Historical biogeographers

Historical biogeographers also make use of a tool called an area cladogram. This diagram is made by taking a taxonomic tree, which shows various species and their relatedness, and replacing the species names with the geographic location in which those species are found. This new tree allows scientists to determine how the differences in environments have effected the evolutionary history of different species of common origin. A sample area cladogram is shown below:

The Dynamics Of Transcription In Living Mammalian Cells

Transcription is the transfer of DNA’s genetic information through the synthesis of complementary molecules of messenger RNA. It forms the basis of all cellular activities. But the dynamics of the process is not well understood. Scientist do not know how efficient it is or how long it takes. But researchers at the Albert Einstein College of Medicine have measured the stages of transcription in real time. Their unexpected and surprising findings have fundamentally changed the way transcription is understood.

The study focused on the ensyme responsible for transcription, RNA polymerase II. During transcription, numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides.

3 phases of Transcription

To visualize the transcription process, the researchers used living mammalian cells, each of which contained 200 copies of an artificial gene that they had inserted into one of the cell’s chromosomes. Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process:

• binding of the enzyme molecules to DNA,
• initiation (when the enzyme links the first few RNA nucleotides together) and
• elongation (construction of the rest of the RNA molecule).

The result of the observation
As they observed the RNA polymerase II molecules attaching to DNA and making new RNA, they saw many cases where enzyme molecules attached — and then promptly fell off.

Transcription is inefficient
During the first two phases the transcription process is really inefficient. It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule.

Transcription may be inefficient for a reason. All the factors needed for transcription have to come together at the right time and the right place, so there’s a lot of falling off and adding on of polymerases until everything is precisely coordinated.

The researchers observed that

• the binding phase of transcription lasted six seconds and
• initiation phase lasted 54 seconds.
• the elongation phase lasted 517 seconds (about eight minutes).

Pausing and Elongation
The “lead” polymerase on the growing polymerase II enzyme sometimes “paused” for long periods, retarding transcription in the same way that a Sunday driver on a narrow road slows down all traffic behind him.
But in the absence of pausing, elongation proceeded much faster — about 70 nucleotides synthesized per second — than has previously been reported.

These two phenomena — pausing and rapid RNA synthesis during elongation — may be crucial for regulating gene expression. Once the ‘paused’ polymerase starts up again, in a very short time you could synthesize a new batch of messenger RNA molecules that might suddenly be needed for making large amounts of a particular protein.

Biogeorgraphic Distributions

The geographic distributions of species can be of a number of types
Consider the distribution of three species of toucans in the genus Ramphastos.
• Endemic distributions
Two of the species, R. vitellinus and R. cluminatus , have endemic distributions: they are limited to a particular area. Endemic distributions can be more or less widespread.
• Cosmopolitan distributions
The extreme case of species that are found on all continents of the globe are called cosmopolitan. The pigeon, for example, is found on all continents except Antarctica; on a strict definition, the pigeon (pictured opposite) might not be allowed to be cosmopolitan, but the term is usually intended less strictly - and the pigeon is called a cosmopolitan species.
• Disjunct distributions
Other species, like R. ariel , are not confined to a single area, but are distributed in more than one region with a gap between them: these are called disjunct distributions.
Maps can be drawn for a taxonomic group at any Linnaean level: just as species have geographic distributions, so too do genera, families, orders. Biogeography aims to explain the distributions of the higher taxa too, in addition to those of species; and different explanatory processes are often appropriate at different levels.
Short-term movements of individuals influence the distributions of populations and species, whereas slower acting geological processes may control the biogeography of higher taxa.

Genetic Chromosome Breaking

Researchers in genome stability have observed that many kinds of cancer are associated with areas where human chromosomes break. Its been hypothesized, but not proven, that slow or altered replication led to the chromosomes breaking.

But now a study at Tufts University two molecular biologists have used yeast artificial chromosomes to prove that hypothesis. They found a highly flexible DNA sequence that increases fragility and stalls replication, which then causes the chromosome to break.

Cancer Causing Areas
The area in question is an area that has a tumor suppressor gene -- a gene whose absence can cause tumors. If you delete that gene or delete part of that gene so it doesn't work anymore, that can lead to tumors. The fact that there is fragility in the same region that this gene is located is a bad coincidence. Fragility can cause deletions and deletions can cause cancer, so you want to understand the fragility because that might be what's causing cancer.

DNA structure leads to fragility
Past research had predicted the flexibility of the DNA helix in this particular common fragile site by calculating the twist angle between consecutive base pairs and found that there were several points of high flexibility, suggesting that the flexibility was connected to the fragility.
Freudenreich and Zhang used yeast artificial chromosomes to test this idea because it allowed them to look at the region in a more detailed way than looking at human chromosomes and to monitor the replication process. They expect the results will be similar when tested in human cells based on previous research using yeast chromosomes.

How the research was conducted
Two regions of predicted high flexibility, plus a region near a cancer cell breakpoint and a control region were tested to see whether any of these regions could cause breakage of a yeast chromosome. They found that one did. This is the first known sequence element within a human common fragile site shown to increase chromosome breakage. What is intriguing is that the sequence that breaks, in addition to being flexible, is predicted to form an abnormal DNA structure." The result is that when replication stalls, chromosomes can break.

How did the chromosomes break?
From past studies, they hypothesized that breakage was connected to replication. Replication is just the duplication of DNA in side the cells as they divide, the DNA inside those cells must duplicate. The research showed that the chromosomes were breaking because replication was stalled.

The problem arises when they do not heal correctly and instead are deleted or rearranged, Cancer cells almost always have some sort of deletions or rearrangements. Something is wrong with their chromosomes that then messes up the genes that are in those areas.

Replication process stalled
The researchers also noticed that this particular sequence was an AT-rich region, where the DNA was composed mostly of the bases adenine (A) and thymine (T), rather than the other bases cytosine (C) or guanine (G). Freudenreich and Zhang found the longer the AT-repeat, the more the replication process was stalled, something they would like to follow up on with further research.

Some researchers believe that the longer the repeat, the more the abnormal the DNA structure forms, and the more fragile the chromosome becomes. What is still up in the air is whether people with longer repeats are more prone to deleting that tumor suppressor gene and getting cancer as a result. Does this correlation between chromosome breaks and cancer has a medical consequence.

BioGeorgraphy and Range Limitations?

What factors limit the geographic range of a species?
Ecological factors
The distributional limits of a species are set by its ecological attributes:

• Fundamental niches
If a species is able to tolerate a certain range of physical factors such as temperature, humidity, and so on and it has the capacity in theory live anywhere within these tolerance limits, this is its fundamental niche.

• Realized niches - Competing species
However, if there are competing species that occupy part of this range the competition may be too strong to permit both species to exist. The near extinction of the red squirrel in Britain due to competition from the grey squirrel is a good example. Each species' realized niche will be smaller than its physiology makes possible. In other words each species will occupy a smaller range than it otherwise would in the absence of competition.

Genetic Factors Strongly Shape How Peers Are Chosen

The company we keep may be more influenced by genetics than previously thought. Researchers report that as individuals develop, genes become more important in influencing how they choose their peer groups. The findings offer insight into which individuals may be at risk for future substance use or other externalizing behaviors such as conduct and antisocial personality disorder.

The study involved 1,800 male twin pairs from mid-childhood to early adulthood, between 1998 and 2004.

Through a series of interviews, researchers found that genetic factors increasingly impact how male twins make choices as they mature and develop their own social groups. Their finding include that the path from genes to behaviors like drug use and antisocial behaviors is not entirely direct or biological. Rather an important part of this pathway involves the genetics, which influences our own social environment, which in turn impacts on our risk for a whole host of deviant behaviors. Results demonstrate clearly that a complete understanding of the pathway from genes to antisocial behaviors, including drug abuse, has to take into account self-selection into deviant versus benign environments. The effects of peers in adolescence can be quite powerful, either encouraging or discouraging deviant behaviors. Peers also provide access to substances of abuse.

Molecular evolution

Molecular evolution is the process of evolution at the scale of DNA, RNA, and proteins.

Some of the key topics that spurred development of the field have been

• the evolution of enzyme function,
• the use of nucleic acid divergence as a "molecular clock" to study species divergence,
• and the origin of non-functional or junk DNA.

Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.