Category Archives: Biotechnology

Cells, tissues and organs

Posted on by

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. Humans contain about 10 trillion cells.

Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals).

All cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.

There are two types of cells: eukaryotic and prokaryotic. There are about 210 distinct human cell types. The process by which cells specialise from progenitor cells into the enormous  variety of cell types that make up the body is termed differentiation. Unspecialised cells (called Stem Cells) produce cells with specialised structures. The final mature cells may be white blood cells of the immune system; neurons of the central nervous system with dendritic ‘trees’ connecting to thousands of other nerve cells, contractile cells of skeletal muscle or of smooth muscle.

A gamete is a cell that fuses with another cell (ovum and sperm) during fertilization (conception) in organisms that reproduce sexually. A zygote is the initial cell formed when two gamete cells are joined. In multicellular organisms, it is the earliest developmental stage of the embryo.

Early embryos consist of Stem Cells that can produce any type of cell. These cells are described as Totipotent. Stem Cells are also found in a few places in adults, but these can only differentiate into a limited number of types of cell and are called Multipotent.

Cells that work together to perform a particular function are organised into Tissues which are grouped into four main categories :

  •  Epithelial Tissue – Linings and layers
  •  Connective Tissue – Holding structures together
  •  Muscle Tissue – Actuation of movement
  •  Nervous Tissue – Communication via electrical signal

Tissues that work together to perform a larger function are organised into Organs (Leaves, heart, kidneys, …). Organs may be further organised into Organ Systems, that carry out an overall function (Circulatory System, Nervous System, Reproductive System, …).

How do cells become specialized even though DNA is identical in every cell ? The short answer is that not every gene that is encoded by the DNA is expressed in every cell. All cells express a certain set of genes, often called “housekeeping” genes. These genes encode proteins that are essential for every type of cell. Each specialized type of cell also expresses a tissue-specific set of genes, which are unique to that particular tissue or organ. The cells become specialized for a particular function during the development of the organism.

DNA sequencing and bioinformatics

Posted on by

DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA. The chain-termination method developed by Frederick Sanger and coworkers in 1977 at the University of Cambridge in England became the method of choice for DNA sequencing.

Once a DNA sequence has been obtained from an organism, it is stored in silico in digital format. In silico is used as an analogy to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology. It means performed on computer. Usually the DNA sequences are stored in sequence databases that can be searched using a variety of methods. One of these methods is BLAST (Basic Local Alignment Search Tool), a registered trademark of the National Library of Medicine.

The application of computer science and information technology to the field of biology and medicine is called Bioinformatics. A renowned Genome Bioinformatics website is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC).

A sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.

A list of links to some biological databases and software tools is shown below :

  •  BLAST : Basic Local Alignment Search Tool
  • ENCODE : Encyclopedia of DNA Elements Consortium – an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)
  • Neanderthaler Project : Neandertal Genome Analysis Consortium Tracks
  • Genome Browser : this program zooms and scrolls over chromosomes, showing the work of annotators worldwide
  • Gene Sorter : this program displays a sorted table of genes that are related to one another
  • Blat : this program quickly maps a sequence to the genome
  • Table Browser : this program retrieves data associated with a track in text format
  • Visi Gene : this program is a virtual microscope for viewing in situ images
  • Genome Graphs : this program is a tool for displaying genome-wide data sets
  • Mouse Genome Informatics : the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease

Genetics

Posted on by

Genetics is the science of genes, heredity, and variation in living organisms. It’s a discipline of biology and can be applied to the study of all living systems, from viruses and bacteria, through plants and domestic animals to humans. The modern science of genetics, which seeks to understand the process of inheritance, began with the work of Gregor Mendel in the mid-19th century.

The molecular basis for genes is deoxyribonucleic acid (DNA). Genes correspond to regions within DNA, a molecule composed of a chain of four different types of nucleotides :

  • adenine (A)
  • cytosine (C)
  • guanine (G)
  • and thymine (T)

Genetic information exists in the sequence of these nucleotides. DNA exists as a double-stranded molecule, coiled into the shape of a double-helix. Each nucleotide in DNA  pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs with G. Thus, in its two-stranded form, each strand contains all necessary information, redundant with its partner strand.

Genes are arranged linearly along long chains of DNA base-pair sequences. Eukaryotic organisms, which include plants and animals, have their DNA arranged in multiple linear chromosomes. These DNA strands are often extremely long; the largest human chromosome is about 247 million base pairs in length.

The full set of hereditary material in an organism (the combined DNA sequences of all chromosomes) is called the genome.

Google Body and Biodigital Human

Posted on by

Last update : August 9, 2012

Google Body

Google Bodybrowser

On December 15th, 2010, Google announced the launch in Google Labs of an interesting WebGL application called Body Browser, which lets you explore the human body just like you can explore the world in Google Earth.

Google Body (Google Human) is a detailed 3D model of the human body. You can peel back anatomical layers, zoom in, click to identify anatomy, or search for muscles, organs, bones and more. You can also share the exact scene you are viewing by copying and pasting the URL.

To view the body application, you need a Web browser that supports WebGL. I use Google Chrome.

The 3D body data was provided by the Zygote Media Group, Inc., a leading company in the development of Bio-Medical 3D content (since 1994).

Zygote offers stock 3D models, images and animation of the Human Anatomy Collections through the website 3DScience.com. These collections are the best and most comprehensive available. The artistic and illustrative value is unquestionable while remaining medically accurate.

3D anatomy collection of Zygote

Late 2011, the Google Body application was disabled. A commercial 3D platform BioDigital Human that simplifies the understanding of anatomy, disease and treatments has been launched in the meantime by Biodigital. Founded in 2002, BioDigital is the leading developer of state of the art biomedical visualization systems.