April 23, 2008

The Ups and Downs of Mechanical Ventilation

Posted in Articles of Interest tagged , , , , , at 10:25 am by D. Borst

So mechanical ventilators are perhaps one of the most important advances in critical care medicine ever. Critically ill patients get too ill to manage their own breathing, and to make sure that their bodies get enough of an air supply, hooking them up to a machine for hours or days has saved countless lives. It has also enabled many invasive surgeries that require the use of drugs that suppress the respiratory drive along with consciousness.

But as with all medical advances, ventilators do come with a cost. When a ventilator is put in, the physician sticks a tube down the patients trachea to make sure that air is going into the patients lungs and not into her stomach. Having a tube stuck down one’s throat precludes much movement, and also slightly abrades the surfaces it comes in contact with. This is postulated to cause the increase in nosocomial, or hospital acquired, infections such as pneumonia.

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Designer Enzymes

Posted in Articles of Interest, Biochemistry tagged , , , at 10:01 am by D. Borst

Harnessing the power of enzymes for commercial reactions is one of the ultimate Holy Grails of synthetic chemistry. It looks like its achievement may have come one step closer. Head on over to Biosingularity for the report on how Kendall Houk of UCLA has begun to make the first successful prototypes of such molecules.

I got to listen to Dr. Houk speak at PSU in February. He is doing some pretty cool organic chemistry intensive stuff, way over my head. But essentially what they did was use quantum mechanical models of the transition state for the reaction they wanted to catalyze, and designed an active site which would stabilize that active site. This is coherent with the transition state stabilization model of enzymatic catalysis. Instead of using amino acids and proteins, they were using complex organic molecules which would do the same things that amino acids would.

This challenge is straightforward, if not simple, in theory. We have the theories to predict all chemical reactions. What we don’t have is the processing power to do the incredibly complex calculations that arise because of the theory. The art of the science is to develop shortcuts and assumptions that will allow one to simplify the calculations to the point where they can be done.

April 22, 2008

Update to Theme

Posted in Uncategorized at 11:52 pm by D. Borst

Don’t be scared. I was just looking for a lighter theme to use in place of the old one. Same great Science Content.

Genes and Dominance

Posted in Genetics tagged , , , , , , at 10:45 am by D. Borst

Why are some genes recessive?

So in genetics class, we learn that Mendel began the study of genetics with his study of peas. One of the notions that he developed was that of Dominant and Recessive genes. But in this age of molecular genetics, what does it mean to be dominant or recessive?

Further inquires into the topic have also led to more controversy. Some genes are “incompletely dominant” and some share “codominance.” Mendel’s Law of independent assortment turned out to not be entirely true. Some traits seemed to be inherited only from the mother.

On the other hand, the discovery that we have a diploid genotype provided a very obvious explanation for the presence of two alleles of a gene, and the nature of meiosis explains why alleles separate during the production of gametes. Today I want to focus on what factors, from a molecular biology standpoint, produce genes that act recessive and dominant. The key is the level of expression.

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Ken Miller: Intelligent Design

Posted in Mad Scientist, Policy tagged , , , , , , at 4:38 am by D. Borst

In the below video, (its about 2 hours 70 minutes long, with 50 minutes of questions) Ken Miller of Brown University shows the intellectual pitfalls that are faced by Intelligent Design. It was originally posted 2 years ago, but his points are no less important today than they were then. If you have ever found yourself mystified at how to intelligently and coherently respond to ID advocates, then take a look at this video. Ken Miller nicely skirts the line between respecting those who believe in God yet still maintaining scientific rigor. If you have a spare 2 hours, check it out. It is good.

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Cell Motility: The Flagella, mostly

Posted in Microbiology tagged , , , , at 4:25 am by D. Borst

Thank You cuplantdiversity

Though not universal, one of the oft recognized characteristics of life is that an entity is able to move under its own power. Indeed, such an ability is often necessary for organisms as they need to be able to relocate to areas of greater nutrient concentration, or lower predator concentration.

Microorganisms are no different. Despite their tiny size, microorganisms have developed a number of distinct strategies for controlling their locomotion, which will be the subject of today’s post. By far the most common means of locomotion in microorganisms is the flagella, a long whip like structure that allows microorganisms to propel themselves through the expense of their chemiosmotic gradient. Additionally there is the mysterious movement through a process known as *gliding*, and vertical motion through control of gas vacuoles. While other forms of cell motility exist, these are the three that I shall touch on today, and most of my time will be spent discussing the flagella.

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April 18, 2008

Cell Walls in Microorganisms

Posted in Microbiology tagged , , , , at 10:28 pm by D. Borst

Gram Positive Stain of S. AureusLipid bilayers are relatively weak. Certainly there are stronger forms of these membranes, but as implied by the fluid mosaic model these membranes sacrifice rigidity and strength for the ability to allow proteins to freely disperse within the membrane. A consequence of this is that differences in pressure on the two different sides of the membrane can quickly lead to membrane rupture.

This presents a problem for life, because in order to complete the processes needed many proteins, ions and other molecules are required in a very small space. However, to have all these molecules concentrated within the cell would cause there to be a high osmotic pressure for water to flow into the cell. If the cell is not able to control this water absorption, it will swell to the point where it bursts. In animals, the solution is to keep the cells immersed in a solution that has the same number of osmolites dissolved in it as the cells do. Thus the cell cytoplasm is isoosmotic with the extra-cellular environment.

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Differences between the molecular biology of Prokaryotes and Eukaryotes

Posted in Microbiology tagged , , , at 10:28 pm by D. Borst

So Molecular biology is still progressing pretty slowly, and today we
just focused on basics of molecular biology, but we did cover some of
the differences between prokaryote and eukaryote genetics.

The most obvious difference between the two is that prokaryotic DNA
is generally arranged into circular structures, while eukaryotic DNA
is arranged in linear strands. Furthermore, eukaryotic genomes
contain multiple chromosomes, while prokaryotic genomes only contain
one. This difference may be a result of the massive bloat that has
occurred in eukaryotic genomes. While eukaryotic genes tend to be
longer and more complex than prokaryotic genes, they are also only a
fraction of the total length of the nucleic acid strand. Prokaryotic
genomes are up to 90% coding sequences, while coding sequences in
eukaryotic organisms is often around 3%. Furthermore, eukaryotic
genes are peppered with introns, spans of non-coding sequences within
an operon, while prokaryotic genes are generally free of such nonsense

All of this means that eukaryotes tend to have much more DNA than
prokaryotes. One explanation of the difference in the morphology of
the DNA is simply that as the length of the nucleic acid sequence got
longer, it got too long to be effectively manipulated as a single long
loop. Read the rest of this entry »

Describing Unicellular Morphology

Posted in Microbiology tagged , , , at 10:25 pm by D. Borst

Bacteria, like other organisms, come in a variety of shapes and sizes. Unfortunately, the way scientists have described these unicellular entities does is not necessarily related to how we describe shapes in everyday life. Below, I will discuss some of the basic descriptors used to discuss the form of these cells.

Cocci is a term that is used to describe cells that are spherical. These cells are small and compact, and appear to be small round shapes under a microscope. Coccus bacteria can form many different types of colonies, including pairs, or diplococci; chains, or streptococci; tetrads, a square arrangement of four cells in a plane; sarcina, an arrangement of eight cells with the center of each cell at the vertex of a cube; and in grape like clusters known as staphylococci. You the names of these structures probably remind you of various pathogens such as Staphylococcus aureus and Streptococcus pneumoniae, which are organisms that take the forms relating to their names.

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