iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called “iTIS-PseTNC,” was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method.     

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis.     

Development of a sensitive in vitro method for identifying tumor promoters

The identification and characterization of nongenotoxic carcinogens represents a significant challenge to toxicologists. In vitro methods for identifying tumor promoters with suitable sensitivity and specificity have been particularly elusive. Experiments are described which suggest that the human promyelocytic leukemia cell line HL-60 provides a sensitive indicator of promoter-induced changes to gene regulation and expression. As a result of differentiation these cells undergo a transition from a non-phagocytic suspension culture to an attached fibroblast-like culture which exhibits high phagocytic activity. Fluorescent latex particles were used as sensors to highlight the phagocytic phenotype and permitted the use of flow cytometry to automatically quantitate particle internalization. To evaluate specificity, HL-60 cells were treated with a series of phorbol esters covering a range of in vivo tumor promoting activity. Results indicate that this family of compounds induces HL-60 cells to differentiate in proportion to their in vivo promoting activity. To closely assess the sensitivity of the phagocytic endpoint, HL-60 cells were treated with picogram levels of 12-O-tetradecanoyl phorbol-13-acetate (TPA), whereupon increments as low as 50 pg of TPA per ml caused statistically significant increases in phagocytic activity. The experiments described herein suggest that in vitro differentiation of HL-60 cells may reflect the promoter-dependent modifications to gene expression that are observed in vivo during the promotion phase of carcinogenesis. The described method may represent a sensitive promoter screening assay which is both rapid and economical.     

PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition

The pseudo amino acid (PseAA) composition can represent a protein sequence in a discrete model without completely losing its sequence-order information, and hence has been widely applied for improving the prediction quality for various protein attributes. However, dealing with different problems may need different kinds of PseAA composition. Here, we present a web-server called PseAAC at http://chou.med.harvard.edu/bioinf/PseAA/, by which users can generate various kinds of PseAA composition to best fit their need.     

Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution

In the Post Genome Age, there is an urgent need to develop the reliable and effective computational methods to predict the subcellular localization for the explosion of newly found proteins. Here, a novel method of pseudo amino acid (PseAA) composition, the so-called “amino acid composition distribution” (AACD), is introduced. First, a protein sequence is divided equally into multiple segments. Then, amino acid composition of each segment is calculated in series. After that, each protein sequence can be represented by a feature vector. Finally, the feature vectors of all sequences thus obtained are further input into the multi-class support vector machines to predict the subcellular localization. The results show that AACD is quite effective in representing protein sequences for the purpose of predicting protein subcellular localization.     

Accelerated evolution associated with genome reduction in a free-living prokaryote

Background  

Three complete genomes of Prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. Comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in G+C content. As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the first documented example of such a process in a free-living organism.     

There must be a prokaryote somewhere: microbiology''s search for itself.

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.     

FINS (forensically informative nucleotide sequencing): a procedure for identifying the animal origin of biological specimens.

The keys to identifying different species normally rely heavily on morphological characteristics. However, when an animal has been killed for food or sport, these markers are often destroyed or intentionally removed from the animal. This presents a problem for government agencies who are involved in determining the species origin of an animal or products derived from it in order to enforce conservation and/or health-related regulations. The problem is compounded if the meat of the animal has been processed in any way. We have developed a procedure called FINS (Forensically Informative Nucleotide Sequencing) that overcomes these problems. FINS has four components. First, methods have been developed that can isolate DNA from a wide range of biological samples including processed foods (e.g., canned, partially cooked, pickled, salted or smoked). Second, a specific segment of DNA is amplified using PCR. Third, the nucleotide sequence of the amplified segment of DNA is determined. Fourth, this nucleotide sequence is subjected to a phylogenetic analysis using a database, and the most closely related species is identified. FINS is a rapid, reliable and reproducible procedure that is based on established techniques. This procedure fills the need for an accurate method of determining the species identity of a specimen when this is not possible by conventional means.