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Posts tagged "genetics"


Chromosome 2 - What separates chimps from humans?

At the genetic level chimpanzees are almost indistinguishable from humans, so how did the formation of human chromosome 2 lead to our divergence from our primate relatives?

Geneticist Aoife McLysaght heads to Dublin Zoo to explain more…

via The Royal Institution.

(via kenobi-wan-obi)


A History of Slavery and Genocide Is Hidden in Modern DNA

There are plenty of ways to study history. You can conduct archaeological digs, examining the artifacts and structures buried under the ground to learn about past lifestyles. You can read historical texts, perusing the written record to better understand events that occurred long ago.

But an international group of medical researchers led by Andrés Moreno-Estrada and Carlos Bustamante of Stanford and Eden Martin of the University of Miami are looking instead at a decidedly unconventional historical record: human DNA.

Hidden in the microscopic genetic material of people from the Caribbean, they’ve found, is an indelible record of human history, stretching back centuries to the arrival of Europeans, the decimation of Native American populations and the trans-Atlantic slave trade. By analyzing these genetic samples and comparing them to the genes of people around the world, they’re able to pinpoint not only the geographic origin of various populations but even the timing of when great migrations occurred.

As part of a new project, documented in a study published yesterday in PLOS Genetics, the researchers sampled and studied the DNA of 251 people living in Florida who had ancestry from one of six countries and islands that border the Caribbean—Cuba, Haiti, Dominican Republic, Puerto Rico, Honduras and Colombia—along with 79 residents of Venezuela who belong to one of three Native American groups (the YukpaWarao and Bari tribes). Each study participant was part of a triad that included two parents and one of their children who were also surveyed, so the researchers could track which particular genetic markers were passed on from which parents.

The researchers sequenced the DNA of these participants, analyzing their entire genomes in search of particular genetic sequences—called single-nucleotide polymorphisms (SNPs)—that often differ between unrelated individuals and are passed down from parent to child. To provide context for the SNPs they found in people from these groups and areas, they compared them to existing databases of sequenced DNA from thousands of people globally, such as data from the HapMap Project.

[read more]

(via kenobi-wan-obi)


Fast-Mutating DNA Sequences Shape Early Development; Guided Evolution of Uniquely Human Traits

What does it mean to be human? According to scientists the key lies, ultimately, in the billions of lines of genetic code that comprise the human genome. The problem, however, has been deciphering that code. But now, researchers at the Gladstone Institutes have discovered how the activation of specific stretches of DNA control the development of uniquely human characteristics — and tell an intriguing story about the evolution of our species.

In the latest issue of Philosophical Transactions of the Royal Society B, researchers in the laboratory of Gladstone Investigator Katherine Pollard, PhD, use the latest sequencing and bioinformatics tools to find genomic regions that guide the development of human-specific characteristics. These results offer new clues as to how the activation of similar stretches of DNA — shared between two species — can sometimes result in vastly different outcomes.

"Advances in DNA sequencing and supercomputing have given us the power to understand evolution at a level of detail that just a few years ago would have been impossible," said Dr. Pollard, who is also a professor of epidemiology and biostatistics at the University of California, San Francisco’s (UCSF’s) Institute for Human Genetics. "In this study, we found stretches of DNA that evolved much more quickly than others. We believe that these fast-evolving stretches were crucial to our human ancestors becoming distinct from our closest primate relatives."

These stretches are called human accelerated regions, or HARs, so-called because they mutate at a relatively fast rate. In addition, the majority of HARs don’t appear to encode specific genes. The research team hypothesized that HARs instead acted as “enhancers,” controlling when and for how long certain genes were switched on during embryonic development. Through experiments in embryonic animal models, combined with powerful computational genomics analyses, the research team identified more than 2,600 HARs. Then, they created a program called EnhancerFinder to whittle down that list to just the HARs were likely to be enhancers.



This is the most accurate model yet of what DNA looks like

This is a stunning 3D map that shows how six feet of of DNA can be crammed inside a single chromosome — a space that’s only a hundredth of a millimeter across. Not surprisingly, it looks like something that would go well with meatballs.

Chromosomes, those packages of genetic material found in our cells, were discovered way back in the late 1800s, but scientists have struggled to understand the exact way DNA molecules fold into them across three-dimensions. But a new study conducted by researchers at MIT and the University of Massachusetts Medical school has resulted in the world’s first comprehensive model of the 3D organization of condensed human chromosomes.

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Scientists Discover Parts of Our Bodies Age at Different Rates

Some people age faster than others, but the discovery of a DNA body clock by UCLA researchers now shows that different parts of our bodies age faster than others. The discovery offers important insights into the aging process — and what we might be able to do about it.

This isn’t the first time that biologists have developed a mechanism for assessing age. Earlier “biological clocks” have been derived from data drawn from saliva and hormones. More crucially, there are our telomeres to consider — those fraying tips of our chromosomes that have been linked to cellular expiry dates, and by virtue, our individual rates of aging.

