Hundreds Of Domains Research Articles

Bombyx moriTranscription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

Transcription factors are present in all living organisms, and play vital roles in a wide range of biological processes. Studies of transcription factors will help reveal the complex regulation mechanism of organisms. So far, hundreds of domains have been identified that show transcription factor activity. Here, 281 reported transcription factor domains were used as seeds to search the transcription factors in genomes of Bombyx mori L. (Lepidoptera: Bombycidae) and four other model insects. Overall, 666 transcription factors including 36 basal factors and 630 other factors were identified in B. mori genome, which accounted for 4.56% of its genome. The silkworm transcription factors' expression profiles were investigated in relation to multiple tissues, developmental stages, sexual dimorphism, and responses to oral infection by pathogens and direct bacterial injection. These all provided rich clues for revealing the transcriptional regulation mechanism of silkworm organ differentiation, growth and development, sexual dimorphism, and response to pathogen infection.

A mathematical model for generating bipartite graphs and its application to protein networks

Complex systems arise in many different contexts from large communication systems and transportation infrastructures to molecular biology. Most of these systems can be organized into networks composed of nodes and interacting edges. Here, we present a theoretical model that constructs bipartite networks with the particular feature that the degree distribution can be tuned depending on the probability rate of fundamental processes. We then use this model to investigate protein-domain networks. A protein can be composed of up to hundreds of domains. Each domain represents a conserved sequence segment with specific functional tasks. We analyze the distribution of domains in Homo sapiens and Arabidopsis thaliana organisms and the statistical analysis shows that while (a) the number of domain types shared by k proteins exhibits a power-law distribution, (b) the number of proteins composed of k types of domains decays as an exponential distribution. The proposed mathematical model generates bipartite graphs and predicts the emergence of this mixing of (a) power-law and (b) exponential distributions. Our theoretical and computational results show that this model requires (1) growth process and (2) copy mechanism.

Google's Deep Web crawl

The Deep Web, i.e., content hidden behind HTML forms, has long been acknowledged as a significant gap in search engine coverage. Since it represents a large portion of the structured data on the Web, accessing Deep-Web content has been a long-standing challenge for the database community. This paper describes a system for surfacing Deep-Web content, i.e., pre-computing submissions for each HTML form and adding the resulting HTML pages into a search engine index. The results of our surfacing have been incorporated into the Google search engine and today drive more than a thousand queries per second to Deep-Web content. Surfacing the Deep Web poses several challenges. First, our goal is to index the content behind many millions of HTML forms that span many languages and hundreds of domains. This necessitates an approach that is completely automatic, highly scalable, and very efficient. Second, a large number of forms have text inputs and require valid inputs values to be submitted. We present an algorithm for selecting input values for text search inputs that accept keywords and an algorithm for identifying inputs which accept only values of a specific type. Third, HTML forms often have more than one input and hence a naive strategy of enumerating the entire Cartesian product of all possible inputs can result in a very large number of URLs being generated. We present an algorithm that efficiently navigates the search space of possible input combinations to identify only those that generate URLs suitable for inclusion into our web search index. We present an extensive experimental evaluation validating the effectiveness of our algorithms.

Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations

Atomic force microscopy and steered molecular dynamics investigations of the response of so-called mechanical proteins like titin, tenascin or their individual immunoglobulin and fibronectin type III domains have lead to qualitative insights about the relationship between the β sandwich domain architecture and the function of this class of proteins. The proteins, linear segments of up to hundreds of domains, through strain induced shape changes, unfolding and refolding, maintain order and elasticity in cellular systems over a nearly tenfold length scale. In this paper we develop a steered molecular dynamics description of the response of the titin immunoglobulin domain I27 at the onset of domain unfolding in quantitative agreement with AFM observations. We show that if forces stronger than 50 pN are applied to the terminal ends the two hydrogen bonds between the antiparallel A and B β strands break with a concomitant 6–7 Å elongation of the protein. If forces strong enough to unfold the domain are applied, the protein is halted in this initial extension until the set of all six hydrogen bonds connecting strands A′ and G break simultaneously. This behavior is accounted for by a barrier separating folded and unfolded states, the shape of which is consistent with AFM and chemical denaturation data. We also demonstrate that steered molecular dynamics simulations which induce unfolding through slow pulling (speed 0.1 Å/ps) predict unfolding forces that are within a factor of two within force values extrapolated from AFM observations.

Characterization of Retention Phenomena of Micron-Size Electrical Domains in Pzt Thin Films

AbstractThe retention phenomena of purposely aligned micron-size domains (defined as “bits”) in Pb(Zr,Ti)O3 thin films were characterized by atomic force microscopy (AFM) combined with a lock-in amplifier. It is found that the retention loss occurs by “region by region” showing local variation of the rate of the loss. Furthermore, the total retention loss can be successfully described by an extended exponential decay, which implies a narrow distribution of the relaxation times of the domains. This probably comes from the fact that the micron-size bits consist a few hundreds of domains. Along with the characterization, the effects of the bit size and the poling time per unit area on the retention characteristics were investigated. Based on our observations, it is concluded that the retention time is proportional to both the poling time per unit area and the bit size. This trend is successfully explained by a kinetic model developed by our group.

RNA polymerase II transcription is concentrated outside replication domains throughout S-phase

Transcription and replication are, like many other nuclear functions and components, concentrated in nuclear domains. Transcription domains and replication domains may play an important role in the coordination of gene expression and gene duplication in S-phase. We have investigated the spatial relationship between transcription and replication in S-phase nuclei after fluorescent labelling of nascent RNA and nascent DNA, using confocal immunofluorescence microscopy. Permeabilized human bladder carcinoma cells were labelled with 5-bromouridine 5'-triphosphate and digoxigenin-11-deoxyuridine 5'-triphosphate to visualize sites of RNA synthesis and DNA synthesis, respectively. Transcription by RNA polymerase II was localized in several hundreds of domains scattered throughout the nucleoplasm in all stages of S-phase. This distribution resembled that of nascent DNA in early S-phase. In contrast, replication patterns in late S-phase consisted of fewer, larger replication domains. In double-labelling experiments we found that transcription domains did not colocalize with replication domains in late S-phase nuclei. This is in agreement with the notion that late replicating DNA is generally not actively transcribed. Also in early S-phase nuclei, transcription domains and replication domains did not colocalize. We conclude that nuclear domains exist, large enough to be resolved by light microscopy, that are characterized by a high activity of either transcription or replication, but never both at the same time. This probably means that as soon as the DNA in a nuclear domain is being replicated, transcription of that DNA essentially stops until replication in the entire domain is completed.