literally hundreds of decisions need to be made before hay is marketed in 1989. since these decisions will be made by a group of people (a producer Board of Directors and the KY Department of Agriculture personnel) what is written here is only an approximation of what will probably happen

Marketing Alternatives for Kentucky Alfalfa: Needs, Challenges and Opportunities

There are unquestionable needs for more high quality alfalfa in the Southeastern U.S. From these needs arise the challenge and opportunities for those who are researching, informing, teaching, and even promoting alfalfa. Likewise, there are income opportunities for those who own resources which could be used in producing and marketing alfalfa. This paper will discuss some of the factors which should be considered in hay marketing, i.e., (1) a dependable supply of hay; (2) producing high quality hay; and (3) planning to supply the highest quality hay to the highest priced market

Genomic DNA from animals shows contrasting strand bias in large and small subsequences

Abstract Background For eukaryotes, there is almost no strand bias with regard to base composition, with exceptions for origins of replication and transcription start sites and transcribed regions. This paper revisits the question for subsequences of DNA taken at random from the genome. Results For a typical mammal, for example mouse or human, there is a small strand bias throughout the genomic DNA: there is a correlation between (G - C) and (A - T) on the same strand, (that is between the difference in the number of guanine and cytosine bases and the difference in the number of adenine and thymine bases). For small subsequences – up to 1 kb – this correlation is weak but positive; but for large windows – around 50 kb to 2 Mb – the correlation is strong and negative. This effect is largely independent of GC%. Transcribed and untranscribed regions give similar correlations both for small and large subsequences, but there is a difference in these regions for intermediate sized subsequences. An analysis of the human genome showed that position within the isochore structure did not affect these correlations. An analysis of available genomes of different species shows that this contrast between large and small windows is a general feature of mammals and birds. Further down the evolutionary tree, other organisms show a similar but smaller effect. Except for the nematode, all the animals analysed showed at least a small effect. Conclusion The correlations on the large scale may be explained by DNA replication. Transcription may be a modifier of these effects but is not the fundamental cause. These results cast light on how DNA mutations affect the genome over evolutionary time. At least for vertebrates, there is a broad relationship between body temperature and the size of the correlation. The genome of mammals and birds has a structure marked by strand bias segments.</p

Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression

<p>Abstract</p> <p>Background</p> <p>On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication.</p> <p>Results</p> <p>The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not.</p> <p>Conclusion</p> <p>The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.</p

Marketing Kentucky Hay — An Update

Based on soil capabilities, Kentucky could grow 2-million acres of alfalfa while increasing the acreage of corn and soybeans. Even more than 2-million acres could be grown if Kentucky grown alfalfa should show market demands making it economically competitive with corn and soybeans. Marketing is the key to developing demand which could make hay a $1-billion Kentucky crop. Many of you have heard or read my comments on marketing hay. In this presentation, I will present a brief review of what I have previously said and then bring you up to date on hay marketing activities since the alfalfa conference in February 1986

Marketing Kentucky Hay

That more income is needed by Kentucky farmers is a well established and accepted fact. Although, the tobacco program appears to be yet viable, we have long needed to supplement the tobacco income with income from the remainder of the farm. I think this audience is also well aware of the potential· for producing hay in Kentucky, particularly alfalfa. Estimates in the University of Kentucky potential study indicate that we could have in this state two million acres of alfalfa with a projected potential income of a billion dollars a year generated for our farmers. This potential income should not be interpreted as an objective since the big determinant in generating the income is marketing. Kentucky farmers have never considered hay as a cash crop. Probably less than 7% of the hay production is sold off of the farm on which it is produced. Sales generally are to a neighbor or someone near the site of production. Any successful marketing program must contain several features. I will discuss briefly some of these features and point out where we are in Kentucky in the development of a system for marketing Kentucky hay

Marketing Programs and Strategies

Hay has never been widely perceived as a cash crop, therefore, it has historically accounted for a very small part of the total cash sales by farmers. It has been estimated that more than 90% of all hay baled in the state is retained on the producing farms. Most of that which is sold is transported very short distances and of course if one farmer in a community has a good hay year, all do. Organized marketing efforts have been minimal in both scope and successes. In 1978, efforts were initiated toward a more organized system of marketing Kentucky hay. In the following few minutes I will discuss marketing organization, surveys to locate potential buyers, the national quality assessment system which has been approved and one possible hay pricing procedure

Seedbed Preparation for Fall Seeded Alfalfa

With the increased interest developed during the past few years on production of alfalfa hay for cash sales, the acreage seeded each year has increased • And. although UK forage specialists prefer spring seeding of alfalfa to fall seeding. some growers will and should opt for fall seeding. This is particularly true on fields which have a history of legumes and/or are contaminated with Johnsongrass. Those who do so should begin planning now to have the seedbed prepared for planting by mid-August to mid-September

Establishment and Early Management of Alfalfa Stands for Hay and Silage Production

To achieve high levels of productivity and long-lived alfalfa stands, farmers must treat alfalfa as a crop and not as a pasture on the back forty. In this paper we present current recommendations for establishment and early management of alfalfa stands in Kentucky. See AGR-76, Alfalfa-The Queen of Forage Crops, and AGR-64, Establishing Forage Crops, for more detailed information