Conventional Biotechnology Research Articles

Identification of Multiple Subcellular Locations for Proteins in Budding Yeast

Knowing the subcellular locations of a protein helps to explore its functions in vivo since a protein can only play its roles properly if and only if it is located at certain subcellular compartments. Since it is both time-consuming and costly to determine protein subcellular localization purely by means of the conventional biotechnology experiments, computational methods play an important complementary role in this regard. Although a number of computational methods have been developed for predicting protein subcellular localization, it remains a challenge to deal with the multiplex proteins that may simultaneously exist at, or move between, two or more different locations. Here, a new predictor called Sort-PLoc was developed to tackle such a difficult and challenging problem. The key step was to select protein domains to code the protein samples by Incremental Feature Selection method. In each prediction, a series of subcellular locations were sorted descendingly according to their likelihood to be the site where the query protein may reside. Based on the selected domain set, the importance of Gene Ontology (GO) terms and domains in the contribution to the prediction was analyzed that may provide useful insights to the relevant areas. For the convenience of the broad experimental scientists, a user-friendly web-server for Sort-PLoc was established that is freely accessible to the public at http://yscl.biosino.org/. Keywords: Multi subcellular locations, incremental feature selection, sort-PLoc, Gene Ontology, Nearest Neighbor Algorithm, Amino acid, Neighbor Algorithm, pseudo amino acid composition, macromolecular complex

Current status and trends of Japan’s bioindustry

In Japan, the sales of modern biotechnology products and services in 2006 were worth 1,847 billion Japanese Yen (US$ 16.7 billion). The market has shown steady growth since 1989 (Figure 1). Conventional biotechnology products such as beer and sake are not covered in Figure 1. If we cover products of both conventional and modern biotechnology, the market size in 2005 was Yen 7,692 billion (approximately equivalent to US$ 70 billion). Major modern biotechnology products sold in Japan in 2006 are shown in Table 1.

Annual Meeting, Québec, Quebec, 2006, The Canadian Phytopathological Society / Réunion annuelle, Québec, Québec, 2006, La Société canadienne de phytopathologie

Annual Meeting, Québec, Quebec, 2006, The Canadian Phytopathological Society / Réunion annuelle, Québec, Québec, 2006, La Société canadienne de phytopathologie

Agricultural biotechnology R&D and innovations in Nigeria

This study examined the nature and extent of the agricultural biotechnology R&D and innovations in Nigeria. Data were collected from the Directors, Heads of Crop Units and Research Scientists in the agricultural research institutes using structured and unstructured questionnaires and interview schedules. The data collected were analysed using frequencies, means and percentages. The study revealed that there were 48 researchers engaged in the various aspects of agricultural biotechnology R&D, in the research institutes considered. About 32.9% were females, 67.1% were males with mean ages of 38 and 39.5 years, respectively. The majority, 53.2% of the researchers, possessed MSc qualifications with 46.6% specialising in conventional biotechnology. A total of 308 research outputs were recorded in all the research institutes. The most important motivation for embarking on these research projects was the need of the market (72.1%) and the existence of facilities (27.9%). The various bodies responsible for commercialisation of research results were the research institutes (83.3%), entrepreneurs (6.7%), the financial institutions, cooperative farmers and the National Seed Service (3.3%). Only two scientists possessed intellectual property rights and received royalties regularly. However, the majority did not patent their research results because of the lack of interest (45.4%), ignorance (32.0%) and the rigours of the procedure (32.3%).

Three Criteria for Establishing the Usefulness of Biotechnology for Reducing Micronutrient Malnutrition

The fundamental reason that plant breeding using either conventional breeding or biotechnology is so cost-effective is that the benefits of a one-time investment at a central research location can be multiplied over time across nations all over the world. Supplementation and fortification incur the same recurrent costs year after year in country after country. However, each intervention has its own comparative advantages, such that a combination of several interventions is required to substantially reduce micronutrient malnutrition. Improving the density of trace minerals in plants also reduces input requirements and raises crop yields. A simulation model for India and Bangladesh demonstrated that $42 million invested in conventional breeding in developing and planting iron- and zinc-dense varieties of rice and wheat on only 10% of the acreage used for these crops would return $4.9 billion in improved nutrition (including a total of 44 million prevented cases of anemia over 10 years) and higher agricultural productivity.

Parallel Biomolecular Computation: Models and Simulations

This paper is concerned with the development of techniques for massively parallel computation at the molecular scale, which we refer to as molecular parallelism. While this may at first appear to be purely science fiction, Adleman [Ad1] has already employed molecular parallelism in the solution of the Hamiltonian path problem, and successfully tested his techniques in a lab experiment on DNA for a small graph. Lipton [L] showed that finding the satisfying inputs to a Boolean expression of size n can be done in O(n) lab steps using DNA of length O(n log n) base pairs. This recent work by Adleman and Lipton in molecular parallelism considered only the solution of NP search problems, and provided no way of quickly executing lengthy computations by purely molecular means; the number of lab steps depended linearly on the size of the simulated expression. See [Re3] for further recent work on molecular parallelism and see [Re4] for an extensive survey of molecular parallelism. Our goal is to execute lengthy computations quickly by the use of molecular parallelism. We wish to execute these biomolecular computations using short DNA strands by more or less conventional biotechnology engineering techniques within a small number of lab steps. This paper describes techniques for achieving this goal, in the context of well defined abstract models of biomolecular computation. Although our results are of theoretical consequence only, due to the large amount of molecular parallelism (i.e., large test tube volume) required , we believe that our theoretical models and results may be a basis for more practical later work, just as was done in the area of parallel computing. We propose two abstract models of biomolecular computation. The first, the Parallel Associative Memory (PAM) model, is a very high-level model which includes a Parallel Associative Matching (PA-Match) operation, that appears to improve the power of molecular parallelism beyond the operations previously considered by Lipton [L]. We give some simulations of conventional sequential and parallel computational models by our PAM model. Each of the simulations use strings of length O(s) over an alphabet of size O(s) (which correspond to DNA of length O(s log s) base pairs). Using O(s log s) PAM operations that are not PA-Match (or O(s) operations assuming a ligation operation) and t PA-Match operations, we can: 1. simulate a nondeterministic Turing Machine computation with space bound s and time bound 2 O(s) , with t = O(s) , 2. simulate a CREW PRAM with time bound D, with M memory cells, and processor bound P, where here s = O( log (PM)) and t = O(D+s), 3. find the satisfying inputs to a Boolean circuit constructible in s space with n inputs, unbounded fan-out, and depth D, where here t = O(D+s). We also propose a Recombinant DNA (RDNA) model which is a low-level model that allows operations that are abstractions of very well understood recombinant DNA operations and provides a representation, which we call the complex , for the relevant structural properties of DNA. The PA-Match operation for lengthy strings of length s cannot be feasibly implemented by recombinant DNA techniques directly by a single step of complementary pairing in DNA; nevertheless we show this Matching operation can be simulated in the RDNA model with O(s) slowdown by multiple steps of complementary pairing of substrings of length 2 (corresponding to logarithmic length DNA subsequences). Each of the other operations of the PAM model can be executed in our RDNA model, without slowdown. We further show that, with a further O(s)/ log (1/ε) slowdown, the simulations can be done correctly with probability 1/2 even if certain recombinant DNA operations (e.g., Separation) can error with a probability ε. We also observe efficient simulations can be done by PRAMs and thus Turing Machines of our molecular models.

Physiology of woody plant under salt condition

Some advances in researches on the physiology of woody plants under salt condition are reviewed, The salt tolerant woody plants can be divided into two main groups: glycophytes and halophytes. They have different mechanisms for maintaining normal metabolism under salt condition. Halophytes usually are salt accumulators and glycophytes are salt excludors. However, the criteria for salt exclusion is not always clear. Although salt responses of different types of woody plants are not the same some major changes are identified in net photosynthesis rate and in growth. Four mechanisms arc proved to be related to the salt resistance of woody plants: (1) Regulation of ion intake. (2) avoidance of toxicity. (3) maintaining membrane integrity and (4) ion compartmentation. Currently, conventional plant breeding and biotechnology are both used to improve salt tolerance of woody plant.