Identification and analysis of gene families from the duplicated genome of soybean using EST sequences

BACKGROUND: Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. However it does have the 6th largest EST collection comprised of ESTs from a variety of soybean genotypes. Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. RESULTS: We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean (Glycine max L. Merr.) using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. CONCLUSION: The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion

Bounding Space

The cognition and description of spatial conditions are essential components of any foundation for design and the visual arts. However, the ability to discern subtle spatial distinctions and the limits of spatial boundaries is often clouded by habit and apparent familiarity with the conditions in question. For example, one thinks one knows the spatial make-up of one\u27s bedroom, but can one real ly see the space of the room from a position outside of this perceived familiarity? Can pre-cognitive knowledge be converted into critical understanding? Or, to invert the question, how can one know a space that one sees with new eyes? Perhaps we need to take Paul Valery to heart when he suggests that; to see is to forget the name of the thing one sees

Predicting Stag and Hare Hunting Behaviors Using Hidden Markov Model

In this paper, we used Hidden Markov Model (HMM) to describe the gaming behaviors of students and whether they will exhibit “stag” or “hare” hunting behavior in a mobile game for mathematics learning. We found that there is a 99% probability that the students will stay either as stag or hare hunters. Our results also suggest that they would choose arithmetic problems involving addition. These game behaviors are not beneficial to learning because they are only exhibiting mathematical skills they already know. The results of the study show that stag and hare hunters have unique traits that separate the one from the other

Variation in the Performance of Larvae Capturing Traps/Substrate during Larviciding on Domasi River in Zomba, Malawi

Research was carried out on performance of larvae capturing traps during larviciding on Domasi River in Zomba. The study was aimed at assessing the impact of Bacillus thuringiensis israelensis (Bti) on black fly larvae colonization of different traps/substrates. Data on black fly larval density on the substrates were collected before and after Bti application. The monitoring was done using three different types of substrates: nylon strips, rocks and debris. The river was divided into three strata and breeding sites were determined

Computing Scalable Multivariate Glocal Invariants of Large (Brain-) Graphs

Graphs are quickly emerging as a leading abstraction for the representation of data. One important application domain originates from an emerging discipline called "connectomics". Connectomics studies the brain as a graph; vertices correspond to neurons (or collections thereof) and edges correspond to structural or functional connections between them. To explore the variability of connectomes---to address both basic science questions regarding the structure of the brain, and medical health questions about psychiatry and neurology---one can study the topological properties of these brain-graphs. We define multivariate glocal graph invariants: these are features of the graph that capture various local and global topological properties of the graphs. We show that the collection of features can collectively be computed via a combination of daisy-chaining, sparse matrix representation and computations, and efficient approximations. Our custom open-source Python package serves as a back-end to a Web-service that we have created to enable researchers to upload graphs, and download the corresponding invariants in a number of different formats. Moreover, we built this package to support distributed processing on multicore machines. This is therefore an enabling technology for network science, lowering the barrier of entry by providing tools to biologists and analysts who otherwise lack these capabilities. As a demonstration, we run our code on 120 brain-graphs, each with approximately 16M vertices and up to 90M edges.Comment: Published as part of 2013 IEEE GlobalSIP conferenc

Political mobilisation by minorities in Britain: negative feedback of ‘race relations'?

This article uses a political opportunity approach to study the relationship of minority groups to the political community in Britain. The main argument is that the British race relations approach established in the 1960s had an important effect that still shapes the patterns of political contention by different minority groups today. Original data on political claims-making by minorities demonstrate that British 'racialised' cultural pluralism has structured an inequality of opportunities for the two main groups, African-Caribbeans and Indian subcontinent minorities. African-Caribbeans mobilise along racial lines, use a strongly assimilative 'black' identity, conventional action forms, and target state institutions with demands for justice that are framed within the recognised framework of race relations. Conversely, a high proportion of the Indian subcontinent minority mobilisation is by Muslim groups, a non-assimilative religious identity. These are autonomously organised, but largely make public demands for extending the principle of racial equality to their non-racial group. Within the Indian subcontinent minorities, the relative absence of mobilisation by Indian, Sikh and Hindu minorities, who have achieved much better levels of socio-economic success than Pakistani and Bangladeshi Muslims, suggests that there is also a strong socioeconomic basis for shared experiences and grievances as Muslims in Britain. This relativises the notion that Muslim mobilisation is Britain is purely an expression of the right for cultural difference per se, and sees it as a product of the paradoxes of British race relations

Age and Growth of Redear Sunfish Lepomis microlophus (Gunthur), from Bob Kidd Lake

Total lengths (62-285mm) and body scales from 75 redear sunfish collected by electroshocking from Bob Kidd Lake during October and November 1985 were used for this study. The length-frequency distribution yielded five age groups, however, the body scale analysis revealed eight age groups. The total length scale radius relationship was estimated as, TL = 17.98 + 0.92 Sr . Lengths attained at earlier ages were estimated by the Fraser-Lee method and the Bertlanffy growth model was fitted to the lengths for ages five through ten, and the resulting equation, L₁ = 295 [1 - exp — 0.29 (t - 1.83)], estimated lengths similar to the back- calculated lengths (r = 0.98)

A Quantitative Study of the Conductivity of Solutions

During the summer of 1963, the author had the privilege of attending an Advanced Placement Chemistry Institute in which the participants built some simple instruments useful in chemistry and studied their usual applications. The A. C. Conductivity Bridge built by the participants seemed to offer some advantages in presenting one of the demonstrations accompanying an experiment used in the Chem-Study course at Roosevelt High School in Des Moines, Iowa where the following activity was conducted