Wednesday, December 15, 2010

Molecular Biology

Molecular Biology
Molecular Biology
Molecular biology is a branch of general biology that deals with DNA manipulation for the point of mutation. Cell biology is the one of the most important branches of general biology. Cell biology concentrates on studying the functions and structure of cells, which is the building blocks that make up all organisms. Combined, these two basics of biology concentrate on the molecular biology of the cell.
• The field of molecular biology was made in the 1930s but no real experimentation of molecular biology was made until the 1950s. When it began, research in molecular biology was done by using x-rays to view molecules within the cell. Studying the proteins within these cells helped scientists to determine how an organism works.
• Cell biology works closely with molecular biology. It deals with all information about the cell including structure, anatomy, death and respiration. The field of cell biology dates back to the 1650s, when Robert Hooke, a English physicist, first invented the term “cell” to describe the cell of a cork tree. Within molecular biology, cells are studied by their various molecules. Proteins are one of the most important molecules in a cell. Each protein functions a certain way and when combined, molecular biology and cell biology work together to determine what those functions are.
• Neither molecular biology or cell biology would be possible without the creation of the microscope. Today’s high-tech microscopes can see the tiniest details of cells.
• The cell theory determined that a cell is the building blocks of all living things. Within cell biology, the cell theory has changed over the years. Today, the cell theory states that all living things are made of cells, old cells diving in two creates new cells, and no two cells are identical. The molecular biology of the cell has created this entire branch of general biology, without which cell could not be studied. Molecular biology could not exist without cell biology, as the two are so closely linked together.
As more progress is made over the years by scientists to further develop the technology of cell biology and microbiology, the cell theory has remained the same for almost 200 years. Watching the cell functions in molecular biology has made it possible for diseases such as cancer to be studied in depth. Due to cell biology, many diseases can be studied and understood.

Genes and protein synthesis

There are many discussions between biologists to find a comprehensive definition of a gene, which is not easy, if possible at all. For our purposes
A gene is a continuous stretch of a genomic DNA molecule, from which a complex molecular machinery can read information (encoded as a string of A, T, G, and C) and make a particular type of a protein or a few different proteins.

This “definition” is not precise, and to better understand it we need to describe the molecular machinery making proteins based on the information encoded in genes. This process is called protein synthesis and has three essential stages: (1) transcription, (2) splicing, and (3) translation.
1. In transcription phase one strand of DNA molecule is copied into a complementary pre mRNA (pre stands for preliminary and m for messenger) by the protein complex RNA polymerase II (see section 2.2 and 2.4). In the process the two-stranded DNA double helix is unwound and information is read only from one strand (sometimes called the W-strand). 
2. Splicing removes some stretches of the pre mRNA, called introns, the remaining sections called exons are then joined together. Note that the removal of introns is a consequence of the way how eukaryote genomes are organised.   The genomic DNA that corresponds to the coding part of genes is not continuous, but consists of exons and introns. Exons are the part of the gene that code for proteins and they are interspersed with non coding introns which must be removed by splicing. The number and  size of introns and exons differs considerably between genes and also between species. Only very few genes in yeast have introns, while  for human threre are about 4 introns per gene on average, and the average size of exons is 150 bp and just above 3400 bp for introns. Prokaryote genes do not have introns and the splicing step is not present. The result of splicing is mRNA. Many eukaryote genes are known to have different alternative splice variants, i.e. the same pre-mRNA producing different mRNAs, known as alternative splicing.

(picture taken from  On-Line Biology Book )
3. Translation is the process of making proteins by joining together amino acids in order encoded in the mRNA. The order of the amino acids is determined by 3 adjacent nucleotides (triplets) in the DNA. This is known as the triplet or genetic code . Each triplet is called a codon and codes for one amino acid. As there are 64 codons and only 20 amino acids the code is redundant, for example histidine is encoded by CAT and CAC.  In cytoplasm the mRNA forms a complex with ribosomes, which are large complexes of proteins and RNA molecules. The precise interactions and functions of all protein in ribosomes are not yet fully understood.

(picture taken from  On-Line Biology Book )
Different transfer or tRNA molecules each carries one specific amino acid to the ribosome and specifically recognises one codon on the mRNA. The amino acid carried by the tRNA is added to the nascent (growing) protein. The translation is a complex process and not all the details are understood. Luckily most of these details are not crucial for understanding of bioinformatics. What is crucial however is to realise that there is nothing magical about proteins synthesis.
The end of translation is the final part of gene expression and the final product is a protein, the sequence of which corresponds to the sequence encoded by the mRNA. Proteins can be post-translationally modified e.g., by adding of sugars or cleavage (chopping), and this affects their location and function.
Biologists used to believe in paradigm - 'one gene - one protein'. Now this is known not to be true - due to alternative splicing and post-translational modifications one gene can produce a variety of proteins. There are also genes that do not encode proteins but encode RNA (for instance tRNA and ribosomal RNA).

Biotechnology and veterinary medicine

Biotechnology and veterinary medicine
Biotechnology and veterinary medicine
While there have been many practical applications for bio technology and humans, there has also been extensive research in bio technology and animals. Biotech research in the field of veterinary medicine has helped to expand the healthy lifespan of our pets and to cure diseases that would have otherwise ended the life our pets prematurely. There is a very real difference between using animals in medical studies for the advancement of human medicine, and using animals in biotech research for the advancement of veterinary medicine. For example, scientists have used biotech research in order to make some dog breeds smaller in size. This may be a benefit to humans, such as city dwellers that don’t have the room for larger dogs. Shrinking breed size may also benefit the animals because it will eliminate such ailments as hip dysplesia.
Using bio technology in order to extend the life spans of our pets, is perhaps an accepted area of study. However, bio technology can also be used to produce a certain type of breed. Researchers could use genetic engineering to produce only the most vicious pit bulls and those dogs could be used for dogs fights or as guard dogs in dangerous parts of the world. There are advancements in bio technology that are meant to help our pets, and then there are those that would only be for human benefit. Scientists, for instance have genetically altered cows, so that they will produce more milk. There are many that feel animals are on the earth for human benefit. However, there are also those that fight for animal rights. Your opinion regarding the ethics of biotech research in regards to animals, would very much depend on where you stand with regard to animal rights.
Biotech research with animals has the possibility of helping both animals and humans. Bio technology can improve the health and lifespan of pets but it can also be used to alter the productivity of animals in the agricultural industry. The applications of bio technology and veterinary medicine are meant to improve the health of our companion animals. Research in the field of bio technology has found some success in curing cancer in dogs and in eliminating common problems associated with certain types of breeds, such as eye problems in Beagles.
Biotech research can produce cures for veterinary medicine that we may not otherwise discover. In striving to improve the lives of our companion animals, we must also remember to treat those animals we use in research humanely. If we don’t follow those principles, we eliminate the point of research meant to improve the quality of life for animals. Too often, scientists in the field of veterinary medicine treat animals in a disgusting manner and behave in a very hypocritical way. While we must realize that biotech research in the field of veterinary medicine is basically performed to sell food, medication or surgical procedures, we must also remember to think of the animals that we are trying to help.


DNA is the main information carrier molecule in a cell. DNA may be single or double stranded. A single stranded DNA molecule, also called a polynucleotide, is a chain of small molecules, called nucleotides . There are four different nucleotides grouped into two types, purines: adenosine and guanine and pyrimidines: cytosine and thymine. They are usually referred to as bases (in fact bases are the only distinguishing element between different nucleotides, see figure below) and denoted by their initial letters, A,C ,G and T (not to be confused with amino acids!).
(picture taken from  On-Line Biology Book )
Different nucleotides can be linked together in any order to form a polynucleotide, for instance, like this

Polynucleotides can be of any length and can have any sequence. The two ends of this molecule are chemically different, i.e., the sequence has a directionality, like this

The end of the polynucleotide are marked either 5' and 3' (this has chemical reasons in the numbering of the –OH groups of the sugar ring); by convention DNA is usually written with 5' left and 3' right, with the coding strand at top. Two such strands are termed complementary , if one can be obtained from the other by mutually exchanging A with T and C with G, and changing the direction of the molecule to the opposite. For instance,
is complementary to the polynucleotide given above.
Specific pairs of nucleotides can form weak bonds between them. A binds to T, C binds to G (to be more precise, two hydrogen bonds can be formed between each A-T pair, and three hydrogen bonds between each C-G pair). Although such interactions are individually weak, when two longer complementary polynucleotide chains meet, they tend to stick together, like this

      5' C-G-A-T-T-G-C-A-A-C-G-A-T-G-C 3'
         | | | | | | | | | | | | | | | 
      3' G-C-T-A-A-C-G-T-T-G-C-T-A-C-G 5'

Vertical lines between two strands represent the forces between them (to be more accurate we could draw triple lines between each C and G and double lines between A and T) as shown below. The A-T and G-C pairs are called base-pairs (bp). The length of a DNA molecule is usually measured in base-pairs or nucleotides (nt), which in this context is the same thing. 

(picture taken from  On-Line Biology Book )

Two complementary polynucleotide chains form a stable structure, which resembles a helix and is known as a the DNA double helix. About 10 bp in this structure takes a full turn, which is about 3.4 nm long.

(picture taken from  On-Line Biology Book )

This structure was first figured out in 1953 in Cambridge by Watson and Crick (with the help of others), and the birthplace of this structure is often thought to be the Eagle pub on Bene't street. Later they got the Nobel Prize for this discovery, for more see the book by Watson – The Double Helix.

Watson and Crick at their DNA model molecule

It is remarkable that two complementary DNA polypeptides form a stable double helix almost regardless of the sequence of the nucleotides. This makes the DNA molecule a perfect medium for information storage. Note that as the strands are complementary, each one of them fully determining the other, therefore for the information purposes it is enough to give only one strand of the genome molecules. Thus, for many information related purposes, the molecule used on the example above, can be represented as CGATTCAACGATGC. The maximal amount of information that can be encoded in such a molecule is therefore 2 bits times the length of the sequence. Noting that the distance between nucleotide pairs in a DNA is about 0.34 nm, we can calculate that the linear information storage density in DNA is about 6x10 8 bits/cm, which is approximately 75 GB or 12.5 CD-Roms per cm.

Complementarity of two strands in the DNA is exploited for copying (multiplying) DNA molecules in a process known as the DNA replication , in which one double stranded DNA is replicated into two identical ones. (The DNA double helix unwinds and forks during the process, and a new complimentary strand is synthesised by specific molecular machinery on each branch of the fork. After the process is finished there are two DNA molecules identical to the original one.)   In a cell this happens during the cell division (see Section 1) and a copy identical to the original goes to each of the new cells.

Note that mismatched components between polynucleotide strands are possible, if the total sum of weak forces between the complementary nucleotides are strong enough. So the molecules like

| | | ~ | | | ~ | | | ~ | | |
are chemically possible, though they may be rare in a living cell. More bonds, i.e., more complementary pairs, makes the molecule more stable. If there are not enough bonds, the two stranded molecular structure may become weak and the strands may come apart. The number of links needed to keep the double-helix together depends on the temperature (so-called melting temperature) and other environmental factors. DNA which is no longer in the helical form is said to be denatured.

Molecules of life : Small molecules

These can be the building blocks of the macromolecules or they can have independent roles, such as signal transmission or being a source of energy or material for a cell. Some important examples besides water are sugars, fatty acids, amino acids and nucleotides. For instance, biological membranes are constructed from fatty acids, into which macromolecules are embedded. There are 20 different amino acid molecules, which are the building blocks for proteins (to be more precise, there are 19 amino acids and one which has a slightly different structure and therefore is called imino acid).

These are three examples of amino acid moleclues, there are 17 more. They differ by R side chains which determine their properties and the order of these different amino acids within the protein determines the three dimensional structure of the protein. There is a convention that each amino-acid is denoted by a letter in Latin alphabet, for instance arginine  is denoted by R, histidine by H, lysine by L and there are 20 such letters .


Proteins are the main building blocks and functional molecules of the cell, taking up almost 20% of a eukaryotic cell’s weight, the largest contribution after water (70%). Among others, there are
  • Structural proteins, which can be thought of as the organism's basic building blocks. An example is collagen, which is the major structural protein of connective tissue and bone.
  • Enzymes, which perform (catalyse) a multitude of biochemical reactions, such as altering, joining together or chopping up other molecules. Together these reactions and the pathways they make up is called metabolism. For example the first step in the glycolysis pathway, which is the conversion of glucose to glucose 6-phosphate, is catalysed by the enzyme hexokinase. Usually enzymes are very specific and catalyse only a single type of reaction, however the same enzyme can play role in more than one pathway.
  • Transmembrane proteins are key in maintenance of the cellular environment, regulating cell volume, extraction and concentration of small molceules from the extracellular environment and generation of ionic gradients essential for muscle and nerve cell function. An example is the sodium/potassium pump.

Proteins have complex three dimensional (3D) structure (see figure below). Four levels of protein structure are distinguishable:
  1. Proteins are chains of 20 different types of amino acids, which in principle can be joined together in any linear order, sometimes called poly-peptide chains. This sequence of amino-acids is known as the primary structure, and it can be represented as a string of 20 different symbols  (i.e., a word over the common alphabet of 20 letters). Information about various protein sequences and the functional roles of the respective proteins, can be found in UniProtKB/Swiss-Prot database. UniProtKB/Swiss-Prot is a joint project between the EBI and the Swiss Institute of Bioinformatics (SIB). The length of the protein molecule can vary from few to many thousands of amino-acids. For example insulin is a small protein and it consists of 51 amino acids, while titin has ~28,000 amino acids.
  2. Although the primary structure of a protein is linear, the molecule is not straight, and the sequence of the amino acids affects the folding. There are two common substructures often seen within folded chains - alpha-helices and beta-strands. They are typically joined by less regular structures, called  loops. These three are called secondary structure elements.
  3. As the result of the folding, parts of a protein molecule chain come into contact with each other and various attractive or repulsive forces (hydrogen bonds, disulfide bridges, attractions between positive and negative charges, and hydrophobic and hydrophilic forces) between such parts cause the molecule to adopt a fixed relatively stable 3D structure. This is called tertiary structure. In many cases the 3D structure is quite compact.
  4. A protein may be formed from more than one chain of amino-acids, in which case it is said to have quaternary structure. For example haemoglobin, is made up of four chains each of which is capable of binding an iron molecule.
Proteins are much too small to be seen in an optical microscope - a characteristic protein size varies from about 3 to 10 nanometers (nm), i.e., 3 to 10 times 10-9 m, and solving (i.e., discovering) their structure is a difficult and expensive exercise (approximately €50,000 - €200,000 per novel structure), which is done by a variety of methods including X-ray crystallography, nuclar-magnetic resonance spectroscopy, and advanced electron microscopy. PDbe is a database of known protein structures, which is housed and developed at the EBI. The images below shows the structure of triosephosphate isomerase visualised by RasMol software package, a 3D viewer for PDBe structures.
In this image the magenta coloured bits are alpha-helices, while yellow bits are beta-strands.
An alternative view in which the two monomer units are highlighted. The size of this protein in a crystallised state is about 13 x 7 x 5 nm. The images above are only models of these molecules, as the molecules are two small to have a ‘real’ image. For instance they cannot have any conventional colour, they are in constant motion, and when we start zooming in into a finer structure, quantum effects, such as Heisenberg uncertainty principle start playing role. 
There are roughly 15,000 protein structures deposited in public databases, though many of them are very similar to each other. Whether to consider two protein structures  similar or different depends on the similarity threshold (as with cell types). Structural biologists think that currently there are about 1,500 different representative protein structures known. 
All four structural levels are essentially determined by the primary structure (i.e., the amino-acid sequence) plus the physico-chemical environment where the molecule is placed. Predicting protein structure from the amino-acid sequence is one of the most important problems of computational biology (another name for bioinformatics, though some try to make a distinction between these two terms) and is far from being solved. Characteristic, frequently reoccurring structural elements are called protein domains. Sometimes it is possible to identify these domains in proteins of unknown structure, if their sequence is similar to that of a known structural domain. Structural domains are often associated with a particular protein function. Protein similarity is also deemed to be the result of evolutionary relationship.
What are the comparative sizes of proteins and cells? There is a proverb saying that size does not matter. Still comparative sizes may matter, particularly if we try to imagine the cellular processes described in the next sections. A typical linear dimension (diameter) of a globular protein is about 5 x 10 -9 m, while of a eukaryotic cell about 5 x 10 -5 m. This means the a cell is about a 10,000 times larger than a protein linearly. Alternatively, if we estimate the average weight of a human cell as about 10 -9 g, and remember that proteins constitute about one fifth of cell mass, then assuming the weight of an average protein to be about 10 -19 g (say hemoglobin is 64,500 atomic units, each of which is 1.66 x 10 -24 g), we see that there are 0.2 x 10 -9 / 10 -19 proteins per cell, which equals two billion (2 x 10 9 ). These of course are very rough estimates which would vary from cell to cell. If we remember that there are about 6 x 10 13 cells, we see that there are 30,000 times more cells per human, than proteins per cell. This may be an indication of the relative complexity of a human compared to a single cellular organism (a similar estimate regarding the relative complexity of an elephant or dinosaur and human may not be flattering for a human). 
Although forces such as hydrogen bonds are weak individually, when two or more biological macromolecules with complementary shapes come close to each other, the sum of all such weak forces may cause the molecules interact rather strongly, e.g., to make them stick together. In fact, such weak inter-molecular forces and interactions play a fundamental role in life and are at the basis of virtually all biological processes. For instance many proteins can stick together to form large protein complexes such as yeast RNA polymerase II, which reads and transcribes the genetic information (see Section 3.3), and which has 10 subunits and for which the structure has been solved recently. These weak interactions also underlie how microarrays work, which is discussed in the last section.

Agricultural biotechnology and your dinner table

Plant Biotechnology
Plant Biotechnology
Agricultural biotechnology has successfully altered the food that we eat and even the way that we eat it. Scientists have produced cows that make more milk and in turn, are able to make that milk last longer in our refrigerators. They have used plant biotechnology to grow bigger, longer lasting vegetables. They have even produced plants that can fight diseases or environmental conditions that would have wiped out entire crops in the past. Agricultural biotechnology has improved the quality and quantity of food that we eat. For instance, our tomato plants are stronger and we have more varieties available, thanks in part to plant biotechnology.
Agricultural biotechnology has made advancements in the Health and productivity of farm animals. Thanks to research in these fields, chickens may produce more eggs, cows may have more offspring and sheep’s wool may grow faster. If the wait for sheep’s wool to grow is decreased, so to is the necessity for more sheep. By reducing the amount of sheep necessary to produce the needed wool, we are also decreasing the resources needed to sustain those animals. Those saved resources may be used for other farm animals or even for people.
Agricultural biotechnology has been able to prevent some starvation in third world countries. Through the study of plant biotechnology, they have found ways to make crops stronger. For instance, imagine a village that experiences extreme drought with great frequency throughout the year. In the past, it would have been difficult for that village to sustain life with the limited crops available for growth in drought areas. However, the study of plant biotechnology, has produced a varied array of plants that not only survive drought, but thrive in it. In the past, that village may have suffered from a deficiency in vitamin C because they had no food that contained that vitamin. However, advancements in agricultural biotechnology have produced plants that are more hardy, and therefore that village now has a wider array of vitamin rich food available to them. The village is now able to sustain life with the crops that they can grow on their own. They may even have enough to sell to other villages, thereby aiding their economy as well.
The field of agricultural biotechnology has made many advancements in enriching and protecting our food sources. Plant biotechnology has made plants stronger and we are now offered a wider variety of choice in fruits and vegetables. In the past you may not have been able to grow a certain crop in a certain geographical area, however that is becoming less true with advancements made in plant biotechnology. As a direct result of improved plant health, there is a positive impact on human health. It must also be noted, that a wider variety of crop choice may also increase production for farmers, thereby increasing their profits and helping the economy. The positive ripple effects of Agricultural biotechnology can be felt worldwide.

