Identification of metal (iron) transporters in plants and human via database search and analysis

Identification of metal (iron) transporters in plants and human via database search and analysis

 

Objectives

 

• Learn to identify genes, search gene information and gene analysis using different databases.
• Identify metal transporters in plants and human via those approaches.

 

Introduction

Today, most researchers would find it difficult to imagine a time when sequence databases and search tools were not a ubiquitous and accessible part of the research landscape.  Biological data, and DNA sequence data in particular, are accumulating at a phenomenal rate.  Today, collectively, the entire cast of many genome research center can sequence close to 2000 bases every second–that’s 7.2 million per hour, 172 million per day, every day, 365 days a year–counting all the sequencing machines in all the labs responsible for the human genome effort. This capacity could translate into a first pass at sequencing about two big mammalian genomes a year, if all players turned their machines on the same species. Several of the major genome centers have begun to move on to sequence more organisms.  In order to exploit the wealth of DNA sequences and other biological data, a new science has developed that fuses biology with mathematics and computer science- “bioinformatics”.

To find the genes within the genomic sequence is a massive task in itself.  Once apparent, otherwise uncharacterized coding regions must be assigned a function.  Therefore, the interactions between genes and gene products must be understood at all levels, not merely in the context of the pathway within and between cells but also in terms of the evolution of gene families within and between species.  Those questions can all be addressed using bioinformatics.

Bioinformatics is the convergence of two technology revolutions: the explosive growth in biotechnology, paralleled by the explosive growth in information technology.  The amount of biological information accessible via the World Wide Web (WWW) is truly astonishing, and the volume of data is increasing at a fast pace.  It is important for the bench scientist to have easy and efficient ways of wading through the data and finding what is important to his or her research.  Although one can browse the data, a far more efficient access method is to perform a search.

Depending on the type of data at hand, there are two basic ways of searching:

1. Using descriptive words to search text databases
2. or using a nucleotide or protein sequence to search a sequence database.

The cells of organisms, such as plants and animals, are separated from their variable external environment by a plasma membrane.  It must accommodate and promote continual inward and outward traffic of molecules and ions, as the cells takes up nutrients and export wastes.  The same is true for the membranes of organelles that separate the various compartments within each cell.  Therefore, cell membranes contain specialized transport proteins – channels, carriers, pumps and transporters- to carry out transport functions. Since the transport processes are involved in almost all essential biological processes in the life cycle of all organisms, about 5-15 % genes of various organisms are found encoding transport proteins.

 

we will look through number of major plant and human gene databases and learn to search metal transporter genes and to analyze their potential structure and functions of these genes.

 

 

Procedures

1. Text-based database searching

There are three commonly used tools – Entrez, the Sequence Retrieval System (SRS) and DBGET – that allow text searching of multiple molecular biology databases and provide links to relevant information for entries that match the search criteria.

These retrieval systems are indispensable to the scientist in search of information.  In using any of these systems, queries can be as simple as entering the accession number of a sequences or as complex as searching multiple database fields for specific terms.  The advantage of Entrez, the Sequence Retrieval System (SRS) and DBGET is that they are not only return matches to a query, but also provide handy pointers to additional important information in related database.

 

NCBI

The literature database, PubMed, provides excellent and easy access to MEDLINE articles.  Through PubMed, anyone can access Medline’s 10,000,000 bio-medical journal citations to research questions.

 

Entrez, a molecular biology database and retrieval system, was developed by the National Center for Biotechnology Information (NCBI).  It is entry point for exploring distinct but integrated databases.  The entrez system provides access to nucleotide and protein sequence databases, a molecular modeling 3-D structure database (MMDB), a genomes and maps database and the literature.

 

The taxonomy database contains more than 23000 different species and allows retrieval of DNA and protein sequences for any taxonomic group.

 

1. Open the National Center for Biotechnology Information (NCBI) Entrez home:

http://www.ncbi.nlm.nih.gov/Entrez/

1. Search the information (review and research papers) about different metal transporters using PubMed.
2. Search the genes of different metal transports using Nucleotide sequence database (Genbank).

1. Search the genes of different metal transports using Protein sequence database.

1. Sequence based database search

 

2. 2. Efficient DNA sequencing methods make it much easier to obtain information on the amino acid sequence of proteins than on their structures and functions. The sequences of homologous proteins can diverge greatly over time, even though the structure or function of the proteins changes little.  Thus, much can be inferred about an uncharacterized protein when significant sequence similarity is detected with a well-studied protein.  Search homologue genes and/or aligning novel sequences with previously characterized genes or proteins can provide important insights into their common attributes and evolutionary origins.

 

Planning a good experiment requires an understanding of the methods being applied.  Fundamentally, database searches are a simple operation: a query sequence is logically aligned with each of the sequences (called targets) in a database.  Blast and Fasta are very commonly used for this propose.

 

1. log in http://www.ncbi.nlm.nih.gov/Tools/index.html
2. Use a transporter DNA sequence to search databases using Blast.

 

Results and Discussion:

Write a lab report (see How to write scientific report ).

In the Results and Discussion section of your lab report, you need to present the information of three plant and three human transporter genes including Gene ID, Gene Family and one reference list for each transporters. You need to discuss the keys for a successful database search

 

 

 

 

How to write scientific report:

The steps of scientific approach

In general, if you undertake a scientific project, you need to apply the scientific methods and go through the following seven steps:

1. General question: You should start with learning the background of the field that you are going to work on. Via read books and review papers you will obtain the knowledge about :

(a) What is going on in this field?

(b) What are the major questions and problems?

(c) How other researchers study those questions and problems?

(d) What do you want to do and how do you perform the research?

2. Hypothesis: Based on the question(s) you want to solve, you need to read more review and research papers to know the question better, then you should develop a hypothesis and make predictions based on your hypothesis.
3. Experimental design: Read more research papers and ask experts to find the proper experimental methods and techniques, and design you experiments to test the validity of your hypothesis. Three Factors are essential for good experimental design:
   • You must have proper control into each experiment. A control group has the same treatment and experimental condition as the experimental group except that the factor being tested, the specific tested factor is only applied to the experimental group.

(b) Experiments must be repeated enough times or have enough replications to allow comparisons between experimental and control groups. Through such repetition, the data can be compared statistically and the results will be very accurate.

©   You must avoid bias in your experimental design, you must prevent personal opinion about a hypothesis from influencing how test are made. You must objective!

4. Collecting data: While you perform the tests following your experimental design, you must take detailed notes in a record book that becomes a scientific diary of the research in process. It must be clearly recorded so that anyone could read and check your experimental processes and results.
5. Analyzing data: You need to objectively calculate, examine and compare your data, make proper Figures, tables or photo plates.
6. Interpretation: You should ask critical questions, and to determine the cause and effect of experimental observations
7. Communication: A hypothesis must be tested by independent researchers, thus science is a powerful group activities. Scientists must communicate their work or findings via presenting seminars, presentations in meetings or publishing in a scientific journal.  Other researchers will have an opportunity to read and learn the work, so they can make independent testing and for further approaches.