Wednesday, 24 July 2013

Advanced Molecular Biology and Genetics

In advanced molecular biology and genetics, the genome is the whole of an organism’s hereditary information. It is encoded either in DNA, or, for several types of viruses, in RNA. The genome takes in both the genes and the non-coding sequences of the DNA/RNA. 

Genome Repair describes how the genome of the bacterium Deinococcus radiodurans gets reassembled after being crushed by-dose radiation. 

Repair of DNA damage is vital for protection against cancer and other age related diseases. Such diseases are supposed to be started by mutations and rearrangements of the DNA sequence. DNA damage produced by ionising radiation, simple alkylating agents or endogenously hydrolytic and oxidative processes is repaired by the base excision repair (BER) pathway.

Monday, 4 March 2013

Genomics

Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes. The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.

Friday, 13 July 2012

Doggie DNA

With all this talk of Pit Bulls and breed confusion, I have seized upon the opportunity to commission a breed analysis for Genomic RepairDog since he looks like every breed of small dog that we put him up next to. I swabbed his cheek and sent off the cotton swab in the mail and am awaiting his results. Plus I love the fact they are using breed specific SNPs to give you the animal's breed makeup.

Tuesday, 6 March 2012

Genetics

Genetics (from Ancient Greek γενετικός genetikos, "genitive" and that from γένεσις genesis, "origin"), a discipline of biology, is the science of genes, heredity, and variation in living organisms.
Genetics deals with the molecular structure and function of genes, gene behavior in context of a cell or organism (e.g. dominance and epigenetics), patterns of inheritance from parent to offspring, and gene distribution, variation and change in populations. Given that genes are universal to living organisms, genetics can be applied to the study of all living systems, from viruses and bacteria, through plants and domestic animals, to humans (as in medical genetics).

The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. However, the modern science of genetics, which seeks to understand the process of inheritance, only began with the work of Gregor Mendel in the mid-19th century. Although he did not know the physical basis for heredity, Mendel observed that organisms inherit traits via discrete units of inheritance, which are now called genes.

Genes correspond to regions within DNA, a molecule composed of a chain of four different types of nucleotides—the sequence of these nucleotides is the genetic information organisms inherit. DNA naturally occurs in a double stranded form, with nucleotides on each strand complementary to each other. Each strand can act as a template for creating a new partner strand. This is the physical method for making copies of genes that can be inherited.
The sequence of nucleotides in a gene is translated by cells to produce a chain of amino acids, creating proteins—the order of amino acids in a protein corresponds to the order of nucleotides in the gene. This relationship between nucleotide sequence and amino acid sequence is known as the genetic code. The amino acids in a protein determine how it folds into a three-dimensional shape; this structure is, in turn, responsible for the protein's function. Proteins carry out almost all the functions needed for cells to live. A change to the DNA in a gene can change a protein's amino acids, changing its shape and function: this can have a dramatic effect in the cell and on the organism as a whole.

Although genetics plays a large role in the appearance and behavior of organisms, it is the combination of genetics with what an organism experiences that determines the ultimate outcome. For example, while genes play a role in determining an organism's size, the nutrition and health it experiences after inception also have a large effect.

Friday, 27 January 2012

NASA's Kepler Announces 11 Planetary Systems Hosting 26 Planets

NASA's Kepler mission has discovered 11 new planetary systems hosting 26 confirmed planets. These discoveries nearly double the number of verified Kepler planets and triple the number of stars known to have more than one planet that transits, or passes in front of, its host star. Such systems will help astronomers better understand how planets form.

The planets orbit close to their host stars and range in size from 1.5 times the radius of Earth to larger than Jupiter. Fifteen of them are between Earth and Neptune in size, and further observations will be required to determine which are rocky like Earth and which have thick gaseous atmospheres like Neptune. The planets orbit their host star once every six to 143 days. All are closer to their host star than Venus is to our sun.

"Prior to the Kepler mission, we knew of perhaps 500 exoplanets across the whole sky," said Doug Hudgins, Kepler program scientist at NASA Headquarters in Washington. "Now, in just two years staring at a patch of sky not much bigger than your fist, Kepler has discovered more than 60 planets and more than 2,300 planet candidates. This tells us that our galaxy is positively loaded with planets of all sizes and orbits."

Kepler identifies planet candidates by repeatedly measuring the change in brightness of more than 150,000 stars to detect when a planet passes in front of the star. That passage casts a small shadow toward Earth and the Kepler spacecraft.

“Confirming that the small decrease in the star's brightness is due to a planet requires additional observations and time-consuming analysis," said Eric Ford, associate professor of astronomy at the University of Florida and lead author of the paper confirming Kepler-23 and Kepler-24. “We verified these planets using new techniques that dramatically accelerated their discovery.”

Each of the new confirmed planetary systems contains two to five closely spaced transiting planets. In tightly packed planetary systems, the gravitational pull of the planets among themselves causes one planet to accelerate and another planet to decelerate along its orbit. The acceleration causes the orbital period of each planet to change. Kepler detects this effect by measuring the changes, or so-called Transit Timing Variations (TTVs).

