Monday, May 26, 2008

BAC: Super-Sized Inserts

Bacterial Artificial Chromosomes (BAC) have been developed to hold much larger pieces of DNA than a plasmid can. BAC vectors were originally created from part of an unusual plasmid present in some bacteria called the F’ plasmid.

The F’ plasmid allows bacteria to have “sex” (well, sort of: F’ helps bacteria give its genome to another bacteria but this only happens rarely when bacteria are under a lot of stress). F’ had been studied extensively and it was found that it could hold up to a million basepairs of DNA from another bacteria. Also, F’ has origins of replication and bacteria have a way to control how F’ is copied.

Friday, May 16, 2008

Mitochondrial Eve

'Mitochondrial Eve' Research: Humanity Was Genetically Divided For 100,000 Years
A Picture of the Ancient Past
Finding:
Based on Anthroopological genetic research, researchers believe that about 60,000 years ago, modern humans started the journey to populate the world. However, relatively little is known about the demographic history of our species over the previous 140,000 years in Africa.

The current study focuses on Africa and refines the understanding of early modern Homo sapiens history. These early human populations were small and isolated from each other for many tens of thousands of years.

The research was based on a survey of African mitochondrial DNA (mtDNA) and is the most extensive survey of its kind. It included over 600 complete mtDNA genomes from indigenous populations across the continent.

How Old Was “Mitochondrial Eve”?

MtDNA, inherited down the maternal line, was used in 1987 to discover the age of the “Mitochondrial Eve,” the most recent common female ancestor of everyone alive today. This work has since been extended to show unequivocally that “Mitochondrial Eve” was an African woman who lived sometime during the past 200,000 years.

Recent data suggests that Eastern Africa went through a series of massive droughts between 90,000 and 135,000 years ago. It is possible that this climate shift contributed to the population splits. What is surprising is the length of time the populations were separate — for as much as half of our entire history as a species.

The study shows that tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA.

Monday, April 28, 2008

Last Common Ancestor Of Neanderthals And Humans

Finding: Fossil Found In Europe, 1.2 Million Years Old

That's 500,000 years older than the previous oldest known humanlike fossils from the area. The new find bolsters the view that Homo reached Europe not long after leaving Africa almost 2 million years ago.

It seems probable that the first European population came from the region of the Near East, the true crossroads between Africa and Eurasia, and that it was related to the first demographic expansion out of Africa.

The researchers tentatively classified the new fossil as an earlier example Homo antecessor (Pioneer Man), the species represented by the previous oldest fossils and thought to be the last common ancestor of Neanderthals and modern humans.

Sunday, April 6, 2008

Early Human Populations Evolved Separately For 100,000 Years

Finding:
A team of Genographic researchers and their collaborators have published the most extensive survey to date of African mitochondrial DNA (mtDNA). Over 600 complete mtDNA genomes from indigenous populations across the continent were analyzed by the scientists. Analyses of the extensive data provide surprising insights into the early demographic history of human populations before they moved out of Africa, illustrating that these early human populations were small and isolated from each other for many tens of thousands of years.

MtDNA, inherited down the maternal line, was used to discover the age of the famous 'mitochondrial Eve' in 1987. This work has since been extended to show unequivocally that the most recent common female ancestor of everyone alive today was an African woman who lived in the past 200,000 years. Paleontology provides corroborating evidence that our species originated on this continent approximately 200,000 years ago.

The migrations after 60,000 years ago that led modern humans on their epic journeys to populate the world have been the primary focus of anthropological genetic research, but relatively little is known about the demographic history of our species over the previous 140,000 years in Africa. The current study returns the focus to Africa and in doing so refines our understanding of early modern Homo sapiens history.

There is strong evidence of ancient population splits beginning as early as 150,000 years ago, probably giving rise to separate populations localized to Eastern and Southern Africa. It was only around 40,000 years ago that they became part of a single pan-African population, reunited after as much as 100,000 years apart.

Recent paleoclimatological data suggests that Eastern Africa went through a series of massive droughts between 135,000-90,000 years ago. It is possible that this climatological shift contributed to the population splits. What is surprising is the length of time the populations were separate - as much as half of our entire history as a species.

Friday, March 14, 2008

Two Explosive Evolutionary Events Shaped Early History Of Multicellular Life

The Avalon Explosion suggests that more than one explosive evolutionary event may have taken place during the early evolution of animals. Using rigorous analytical methods, scientists have identified another explosive evolutionary event that occurred about 33 million years earlier among macroscopic life forms unrelated to the Cambrian animals.