Organisms and cells

All organisms consist of small cells, typically too small to be seen by a naked eye, but big enough for an optical microscope . Each cell is a complex system consisting of many different building blocks enclosed in membrane bag. There are unicellular (consisting only of one cell) and multicellular organisms. Bacteria and baker’s yeast are examples of unicellular organisms - any one cell is able to survive and multiply independently in appropriate environment.
There are estimated about 6x1013 cells in a human body, of about 320 different types. For instance there are several types of skin cells, muscle cells, brain cells (neurons), among many others. The number of cell types is not well-defined, it depends on the similarity threshold (what level of detail we would like to use to distinguish between the cell types, e.g., it is unlikely that we would be able to find two identical cells in an organism if we count the number of their molecules). The cell sizes may vary depending on the cell type and circumstances. For instance, a human red blood cell is about 5 microns (0.005 mm) in diameter, while some neurons are about 1 m long (from spinal cord to leg). Typically the diameter of animal and plant cells are between 10 and 100 microns.
There are two types of organisms - eukaryotes and prokaryotes, and two types of cells respectively. Bacteria belong to the prokaryotes. However, most organisms which we can see, such as trees, grass, flowers, weeds, worms, flies, mice, cats, dogs, humans, mushrooms and yeast are eukaryotes. The distinction between eukaryotes and prokaryotes is rather important, because many of the cellular building blocks and life processes are quite different in these two organism types. This is believed to be the result of different evolutionary paths. Evolution is an important concept in biology, there is a proverb saying that things only make sense in biology in the context of evolution. Most scientists believe that life first emerged on Earth around 3.8 billion years ago. The oldest fossilised bones that have been found resembling bones from anatomically modern humans are about 100,000 – 200,000 years old. Nobody really knows how life emerged on Earth, but there is lots of scientific evidence regarding how it may have evolved.
Viruses are not quite living organisms, but when inside a living host cell they show some features of a living organism. Viruses are too small to be seen in an optical microscope, but are big enough to reveal their structure in an electron microscope (the characteristic size of the virus is about 0.05-0.1 micron, while the wavelength of green light is about 0.5 micron).
Prokaryotic cells are smaller than eukaryotic cells (a typical size of a prokaryotic cell is about 1 micron in diameter) and have simpler structure (e.g., they do not have any inner cellular membranes that are always present in Eukaryotes, see below). Prokaryotes are single cellular organisms, but note that being a single cell does not mean that an organism is a prokaryote. Being smaller than eukaryotes does not mean that prokaryotes are any less important – for instance it is quite likely that the number of bacteria living in the mouth and digestive tract of a human  are larger than the number of eukaryotic cells in the same individual and many of these bacteria are necessary for a human being to live a normal life (these numbers are rather difficult to estimate, rather a hypothesis). Prokaryotes are sometimes also known as microbes.
eukaryotic cell
A model of a eukaryotic cell (picture taken from On-Line Biology Book )
A eukaryotic cell has a nucleus, which is separated from the rest of the cell by a membrane. The nucleus contains chromosomes, which are the carrier of the genetic material (Section 3). There are internal membrane enclosed compartments within eukaryotic cells, called organelles, e.g., centrioles, lysosomes, golgi complexes, mitochondria among others (see picture above), which are specialised for particular biological processes. The mitochondria are found in all eukaryotes and are specialised for energy production (respiration). Chloroplasts are organelles found in plant cells which produce sugar using light. Light is the ultimate source of energy for almost all life on Earth. The area of the cell outside the nucleus and the organelles is called the cytoplasm. Membranes are complex structures and they are an effective barrier to the environment, and regulate the flow of food, energy and information in and out of the cell. There is a theory that mitochondria are prokaryotes living within eukaryotic cells.
An essential feature of most (prokaryote and eukaryote) living cells is their ability to grow in an appropriate environment and to undergo cell division. The growth of a single cell and its subsequent division is called the cell cycle. However, not all cells continually grow and divide, for example neurons only undergo an initial growth phase. Prokaryotes, particularly bacteria, are extremely successful at multiplying - it is likely that natural selection has favoured single celled organisms able to grow and divide quickly. Multicellular organisms typically begin life as a single cell, usually as a result of fusion of a male and a female sex cell (gametes). The single cell has to grow, divide and differentiate into different cell types to produce tissues and in higher eukarotyes, organs. Cell division and differentiation need to be controlled. Cancerous cells grow without control and can go on to form tumours. Development of single cells into complex organisms is in itself an area of study called developmental biology. This year’s  Nobel prize for Physiology or Medicine has been awarded to scientists for the discoveries of key regulators of the cell cycle.

Cells consist of molecules.

Human ecology and biology

Human ecologists
Human ecologists
Like nature, the human body must maintain a fragile balance in order to thrive. The smallest factor can effect human ecology. Human ecology can be thought of in two ways. There is human ecology in the sense that humans effect their environment and vice verse. However, their is also a fragile ecology inside the human body. This type of human ecology can be thought of as biology ecology. While humans can effect their natural environment the same cant always be said for our effect on our biology ecology. In some sense humans have control over their biology ecology. However, our environment and heredity can also directly effect the fragile balance in our bodies.
Getting lung cancer is an example that could be explained in either way. Human ecology might say that a person got lung cancer because they were a heavy smoker throughout their lifetime or where exposed to known cancer causing material such as asbestos. These days, people are aware of the effects of smoking on the human body and should act accordingly. By smoking or exposing ourselves to known carcinogens, we as the subject, caused ourselves to get lung cancer. However, lung cancer can also be explained through biology ecology. Certainly if the subject smoked and introduced a foreign substance into the human body, they caused the effect on the biology ecology of that subject. However, it could also be said that that persons biology effected the outcome of cancer. There are people that never smoke or purposefully exposed themselves to known carcinogens and they still get lung cancer. Those people may have not had a balance in their biology ecology and could complete no outside action (human ecology) to directly effect the outcome of lung cancer. We cannot always be held responsible for our biology or how it effects us. Regardless of the type of ecology, balance is always a necessity for an organism to thrive.
Human ecology may study the social reason for our smoking habit. It may also study the reason that society has allowed known carcinogens such as lead, to remain in our environment. In studying the social interaction between humans and their environment, human ecologists are able to find solutions to problems that are caused as a direct result of interaction between humans and their environment. Biology ecology may study biological factors in the human body that are out of our control. By studying the relationship between humans and their bodies, ecologists can sometimes find links in other types of ecology and find ways to produce a positive outcome.
Human health depends on many ecological factors. In many cases, humans have the ability to effect those factors. Humans can usually change their environmental factors through geography or through direct environmental contact. While we can not always change our biology, we can change environmental factors that will effect our biology. Humans have the ability to change many factors that effect us both directly and indirectly.

Ecosystems and balance


Ecosystems must maintain a fragile balance for the health of all of the organisms contained within. There are different ecosystems throughout the world and each has its own unique residents. For instance, the ecosystem in a rain forest will have some species of frog that are not found in any other ecosystem in the world. There are also some species of frog that are common to many ecosystems worldwide. Many things can destroy the health of an ecosystem. For instance, pollution can adversely effect an ecosystem. Habitat destruction is also an issue for organisms within an ecosystem. Food scarcity is also an issue for the health of any ecosystem.
Every organism contained within an ecosystem has a purpose. However, there are sometimes foreign entity’s introduced into an ecosystem. This can have a devastating effect on the ecosystem. Organisms work together to create optimal conditions for those that live in that ecosystem. For example, it is likely that each organism is a food source for another organism. While there will be some organisms at the top of the food chain, there must also be some at the bottom. Certain creatures, such as worms, eat organisms that are too small for the human eye to see, while larger creatures will feed on creatures that we are more familiar with, such as a lion eating a bird. Because of the food chain, the health of even the smallest creature will have an effect on the largest of creatures. If the creatures at the bottom of the food chain have poor health or carry disease, this will directly effect the health of the creatures that use them as a food source. If a creature at the top of the food chain becomes ill and die, the population of other creatures may grow too large.
There is an obvious ripple effect on an ecosystem when even one resident is effected by a single environmental factor. If for example, the population of one species were to exceed its usual numbers, they would in turn, require more abundant food sources. When their food sources begin to dwindle, they may begin looking for new food sources, directly effecting the food sources of another organism. A good example of this is the population of the white-tailed deer in New Jersey and surrounding states. If allowed to continue to produce at their current rate, deer would starve to death and succumb to disease at a much higher rate than if their numbers were as they should be. One solution to cutting the number of the deer in the area is hunting. Another solution is to introduce birth control. However, the population has already caused havoc for its ecosystem. Deer have run out of food in some areas, thereby, effecting the food source of other creatures, such as rabbits. The ecosystem cannot support deer at their current population without adverse effects for the rest of the ecosystem.
Ecosystems around the world have issues that adversely effect their health. While some of these disruptions are due to environmental factors, many are cause by human interference. We must work to live our lives with minimal interference to our surrounding ecosystems. This in turn, assures the health of ours.

Endangered species

Endangered species
Endangered species
There are many endangered species around the globe. Many things effect the survivability of a species. There are genetic components which effect their ability to adapt to their environment as well as mutations that can directly result in their destruction. Pollution is another cause of species disappearing from the planet. While some factors that effect a species survival are beyond our control, there are things we can do to slow the process. Invasive species are a problem worldwide and in a lot of ways, it is our fault. Whether or not we directly introduced an invasive species into an environment, we can be responsible for controlling or eradicating it once it is introduced.
Some invasive species arrive on their own by hitching a ride with either another species or with humans. There has been an indirect introduction of many species through travel. Creatures come with us on airplanes, boats, trains and cars. In some cases, it is because a passenger does so on purpose, by concealing the creature to bring home as a pet. But more frequently, we may not notice the extra passengers when we leave for our destination.
Invasive species take over food sources, fight for habitat and can also carry or spread disease that can wipe out entire populations. While a grey squirrel in the US may have a natural immunity to a disease, one in the UK may not. By introducing that disease to the UK, you may inadvertently wipe out the entire squirrel population in the UK. In the UK the red squirrel is an endangered species, while the grey squirrel is an invasive species which has caused many difficulties in the survival of the red squirrel including the spread of disease.
We have also introduced some invasive species on purpose. When you are planting seeds in your garden, do you wonder how that plant will do in your climate? If there is any question as to the viability of a plant in your region, chances are, the plant shouldn’t be here. That plant may spread and take over large areas of land and it may also put other species in danger . We have also introduced invasive species in order to destroy another. Some places have introduced predators to lower the population of a prey animal. While it may be effective at first, it is possible that the new species has no natural predator in its new habitat and its population will also get out of control. It is also possible that he introduced species will find a new food source and over indulge. This process has been linked to the placement of several species on the endangered species list.
Two problems for any ecosystem are endangered species and invasive species. While they are two opposite sides of the coin, the two can have a direct correlation. Invasive species can be the cause of another becoming an endangered species. As with many environmental factors, gaining or losing a species can have a devastating effect on the health of any ecosystem.

Human Biology

Human Biology
Human Biology
Learning the basics of human biology can be a complicated process. However, although difficult, biology genetics are considered to be a very interesting field to research, because of the nature of the work. Human biology is known as the scientific study of the body itself: how it works and what its made of. Unlike many other areas of biology which combines several areas into one, human biology concentrates specifically on people.
• The systems of the human body is considered to be part if its structure. Studying human biology is based on studying the bodily structure of a person. The building block of a living organism is called a cell. Cells combine to form larger structures called tissue. When learning about human biology, an individual may be required to do research with a microscope to look at these cells and tissues. A microscope is considered to be the most important tool to use when learning about human biology and biology genetics.
• One of the first things that an individual learns about human biology is that there are ten systems within the human body. These are the skeletal system, the excretory system, the reproductive system, the muscular system, the digestive system, the nervous system, the respiratory system, the immune system, and the endocrine system. A human being needs all those systems to be working in order to live, with the exception of the reproductive system. Human biology is often studied to learn about the causes, effects, and possible treatments of different diseases. Diseases will attack one of these systems when they begin to form. Some effects of a disease will be minor and others serious: this depends on the placement and the strength of the disease.
• Human biology concentrates on how the bodies’ cells, tissues, organs, and systems work together to form a human body. In biology, genetics is the type of study that covers the heredity and evolution of all life forms. Genetics is a cornerstone of human biology knowledge and study. Scientists have discovered that humans mostly all have the similar characteristics of things like eyes, a mouth and a nose. But in biology, genetics control how individuals look and live. Human biology relies particularly heavily on genetics since a humans genes determine peoples’ differences like eye color and hair color.
When studying biology, genetics and human biology is two complicated yet important subjects. Understanding how the different systems within the human body reacts with each other is an important part of understanding any basic knowledge of human biology.

RNA biology in eukaryotes

The Virtanen lab has moved to the Molecular Biology program. The new webpage can be found at
cleavage_small.gif (40K)

Cell Biology of the Synapse

Our research deals with the molecular cell biology of the synapse, the type of cell-cell junction specialized on signal transmission between nerve cells. Our laboratory has newly identified a number of protein components of synapses, and we now investigate how these proteins contribute to the formation and functioning of the nervous system. Our work has also contributed to the understanding of nervous system diseases. Dealing with the molecular functioning of a biological system as complex as the nervous system, our research is very interdisciplinary, employing molecular, morphological, electrophysiological and genetic techniques, and spans several levels of complexity (protein structure, protein interactions, regulatory mechanisms, cellular physiology, whole organisms in the form of genetically modified mice).

Acz-Doppel-Synapse.jpg (423K) cover1a.jpg (1345K)
The protein, aczonin, concentrates at the active zones of two synaptic terminals contacting a dendrite (immuno electron microscopic image by M.M. Laue)Overexpression of the protein, paralemmin, induces fibroblasts to form dendritic processes and long filopodia (immunofluorescence microscopic image by C. Kutzleb)

New Population Of Iberian Lynx Raises Hope For Species' Survival

ScienceDaily (Oct. 26, 2007) — Spanish authorities have announced they have discovered a previously unknown population of Iberian lynx, triggering hope for one of the world's most endangered cat species, said World Wildlife Fund.

"We are excited and amazed by this discovery," said Luis Suarez, head of WWF's Species Program in Spain. "However, we are a long way from saving the Iberian lynx from imminent extinction."
It appears that the new population was discovered in previously unsurveyed estates in Castilla - La Mancha (Central Spain). This Iberian community is one of the most sparsely populated of Spain's autonomous communities.
At present, the exact numbers and location of the newly discovered population are being kept confidential, but the population is thought to be made up of both adults and cubs.
Until the exact location is known, conservationists cannot confirm if this population is genetically distinct from the larger and more stable population of lynx found in Andujar (South).
According to the most recent comprehensive survey prior to this discovery, there were about 100 adult Iberian lynx in two isolated breeding populations in southern Spain. The population is thought to have since risen to some 110 adults.
The Iberian Lynx faces myriad threats - a lack of prey, accidental deaths from cars and trucks on Spanish roads, and new construction work destroying habitats.
WWF is calling for all Lynx habitat to be covered by the EU's Natura 2000 Program, which offers the strongest level of protection in Europe, something that still hasn't happened despite years of petition.
"We hope this discovery reinvigorates action in Spain to save the world's most endangered cat species. If Europe cannot take responsibility for Europe's 'tiger', then shame on us all," Suarez added.

Vibrio Bacteria Found In Norwegian Seafood And Seawater


ScienceDaily (Feb. 24, 2009) — While working on her doctorate, Anette Bauer Ellingsen discovered potentially disease-causing vibrios (Vibrio cholerae, V. parahaemolyticus and V. vulnificus) in Norwegian seafood and inshore seawater.

Anette Bauer Ellingsen studied the occurrence of potentially pathogenic vibrios in Norway. These species include the cholera bacterium (V. cholerae) and the lesser-known species V. parahaemolyticus and V. vulnificus. All of these species may cause disease in people who eat raw or lightly-cooked seafood, and they can also cause extremely serious wound infection.

In Japan, V. parahaemolyticus is one of the most common causes of food poisoning, due to the Japanese predilection for sushi. In the USA, food poisoning caused by this bacterium is primarily associated with eating oysters.
Vibrio vulnificus is also associated with oyster eating, and this bacterium causes the greatest number of deaths from seafood poisoning in the USA.
That these bacteria also occur in Norway was previously unknown, and this is the first time that V. cholerae and V. vulnificus have been isolated from the Norwegian environment. All of the three vibrios were demonstrated in Norwegian mussels (at fewer than 100 bacteria /gram) and in Norwegian seawater (up to 30,000/litre) during the course of the study. They were first and foremost demonstrable when the water temperature rose above 20°C.

"Dangerous" and "not so dangerous" forms
It's important to emphasise that there can be big differences in pathogenicity within a species. Both V. cholerae and V. parahaemolyticus have their "dangerous" and "benign" variants, based on the toxins they produce. All V. vulnificus are assumed to be more or less equally dangerous, primarily in people with predisposing illnesses such as diabetes or hepatitis, and for people with weakened immunity.
Part of Anette Bauer Ellingsen's work was to investigate whether the "dangerous" variants of V. cholerae and V. parahaemolyticus occur in Norway. None of the cholera toxin-producing variants of V. cholerae were found among the Norwegian samples. However, it was discovered that some of the V. parahaemolyticus bacteria produce a toxin liable to cause diarrhoea.
The study showed that the danger of food poisoning posed by vibrios in Norwegian food products is extremely small. Nonetheless, toxin-producing V. parahaemolyticus was demonstrated, so one should be careful when eating raw or lightly-cooked seafood, for example, oysters.

Recreational activities and sore infection
In fact, the greatest risk of infection from vibrios is not food. There is possibly a greater chance of being infected in connection with recreational activities such as swimming or handling marine fish and shellfish in periods with high water temperature. All of the bacteria that were discovered during this study are liable to produce serious wound infection, especially in people with reduced immunity.
The study was carried out under the auspices of the Norwegian School of Veterinary Science, The Norwegian Food Safety Authority and the The Fishery and Aquaculture Industry Research Fund.
Anette Bauer Ellingsen B. Sc. (hons) defended her thesis, entitled " Vibrio parahaemolyticus, V. cholerae and V. vulnificus in Norway, with special attention to V. parahaemolyticus", on December 22, 2008, at the Norwegian School of Veterinary Science.

Why a Cloned Cat Isn't Exactly Like the Original: New Statistical Law for Cell Differentiation


ScienceDaily (Dec. 15, 2010) — Why does a cloned cat looks different from the original? A new answer to that question has been found by researchers at the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. Using computer simulations and theoretical calculations they discovered a new statistical law.

It explains the simplest and therefore probably the most widespread mechanism, by which a growing population of genetically identical cells forms groups performing different functions. Under certain conditions, a population of reproducing cells can spontaneously divide into two groups with distinctly different functions. The researchers have since long been looking for the reasons of such a spectacular process but the mechanisms found so far were complicated and did not explain all observed cases.

Theoretical calculations and computer simulations carried out by scientists from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw provided the simplest explanation. "We discovered a statistical law that is responsible for cell differentiation," says Dr Anna Ochab-Marcinek from the IPC PAS.

The new statistical mechanism will possibly illuminate one of the sources of bacteria's resistance to antibiotics and help explain why monozygotic twins and cloned organisms are not their identical copies. A paper describing the discovery has just appeared in the Proceedings of the National Academy of Sciences.
In the middle of the last century, laboratory studies had shown that an Escherichia coli population could divide into two groups with one of them showing expression of a specific gene, e.g., the gene responsible for production of an enzyme to digest a specific type of sugar, whereas in the other group the same gene remained inactive. The effect is known in science as population bimodality. The observation was intriguing, as all the cells had the same DNA and were kept under the same conditions. Moreover, despite the lack of changes in the gene set, subsequent cell generations were able to inherit new functions. The researchers from the IPC PAS set themselves the task of discovering the simplest possible mechanism that could be responsible for such unexpected behaviour in cells. They carried out theoretical calculations followed by a verification with a series of Monte Carlo simulations. The theoretical and computational work involved the most important chemical reactions that take place in a living cell.

The genetic information in cells is contained in the DNA structure, the proteins, however, are synthesised based on the sequences in the messenger RNA (mRNA). To produce a protein encoded in a gene, the information must be first transferred from DNA to mRNA. The transfer process (transcription) is controlled by molecules called transcription factors. After attachment to DNA, these molecules may repress (then they are called repressors) or promote (activators) the gene translation. "A cell is a bag with a plenty of various molecules, moving randomly due to thermal motions. So, it may happen that after cell division one daughter cell will include more transcription factors than the other," describes Dr Anna Ochab-Marcinek from the IPC PAS. Using computer simulations, the researchers analysed, how a different number of repressors or activators affects the cell population.

The computer simulations carried out at the Institute of Physical Chemistry of the PAS mapped fluctuating concentrations of proteins produced by each cell during the development of population. As the number of molecules of a specific type in a cell is relatively low, the cell divisions result in an unequal distribution of repressors or activators among the daughter cells. As a result, the cell population growth leads to appearance of cells that produce a significantly more protein than other cells or do not produce it at all.

The dependence between the production rate of a specific protein and the number of repressors or activators in a cell is not proportional. The effect is referred to as a nonlinearity as the plot showing how the number of protein molecules depends on the number of transcription factors (the so called transfer function) is not a straight line. The researchers from the IPC PAS have shown that the nonlinearity is responsible for formation of two distinct groups in the population: in one of them the gene is active, whereas in the other -- it is not.

The division of a cell population into two groups is of significant evolutionary importance. The differentiation increases the survival chance for a part of the population, if any changes unfavourably affecting one of the groups would occur in the environment. "It is known that bacteria mutate and become more resistant to drugs. We have shown the simplest mechanism by which the very nature of bacteria and the underlying laws of statistics increase the survival probability of at least a part of the population, even if no mutations have occurred," says Dr Ochab-Marcinek.

The researchers from the IPC PAS have also introduced a simple method of geometric construction that can be used to predict when a specific cell population can develop a cell differentiation. The method consists in plotting of a straight line that intersects the axes of the coordinate system at points corresponding to the measured burst frequency of the transcription factor production in a population and the magnitude of these bursts. If the straight line intersects the gene response curve -- known from the laboratory measurements -- then the cell population starts to develop bimodality. With such a simple geometrical operation one can easily explain the results of earlier experiments performed by other research groups, for instance the appearance of bimodality in population only at specific antibiotic concentrations.

"As the mechanism we discovered is the simplest among all possible ones, we suppose that, unavoidably, it is very common in cells," says Dr Marcin Tabaka, a co-discoverer of the phenomenon. "The statistical law we discovered describes how a random disorder inside individual cells transforms into an order leading to a differentiation of population that is of benefit for its survival," sums up Dr Ochab-Marcinek.
The project has been completed under a TEAM Programme of the Foundation for Polish Science, co-founded by the EU European Regional Development Fund (TEAM/2008-2/2).

New Variants Of Diarrhea-Causing Toxins Found In Seafood


ScienceDaily (Mar. 3, 2009) — Trine-Lise Torgersen described in her doctorate new variants of diarrhoea-causing toxins in mussels, oysters and crabs. These variants are assumed to be less virulent than the forms of diarrhoea toxin we are already familiar with and were found in varying amounts in the different types of seafood examined.

For her doctoral thesis, Trine-Lise Torgersen looked at how toxins from algae are taken up and metabolised by mussels and oysters, and also by crabs that eat mussels. During an algal bloom in the ocean, toxins produced by the algae can be taken up by shellfish that filter seawater for food, and the result for the consumer can be diarrhoea, vomiting and nausea. Some of these algal toxins are already well-known.

Torgersen studied how mussels and oysters process some of these toxins, and found that more types of toxin are produced than we previously have been aware of. She also looked at how the toxins are taken up and metabolised by crabs that eat poisonous shellfish. The results indicate that a particularly complex pattern of toxins is formed in these species, and that the levels of modified diarrhoea toxins may be higher than the levels of the known forms, especially in oysters and crabs.
The current procedure for measuring algal toxins involves converting all of the variants back to the original molecule, and then measuring the total amount of original toxin. However, since the modified variants of the toxins can be assumed to be less virulent than the original forms, measuring all of the substances as if they were the original may overestimate the toxicity of the seafood. Therefore, when estimating the risk of food poisoning from shellfish, levels of variants of the original toxin in the various types of seafood should be considered.

In her thesis, Torgersen showed that oysters, mussels and crabs differ regarding the forms of diarrhoea toxin they contained, and also regarding how much of modified variant is present relative to the original toxin. In particular, crabs and oysters contained very little of the original substances and nearly all of the toxin had been converted to other forms. Torgersen therefore recommends that different types of seafood need to be considered individually when estimating the risks of food poisoning from seafood.

Secrets Of Red Tide Revealed


In the Aug. 31 cover story of Science, the MIT team describes an elegant method for synthesizing the lethal components of red tides. The researchers believe their method approximates the synthesis used by algae, a reaction that chemists have tried for decades to replicate, without success.
Understanding how and why red tides occur could help scientists figure out how to prevent the blooms, which cause significant ecological and economic damage. The New England shellfish industry, for example, lost tens of millions of dollars during a 2005 outbreak, and red tide killed 30 endangered manatees off the coast of Florida this spring.
The discovery by MIT Associate Professor Timothy Jamison and graduate student Ivan Vilotijevic not only could shed light on how algae known as dinoflagellates generate red tides, but could also help speed up efforts to develop cystic fibrosis drugs from a compound closely related to the toxin. Red tides, also known as algal blooms, strike unpredictably and poison shellfish, making them dangerous for humans to eat. It is unknown what causes dinoflagellates to produce the red tide toxins, but it may be a defense mechanism, possibly provoked by changes in the tides, temperature shifts or other environmental stresses.
One of the primary toxic components of red tide is brevetoxin, a large and complex molecule that is very difficult to synthesize.
Twenty-two years ago, chemist Koji Nakanishi of Columbia University proposed a cascade, or series of chemical steps, that dinoflagellates could use to produce brevetoxin and other red tide toxins. However, chemists have been unable to demonstrate such a cascade in the laboratory, and many came to believe that the "Nakanishi Hypothesis" would never be proven.
"A lot of people thought that this type of cascade may be impossible," said Jamison. "Because Nakanishi's hypothesis accounts for so much of the complexity in these toxins, it makes a lot of sense, but there hasn't really been any evidence for it since it was first proposed."
Jamison and Vilotijevic's work offers the first evidence that Nakanishi's hypothesis is feasible. Their work could also help accelerate drug discovery efforts. Brevenal, another dinoflagellate product related to the red tide toxins, has shown potential as a powerful treatment for cystic fibrosis (CF). It can also protect against the effects of the toxins.
"Now that we can make these complex molecules quickly, we can hopefully facilitate the search for even better protective agents and even more effective CF therapies," said Jamison.
Until now, synthesizing just a few milligrams of red tide toxin or related compounds, using a non-cascade method, required dozens of person-years of effort.
The new synthesis depends on two critical factors-giving the reaction a jump start and conducting the reaction in water.
Many red tide toxins possess a long chain of six-membered rings. However, the starting materials for the cascades, epoxy alcohols, tend to form five-membered rings. To overcome that, the researchers attached a "template" six-membered ring to one end of the epoxy alcohol. That simple step effectively launches the cascade of reactions that leads to the toxin chain, known as a ladder polyether.
"The trick is to give it a little push in the right direction and get it running smoothly," said Jamison.
The researchers speculate that in dinoflagellates, the initial jump start is provided by an enzyme instead of a template.
Conducting the reaction in water is also key to a successful synthesis. Water is normally considered a poor solvent for organic reactions, so most laboratory reactions are performed in organic solvents. However, when Vilotijevic introduced water into the reaction, he noticed that it proceeded much more quickly and selectively.
Although it could be a coincidence that these cascades work best in water and that dinoflagellates are marine organisms, water may nevertheless be directly involved in the biosynthesis of the toxins or emulating an important part of it, said Jamison. Because of this result, the researchers now believe that organic chemists should routinely try certain reactions in water as well as organic solvents.
The research was funded by the National Institute of General Medical Sciences, Merck Research Laboratories, Boehringer Ingelheim, and MIT.
"This is an elegant piece of work with multiple levels of impact," said John Schwab, who manages organic chemistry research for the National Institute of General Medical Sciences. "Not only will it allow chemists to synthesize this important class of complex molecules much more easily, but it also provides key insights into how nature may make these same molecules. This is terrific bang for the taxpayers' buck!"

Earthworms Found To Contain Chemicals From Households And Animal Manure

ScienceDaily (Feb. 27, 2008) — Earthworms studied in agricultural fields have been found to contain organic chemicals from household products and manure, indicating that such substances are entering the food chain.

Manure and biosolids, the solid byproduct of wastewater treatment, were applied to the fields as fertilizer. Earthworms continuously ingest soils for nourishment and can accumulate the chemicals present in the soil.
The chemicals investigated are considered indicators of human and animal waste sources and include a range of active ingredients in common household products such as detergents, antibacterial soaps, fragrances, and pharmaceuticals. Some of the detected chemicals are naturally occurring such as plant and fecal sterols and fragrances. All of these chemicals tend to be concentrated in the municipal waste distribution and disposal process and are referred to as anthropogenic waste indicators (AWI).
U.S. Geological Survey Scientists and their colleague from Colorado State University at Pueblo published their new findings today in Environmental Science and Technology. The results demonstrate that organic chemicals introduced to the environment via land application of biosolids and manure are transferred to earthworms and enter the food chain.
Scientists found 28 AWIs in biosolids being applied at a soybean field for the first time and 20 AWIs in earthworms from the same field. Similar results were found for the field where swine manure was applied. Several compounds were detected in earthworms collected both from the biosolids- and manure-applied fields, including phenol (disinfectant), tributylphosphate (antifoaming agent and flame retardant), benzophenone (fixative), trimethoprim (antibiotic), and the synthetic fragrances galaxolide, and tonalide. Detergent metabolites and the disinfectant triclosan were found in earthworms from the biosolids-applied field, but not the manure-applied field.
Biosolids are made from the sludge generated by the treatment of sewage at wastewater treatment plants. Biosolids are used as fertilizer by farmers, landscapers, and homeowners when it satisfies U.S. Environmental Protection Agency and local regulations for nutrient, metal, and pathogen content. About half of the 8 million dry tons of biosolids produced in the U. S. each year are applied to the land. Biosolids have been found to be rich in AWIs compared to levels in wastewater treatment plant effluent. In addition, the 1.3 million farms raising livestock in the U. S. generate an estimated 500 million tons of manure annually, much of which is also applied to fields as fertilizer for crops.
This study is part of a long-term effort by the USGS Toxic Substances Hydrology Program to determine the fate and effects of chemicals of emerging environmental concern in aquatic and terrestrial environments, and to provide water-resource managers with objective information that assists in the development of effective water management practices. It was funded in part by a Research Corporation Cottrell College Award and a Faculty Research Grant from Eastern Washington University.

New Discoveries Make It Harder for HIV to Hide from Drugs

ScienceDaily (Dec. 15, 2010) — The virus that causes AIDS is chameleon-like in its replication. As HIV copies itself in humans, it constantly mutates into forms that can evade even the best cocktail of current therapies. Understanding exactly how HIV cells change as they reproduce is key to developing better tests and treatments for patients.

In the Journal of Biological Chemistry and Nature Structural & Molecular Biology, MU microbiologist and biochemist Stefan Sarafianos, PhD, reveals new findings that shed light on how HIV eludes treatment by mutating. His discoveries provide clues into HIV's mechanisms for resisting two main families of drugs.
"These findings are important because identifying a new mutation that affects HIV drug resistance allows physicians to make better decisions and prescribe the proper drugs," Sarafianos said. "Without that knowledge, therapy can be suboptimal and lead to early failure."
Patients with HIV are routinely tested to track the levels of the virus and immune cells in their body. Results of the tests help physicians gauge the health of their patients and prescribe the right mix of antiviral drugs. The drugs help prevent the spread of HIV in patients by inhibiting the virus' ability to replicate.
Sarafianos' lab determined the biochemical properties that allow strains of HIV with a specific mutation -- the N348I mutation -- to escape inhibition despite treatment with Nevirapine. The drug is commonly used in combination with other antiviral medications to decrease the amount of HIV in the blood. As a result of Sarafianos' discovery, at least one major company that manufactures HIV mutation-testing kits has modified its test to detect the N348I mutation.
Sarafianos' recent findings resulted from research supported by five National Institutes of Health grants. He recently received another $417,000 award from the NIH to assist him in developing modified antibodies for HIV therapy.
"Our latest efforts to design broadly neutralizing antibodies against HIV will hopefully expand our toolbox against the virus, which remains a constantly moving target," Sarafianos said.
Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.