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(via kenobi-wan-obi)


'Mix and match': Mixing nanoparticles to make multifunctional materials

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have developed a general approach for combining different types of nanoparticles to produce large-scale composite materials. The technique, described in a paper published online by Nature Nanotechnology on October 20, 2013, opens many opportunities for mixing and matching particles with different magnetic, optical, or chemical properties to form new, multifunctional materials or materials with enhanced performance for a wide range of potential applications.

The approach takes advantage of the attractive pairing of complementary strands of synthetic DNA-based on the molecule that carries the genetic code in its sequence of matched bases known by the letters A, T, G, and C. After coating the  with a chemically standardized “construction platform” and adding extender molecules to which DNA can easily bind, the scientists attach complementary lab-designed DNA strands to the two different kinds of nanoparticles they want to link up. The natural pairing of the matching strands then “self-assembles” the particles into a three-dimensional array consisting of billions of particles. Varying the length of the DNA linkers, their surface density on particles, and other factors gives scientists the ability to control and optimize different types of newly formed  and their properties.

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New study changes view about the genetics of leukemia risk
A gene that helps keep blood free of cancer is controlled by tiny pieces of RNA, a finding that may lead to better ways to diagnose blood cancers and even lead to new forms of treatment, Yale School of Medicine researchers report online Oct. 10 in the journal Cell Reports.
In the past few years researchers have identified the crucial role of the gene TET2 in keeping blood cells healthy. Mutations of the gene have been found in about 20% of leukemias and indicate a poor prognosis for patients. However, the gene was thought to be irrelevant in 80% of leukemia cases.
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New study changes view about the genetics of leukemia risk

A gene that helps keep blood free of cancer is controlled by tiny pieces of RNA, a finding that may lead to better ways to diagnose blood cancers and even lead to new forms of treatment, Yale School of Medicine researchers report online Oct. 10 in the journal Cell Reports.

In the past few years researchers have identified the crucial role of the gene TET2 in keeping  healthy. Mutations of the gene have been found in about 20% of leukemias and indicate a poor prognosis for patients. However, the gene was thought to be irrelevant in 80% of leukemia cases.

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$6.4 Million Grant Funds Glaucoma Study in African-Americans

A study led by Robert N. Weinreb, chairman and Distinguished Professor of Ophthalmology at the University of California, San Diego School of Medicine, has received a $6.4 million, 5-year grant from the National Eye Institute, part of the National Institutes of Health, to elucidate the genetics of glaucoma in persons of African descent. 

Glaucoma is the leading cause of blindness in African-Americans. It is four to five times more likely to occur in persons of African descent, and up to 15 times more likely to cause meaningful visual impairment in this group compared to those of European descent.

The overall goal of the study, “ADAGES III: contribution of genotype to glaucoma phenotype in African-Americans,” is to identify glaucoma genes in this high-risk, minority population, particularly persons who have rapidly worsening vision. Weinreb has teamed with Jerry Rotter, MD, Distinguished Professor of Pediatrics, Medicine and Human Genetics at Harbor-UCLA Medical Center, a renowned genetics expert, to identify relevant genes, develop predictive models for glaucoma diagnosis and progression and discover new drug targets for therapies to reduce the visual impact of glaucoma blindness.

Glaucoma results in vision loss due to damage to the optic nerve, which is irreversible if undetected or untreated.  The most common form of glaucoma is called primary open angle glaucoma (POAG). The number of persons with diagnosed POAG in the United States is expected to be more 3.3 million by 2020, with millions more undiagnosed.  While glaucoma affects all races, persons of African descent are disproportionately affected.

“The lack of understanding about the cause of this disease impedes our ability to identify and treat it early in its development,” said Weinreb, who is also director of the Shiley Eye Center, part of the UC San Diego Health System. “Evidence of genetic contribution in the pathogenesis of POAG is well established. Since POAG tends to run in families, it is critical to identify the genetic basis of the disease in order to develop effective therapies for early intervention.”

“A better understanding of the relationship among the stage of disease, the rate of change, ancestry, and other important risk factors being tracked in the ongoing African Descent and Glaucoma Study (ADAGES) will allow us to evaluate the relationship between genetics, visual loss and structural damage in this high-risk group,” added Linda Zangwil, PhD, a professor of ophthalmology at UC San Diego and study co-investigator.

The study will obtain detailed phenotypes – a composite of all observed characteristics or traits of an individual – of more than 2,000 subjects, establish a repository and implement a data-coordinating center at UC San Diego, as well conduct comprehensive genetic studies.

The recruitment, enrollment and phenotyping of both established and new subjects will occur at four clinical centers: UC San Diego School of Medicine; New York Eye and Ear Infirmary; University of Alabama at Birmingham; and a private practice in the Atlanta, Ga. area.

This is how Francis Crick dealt with unwanted solicitations following the discovery of DNA.

When James Watson and Francis Crick unveiled the double-helical structure of DNA, the pair became international celebrities. But with celebrity, can come a lot of unwanted personal attention.

One of the ways Crick dealt with the barrage of letters, personal requests and solicitations that he received throughout the 1960s was the pre-printed, catch-all reply card featured up top.

According to The Francis Crick Archive at the Wellcome Library, the seventeen reply options you see listed here “are a faithful reflection of the requests [Crick] regularly received,” though there was also space to add more if he felt like it. Apparently, unsolicited solutions to “the coding problem” (the question of how just four nucleotides could code for a polypeptide containing up to twenty different amino acids) were pretty common… just not common enough to earn them a spot on the reply card. [For the Record: The Francis Crick Archive at the Wellcome Library via Futility Closet]


Model Organism

by Przemyslaw Gaj  [~Art-de-Viant]

The fruit fly  Drosophila melanogaster – made the jump from nature to laboratory animal in 1901 at Harvard University.

In 1906 Drosophila was adopted by the young evolutionary biologist who would become well known for his work with the flies, Thomas Hunt Morganone of the most influential men in experimental biology during the early twentieth century.  [Wikipedia - History of Model Organisms]

Morgan, who had been at Columbia since 1904, moved to California in 1928 to develop the new Division of Biology at the California Institute of Technology.  In 1933 he received the Nobel Prize in Physiology or Medicine for his work on the role of chromosomes in heredity.  [Wikipedia]


“Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid” was an article published by James D. Watson and Francis Crick in the scientific journal Nature in its 171st volume on pages 737–738 (dated April 25, 1953). It was the first publication which described Rosalind Franklin’s discovery of the double helix structure of DNA. This discovery had a major impact onbiology, particularly in the field of genetics.

This article is often termed a “pearl” of science because it is brief and contains the answer to a fundamental mystery about living organisms. This mystery was the question of how it was possible thatgenetic instructions were held inside organisms and how they were passed from generation to generation. The article presents a simple and elegant solution, which surprised many biologists at the time who believed that DNA transmission was going to be more difficult to detail and understand.

Image Credit: DNA Replication Animation

Happy Birthday DNA!!!!

Squid’s Daily Rhythms Are Controlled by Glowing Symbiotic Bacteria

At nightfall, the Hawaiian bobtail squid digs itself out of the sand and rises into the ocean water like a spaceship taking off. It switches on its cloaking device: glowing bacteria inside its body light up, disguising the squid’s silhouette against the moonlight for any predators swimming below. As sleek a vehicle as it appears, though, the bobtail may not totally outrank its microscopic crewmembers. The bacteria seem to power a clock inside the squid’s body that can’t function without them.

Hiding during the day and hunting at night in shallow Pacific waters, Euprymna scolopes clearly has a working circadian clock. Researchers had noticed, though, that the squid’s light organ—the specialized pocket inside its body that houses its bacterial helpers—seemed to have a rhythm of its own. The Vibrio fischeri bacteria give off fluctuating amounts of light throughout the day, for one thing. And the bacteria have their own daily rhythm of gene expression (when various genes are turned on or off), explains Margaret McFall-Ngai, a microbiologist at the University of Wisconsin, Madison.

McFall-Ngai and her coauthors looked for genes linked to circadian rhythms within the squid. They found two types of “cry" genes, which are known to control internal clocks throughout the animal and plant kingdoms. One gene had a daily cycle of activity in the squid’s head—which is what you’d expect, since animals’ main circadian clocks are in our brains. Other clocks can be elsewhere in the body, though, and this is what researchers found with the second cry gene. It was cycling only within the light organ.

Baby squid, which hadn’t yet collected bacterial friends in their light organs, didn’t show the same cycling. So it seemed that the bacteria themselves were driving the daily rhythms in the light organ. When the researchers let squid fill their light organs with defective, non-glowing bacteria, the cry gene still didn’t cycle properly. This suggested that the glow of the bacteria was the crucial ingredient.

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In ants and bees, there are no sex chromosomes. Instead, sex is determined by whether or not an egg was fertilized. If the egg isn’t fertilized, the offspring is male. If the egg is fertilized, it’s female. So male ants have no fathers, and they have half as many chromosomes as females. Poor little things.


How Mendel’s pea plants helped us understand genetics - Hortensia Jiménez Díaz

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Each father and mother pass down traits to their children, who inherit combinations of their dominant or recessive alleles. But how do we know so much about genetics today? Hortensia Jiménez Díaz explains how studying pea plants revealed why you may have blue eyes.

Lesson by Hortensia Jiménez Díaz, animation by Cinematic Sweden.

by TED Education.


The Immortal Life of Henrietta Lacks, the Sequel

 Rebecca Skloot, author of the extremely popular non-fiction novel “The Immortal Life of Henrietta Lacks,” once again raises important moral and ethical dilemmas behind the ubiquitous HeLa cells, this time surrounding the recent publication of the HeLa cell genome.

LAST week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours.

Now, HeLa cells cells have been back in the news, when researchers published the HeLa cell genome, seemingly without consent from the Lacks family.  This raises new questions surrounding genetic information and privacy.  How much can we learn from a raw human genome?  What are the major ethical issues behind using genetic material in research, and what does it mean to give consent?

I highly recommend Rebecca Skloot’s book, as well as this new article.  Issues behind the dissemination of genetic information, and what sort of laws/oversight need to be used to protect individual privacy are quickly becoming increasingly relevant to the research community and the general public.