The Cambrian explosion event refers to the sudden appearance of most animal groups in a geologically short time period between 542 and 520 million years ago, in the early Cambrian Period. Although there were not as many animal species as in modern oceans, most (if not all) living animal groups were represented in the Cambrian oceans.



Methodology


To test whether other major branches of life also evolved in an abrupt and explosive manner, Virginia Tech scientists analyzed the Ediacara fossils: the oldest complex, multicellular organisms that had lived in oceans from 575 to 542 million years ago; that is, before the Cambrian Explosion of animals. What was notable was that the Ediacara organisms do not have an ancestor-descendant relationship with the Cambrian animals, and most of them went extinct before the Cambrian Explosion.

This group of organisms -- most species -- seems to be distinct from the Cambrian animals. But how did those Ediacara organisms first evolve? Did they also appear in an explosive evolutionary event, or is the Cambrian Explosion a truly unparalleled event. 50 characters were identified and mapped the distribution of these characters in more than 200 Ediacara species. These species cover three evolutionary stages of the entire Ediacara history across 33 million years. The three successive evolutionary stages are represented by the Avalon, White Sea, and Nama assemblages (all named after localities where representative fossils of each stage can be found).

The earliest Avalon stage was represented by relatively few species. These earliest Ediacara life forms already occupied a full morphological range of body plans that would ever be realized through the entire history of Ediacara organisms. In other words, major types of Ediacara organisms appeared at the dawn of their history, during the Avalon Explosion. Then Ediacara organisms diversified in White Sea time and then declined in Nama time. But, despite this notable waxing and waning in the number of species, the morphological range of the Avalon organisms were never exceeded through the subsequent history of Ediacara.

The process involved adapting quantitative methods that had been used previously for studying morphological evolution of animals, but never applied to the enigmatic Ediacara organisms. "We think of diversity in terms of individual species. But species may be very similar in their overall body plan. For example, 50 species of fly may not differ much from one another in terms of their overall shape -- they all represent the same body plan. On the other hand, a set of just three species that include a fly, a frog and an earthworm represent much more morphological variation. We can thus think of biodiversity not only in terms of how many different species there are but also how many fundamentally distinct body plans are being represented.

The approach combined both those approaches. In addition, the method relies on converting different morphologies into numerical (binary) data. This strategy allows us to describe, more objectively and more consistently, enigmatic fossil life forms, which are preserved mostly as two-dimensional impressions and are not understood well in terms of function, ecology, or physiology.


Scientists are still unsure what were the driving forces behind the rapid morphological expansion during the Avalon explosion, and why the morphological range did not expand, shrink, or shift during the subsequent White Sea and Nama stages.

The evolution of earliest macroscopic and complex life also went through an explosive event before to the Cambrian Explosion. It now appears that at the dawn of the macroscopic life, between 575 and 520 million years ago, there was not one, but at least two major episodes of abrupt morphological expansion.

Saturday, February 23, 2008

New Route For Heredity Bypasses DNA

A group of scientists in Princeton's Department of Ecology and Evolutionary Biology has uncovered a new biological mechanism that could provide a clearer window into a cell's inner workings.


What's more, this mechanism could represent an "epigenetic" pathway -- a route that bypasses an organism's normal DNA genetic program -- for so-called Lamarckian evolution, enabling an organism to pass on to its offspring characteristics acquired during its lifetime to improve their chances for survival. Lamarckian evolution is the notion, for example, that the giraffe's long neck evolved by its continually stretching higher and higher in order to munch on the more plentiful top tree leaves and gain a better shot at surviving.

The research also could have implications as a new method for controlling cellular processes, such as the splicing order of DNA segments, and increasing the understanding of natural cellular regulatory processes, such as which segments of DNA are retained versus lost during development. The team's findings will be published Jan. 10 in the journal Nature.
Princeton biologists Laura Landweber, Mariusz Nowacki and Vikram Vijayan, together with other members of the lab, wanted to decipher how the cell accomplished this feat, which required reorganizing its genome without resorting to its original genetic program. They chose the singled-celled ciliate Oxytricha trifallax as their testbed.

Ciliates are pond-dwelling protozoa that are ideal model systems for studying epigenetic phenomena. While typical human cells each have one nucleus, serving as the control center for the cell, these ciliate cells have two. One, the somatic nucleus, contains the DNA needed to carry out all the non-reproductive functions of the cell, such as metabolism. The second, the germline nucleus, like humans' sperm and egg, is home to the DNA needed for sexual reproduction.
When two of these ciliate cells mate, the somatic nucleus gets destroyed, and must somehow be reconstituted in their offspring in order for them to survive. The germline nucleus contains abundant DNA, yet 95 percent of it is thrown away during regeneration of a new somatic nucleus, in a process that compresses a pretty big genome (one-third the size of the human genome) into a tiny fraction of the space. This leaves only 5 percent of the organism's DNA free for encoding functions. Yet this small hodgepodge of remaining DNA always gets correctly chosen and then descrambled by the cell to form a new, working genome in a process (described as "genome acrobatics") that is still not well understood, but extremely deliberate and precise.
Landweber and her colleagues have postulated that this programmed rearrangement of DNA fragments is guided by an existing "cache" of information in the form of a DNA or RNA template derived from the parent's nucleus. In the computer realm, a cache is a temporary storage site for frequently used information to enable quick and easy access, rather than having to re-fetch or re-create the original information from scratch every time it's needed.




"The notion of an RNA cache has been around for a while, as the idea of solving a jigsaw puzzle by peeking at the cover of the box is always tempting," said Landweber, associate professor of ecology and evolutionary biology. "These cells have a genomic puzzle to solve that involves gathering little pieces of DNA and putting them back together in a specified order. The original idea of an RNA cache emerged in a study of plants, rather than protozoan cells, though, but the situation in plants turned out to be incorrect."




Through a series of experiments, the group tested out their hypothesis that DNA or RNA molecules were providing the missing instruction booklet needed during development, and also tried to determine if the putative template was made of RNA or DNA. DNA is the genetic material of most organisms, however RNA is now known to play a diversity of important roles as well. RNA is DNA's chemical cousin, and has a primary role in interpreting the genetic code during the construction of proteins.




First, the researchers attempted to determine if the RNA cache idea was valid by directing specific RNA-destroying chemicals, known as RNAi, to the cell before fertilization. This gave encouraging results, disrupting the process of development, and even halting DNA rearrangement in some cases.




In a second experiment, Nowacki and Yi Zhou, both postdoctoral fellows, discovered that RNA templates did indeed exist early on in the cellular developmental process, and were just long-lived enough to lay out a pattern for reconstructing their main nucleus. This was soon followed by a third experiment that "… required real chutzpah," Landweber said, "because it meant reprogramming the cell to shuffle its own genetic material."




Nowacki, Zhou and Vijayan, a 2007 Princeton graduate in electrical engineering, constructed both artificial RNA and DNA templates that encoded a novel, pre-determined pattern; that is, that would take a DNA molecule of the ciliate's consisting of, for example, pieces 1-2-3-4-5 and transpose two of the segments, to produce the fragment 1-2-3-5-4. Injecting their synthetic templates into the developing cell produced the anticipated results, showing that a specified RNA template could provide a new set of rules for unscrambling the nuclear fragments in such a way as to reconstitute a working nucleus.




"This wonderful discovery showed for the first time that RNA can provide sequence information that guides accurate recombination of DNA, leading to reconstruction of genes and a genome that are necessary for the organism," said Meng-Chao Yao, director of the Institute of Molecular Biology at Taiwan's Academia Sinica. "It reveals that genetic information can be passed on to following generations via RNA, in addition to DNA."




The research team believes that if this mechanism extends to mammalian cells, then it could suggest novel ways for manipulating genes, besides those already known through the standard methods of genetic engineering. This could lead to possible applications for creating new gene combinations or restoring aberrant cells to their original, healthy state

Saturday, February 2, 2008

Oxygen: The Clue To First Appearance Of Large Animals

The sudden appearance of large animal fossils more than 500 million years ago – a problem that perplexed even Charles Darwin and is commonly known as “Darwin’s Dilemma” – may be due to a huge increase of oxygen in the world’s oceans.


In 2002 researchers found the world’s oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth’s earliest known complex life to more than 575 million years ago, soon after the melting of the massive “snowball” glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.

A huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.
Now for the first time, geochemical studies have determined the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon. Studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world’s oceans. Immediately after this ice age there is evidence for a huge increase in atmospheric oxygento at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest large animal fossils.

The close connection between the first appearance of oxygenated conditions in the world’s oceans and the first appearance of large animal fossils confirms the importance of oxygen as a trigger for the early evolution of animals, the researchers say. They hypothesize that melting glaciers increased the amount of nutrients in the ocean and led to a proliferation of single-celled organisms that liberated oxygen through photosynthesis. This began an evolutionary radiation that led to complex communities of filter-feeding animals, then mobile bilateral animals, and ultimately to the Cambrian “explosion” of skeletal animals 542 million years ago.