The artist's rendering depicts the multiple planet systems discovered by NASA's Kepler missionClick image for multiple resolutions and full caption.
Kepler's Planetary Systems: The artist's rendering depicts the multiple planet systems discovered by NASA's Kepler mission. 
Image credit: NASA Ames/Jason Steffen, Fermilab Center for Particle Astrophysics

The image shows an overhead view of orbital positions of the planets in systems with multiple transiting planets discovered by NASA's Kepler mission.
Kepler's Planetary Systems' Orbits: The image shows an overhead view of orbital positions of the planets in systems with multiple transiting planets discovered by NASA's Kepler mission. 
Image credit: NASA Ames/Dan Fabrycky, University of California, Santa Cruz


Planetary systems with TTVs can be verified without requiring extensive ground-based observations, accelerating confirmation of planet candidates. The TTV detection technique also increases Kepler's ability to confirm planetary systems around fainter and more distant stars.

“By precisely timing when each planet transits its star, Kepler detected the gravitational tug of the planets on each other, clinching the case for ten of the newly announced planetary systems,” said Dan Fabrycky, Hubble Fellow at the University of California, Santa Cruz and lead author for a paper confirming Kepler-29, 30, 31 and 32."

Five of the systems (Kepler-25, Kepler-27, Kepler-30, Kepler-31 and Kepler-33) contain a pair of planets where the inner planet orbits the star twice during each orbit of the outer planet. Four of the systems (Kepler-23, Kepler-24, Kepler-28 and Kepler-32) contain a pairing where the outer planet circles the star twice for every three times the inner planet orbits its star.

“These configurations help to amplify the gravitational interactions between the planets, similar to how my sons kick their legs on a swing at the right time to go higher,” said Jason Steffen, the Brinson postdoctoral fellow at Fermilab Center for Particle Astrophysics in Batavia, Ill., and lead author of a paper confirming Kepler-25, 26, 27 and 28.

The system with the most planets among these discoveries is Kepler-33, a star that is older and more massive than our sun. Kepler-33 hosts five planets, ranging in size from 1.5 to 5 times that of Earth and all located closer to their star than any planet is to the sun.

The properties of a star provide clues for planet detection. The decrease in the star's brightness and duration of a planet transit combined with the properties of its host star present a recognizable signature. When astronomers detect planet candidates that exhibit similar signatures around the same star the likelihood of any of these planet candidates being a false positive is very low.

“The approach that was used to verify the Kepler-33 planets shows that the overall reliability of Kepler's candidate multiple transiting systems is quite high," said Jack Lissauer, planetary scientist at NASA Ames Research Center at Moffett Field, Calif., and lead author of the paper confirming Kepler-33. “This is a validation by multiplicity.”

These discoveries are published in the Astrophysical Journal and the Monthly Notices of the Royal Astronomical Society and can be viewed at:
J Lissauer et al - Almost All of Kepler's Multiple Planet Candidates are Planets, and Kepler-33 5-planet system
E Ford et al - Transit Timing Observations from Kepler: II. Confirmation of Two Multiplanet Systems via a Non-parametric Correlation Analysis. Confirms KOI-168=Kepler-23 and KOI 1102=Kepler-24
J Steffen et al - Transit Timing Observations from Kepler: III. Confirmation of 4 Multiple Planet Systems by a Fourier-Domain Study of Anti-correlated Transit Timing Variations
D Fabrycky et al - Transit Timing Observations From Kepler: IV. Confirmation Of 4 Multiple Planet Systems By Simple Physical Models
Ames Research Center in Moffett Field, Calif., manages Kepler's ground system development, mission operations and science data analysis. NASA’s Jet Propulsion Laboratory, Pasadena, Calif., managed the Kepler mission's development.

Ball Aerospace and Technologies Corp. in Boulder, Colo., developed the Kepler flight system and supports mission operations with the Laboratory for Atmospheric and Space Physics at the University of Colorado in Boulder.

The Space Telescope Science Institute in Baltimore archives, hosts and distributes Kepler science data. Kepler is NASA's 10th Discovery Mission and is funded by NASA's Science Mission Directorate at the agency's headquarters in Washington.

For more information about the Kepler mission, visit: http://www.nasa.gov/kepler




Kepler's Planetary Systems in Motion: The animation shows an overhead view of the orbital position of the planets in systems with multiple transiting planets discovered by NASA's Kepler mission. All the colored planets have been verified. More vivid colors indicate planets that have been confirmed by their gravitational interactions with each other or the star. Several of these systems contain additional planet candidates (shown in grey) that have not yet been verified. 
Image credit: NASA Ames/Dan Fabrycky, University of California, Santa Cruz




Transit Timing Variations: The animation shows the difference between planet transit timing of single and multiple planet system. In tightly packed planetary systems, the gravitational pull of the planets among themselves causes one planet to accelerate and another planet to decelerate along its orbit. The acceleration causes the orbital period of each planet to change. Kepler detects this effect by measuring the change known as Transit Timing Variations (TTVs).
Image credit: NASA Ames/Kepler mission

Friday, 11 November 2011

Genomics

Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.

For the United States Environmental Protection Agency, "the term "genomics" encompasses a broader scope of scientific inquiry associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels.