Antibiotic resistant bacteria from the nature

November 28, 2012, 3:39 am

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Antibiotics are naturally or synthetically produced drugs used for treatment of wide spectrum of microorganisms. As a result of uncontrolled antibiotics use, modern society faced antibiotic resistance phenomenon. Genes providing resistance could be transferred inside one or in between different species. Newly developed resistant organism is called superbug and it is usually resistant to more than one antibiotic. Number of newly created drugs couldn’t follow fast tempo of antibiotic resistance development. Medicine doesn’t have a solution for this problem yet; most experiments focused on this issue are dealing with genetic analysis of the resistant bacterial strains. Discovery of resistant microorganisms at the place where they were least expected, could change direction of the further investigation.

Lechuguilla cave is located in the Carlsbad Caverns National Park in New Mexico. It is discovered in 1986 and it is 7th longest known cave (>209 km in length). Due to unique appearance, only specially approved scientific research teams can cross its borders and explore it further. Besides interesting geological formation and cave decorations, chemolithoautotrophic bacteria were found inside. Laboratory experiments on sampled bacterial films revealed one important characteristic - they are antibiotic resistant. Out of 500 bacterial strains, 93 managed to survive medium containing 26 different antibiotics. 70% of 93 tested strains can grow when exposed to 3 or 4 different classes of antibiotics. 3 strains proved to be distant relatives of anthrax species and they managed to survive when exposed to 14 out of 26 tested antibiotics.

Lenchuguilla cave is old between 4 and 7 million years. Specific location and isolated entrance prevented water and modern era inventions from reaching the cave. That means that organisms in the cave have never been exposed to drugs, chemicals and other substances and they didn’t have the reason to develop antibiotic resistance for successful survival in the past. Antibiotic resistance was considered to be consequence of genetic mutation that allows bacterium to survive harsh environmental conditions. Mutated genes are transferred to the next generation through simple cell division, horizontally via plasmids or by viruses. This experiment showed that ancient non-pathogenic bacterial strains contain genes that provide antibiotics resistance even if they never have been exposed to antibiotics. New hypothesis about antibiotic resistant genes emerged: if those genes are not result of genetic mutation as a consequence of selective natural pressure to survive negative environmental conditions, than those genes must have been created during long evolutionary period, probably lasting thousands of years, for some other reason. Question is: why they developed and how those genes managed to reach pathogen strains of bacteria that develop antibiotic resistance in hospitals and animal farms today? Couple theories could explain this riddle. Maybe antibiotic resistant genes are created to provide some other beneficial characteristic essential for bacterial survival and ability to survive antibiotic exposure is simply a coincidence (related traits). Maybe cave contains some natural antibiotic that are still not found. Or, maybe, antibiotic resistant genes emerged when different bacterial species fight against each another in “chemical war” for food and environment. No matter which theory is correct, this revelation is important for future experiments focused on bacterial resistance. Detailed genetic analysis of the newly discovered bacterial strains will provide necessary information on their survival mechanism and possibly help combat future bacterial resistance cases.

Microorganisms resistant to various antibiotics could be seen everywhere in the nature. Unlike Lenchuguilla cave, they are result of careless and incautious human behavior. Garbage and its disposal is problem even when it comes to the medical waste. A lot of drugs end up in the sewage and enter feeding chain easily. Drugs could reach birds living on Antarctica or sharks swimming in the sea. Bacteria found in those animals prove that modified and fortified microorganisms could induce disaster in the natural population of animals as they couldn’t be eliminated by mechanisms that were efficient in the past. Besides affecting one animal species, they could be transferred from one organism to another and even end up in human plate.

Unfortunately, in the battle against antibiotic resistance, microorganisms are still winning. If we want to save human population and the ecosystems throughout the world, we need to find fast and efficient method as soon as possible.

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Decoded domestic pig genome

November 28, 2012, 9:35 am

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Domestic pig (Sus scrofa) originates from the wild boar. It is domesticated ~13 000 years BC. People cultivate pigs mainly for their meat. Their bones and hair are used for brush production. Some types of pigs are popular nowadays as pets. Pigs are intelligent animals that share a lot of anatomical similarities with humans, which is the reason they are used for organ transplantations. Domesticated pigs could be found everywhere. They are the most numerous large mammals on the Earth with over 1 billion pigs present at each moment. Their genome is finally decoded.

Last mutual ancestor for pig and human lived ~ 97 million years ago. Sus scrofa emerged in East Asia ~ 3.5 million years ago. Pig has 18 autosomal chromosome pairs and one sex determining pair. There are 21,640 protein coding genes, and 1,478 mitochondrial genes. Beside protein coding genes, 2,965 non-coding RNA sequences and 380 pseudogenes were identified. 15,072 protein coding sequences are mutual for various species and 3,959 are pig specific. Identification of the porcine endogenous retroviruses (PERVs) was important because they could be transfered to humans during organ transplantations. Their number exceeds 175 in porcine genome. Analysis of 9,000 orthologs (genes that share same ancestor) in six species (dog, human, mouse, horse, cow and pig) provided info on genetic modulation during evolution. 311 proteins in pig were marked as quickly evolving. Genes associated with psychiatric disorders, various cancers, cardiovascular disease, immune diseases and metabolic and neurological disease in humans were easily located in the porcine genome. Altered proteins typical for certain human diseases were analyzed in pigs also. Aligned human and pig orthologous proteins showed 1,393,618 positions where amino acid differ. 112 substitutions are associated with human diseases such as: diabetes, obesity, Parkinson’s disease, Alzheimer’s disease, dyslexia… 32,548 non-sense mutations identified in 48 pigs revealed 6 protein variant that induce disease in humans. Another 157 non-sense mutations in 142 genes result in following human diseases: corneal dystrophy, hemolytic anemia, epidermolysis bullosa, laryngoonychocutaneous syndrome, paroxysmal nonkinesigenic dyskinesia 1, mental retardation, susceptibility to autoimmune disease development and sepsis, congenital contractural arachnodactyly, citrullinemia and pancreatic carcinoma.

Genetic similarity between humans and pigs will help scientists find better therapeutic solutions for existing diseases. Even before genetic similarity between pigs and humans was established, these animals were used as biomodels because their physiology, biochemistry and anatomy match perfectly to humans.

Retinitis pigmentosa is severe degenerative ocular disorder associated with progressive loss of rods, leading to night blindness first (usually in puberty), followed by progressive loss of cones resulting in complete blindness around the age of 40. It is not curable, and until recently, animal model used for disease analysis was transgenic mouse. Besides being too small for surgical operations, number of cones in two species is different. Development of a transgenic pig helped experiments a lot. Disease phenotype resembles human disease completely; first symptoms appear in 5-6 months old pig and complete disease progression is achieved after 20 months.

Cystic fibrosis is another example of severe genetic disorder that was easily established in the pig model. Disease disrupts normal functioning of lungs, pancreas and intestines, and leads to fibrous scars and cyst formation. It is characteristic for caucasians; one out of 25 European descendents carry allele for cystic fibrosis resulting in high prevalence of disease in European Union (one out of 2000-3000 babies will develop cystic fibrosis). Few treatment methods exist but disorder is not curable yet. Again, mice weren’t the perfect models for cystic fibrosis analysis because they don’t exhibit lung and pancreatic disorders (responsible for highest morbidity and mortality rate in humans). Transgenic pigs with cystic fibrosis were easily developed. Viral vector carrying altered genetic particle (delta F508 mutation, responsible for cystic fibrosis) will target cystic fibrosis transmembrane receptor gene in pig fetal fibroblast. Nucleus from the modified fibroblasts will be transferred to oocyte prior fertilization. Once heterozygous pigs (carrying altered cystic fibrosis transmembrane receptor gene) are born, they could serve as ideal models for future studies in the field of cystic fibrosis.

Humans and pigs are tightly connected for thousands of years. These animals were exploited in numerous ways throughout the history. Now when their genome is decoded they will probably accelerate research associated with untreatable human diseases and potentially provide medical solutions in the near future.

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Gluten free wheat is produced!

November 29, 2012, 4:40 am

≫ Next: how predict which aminoacid form secondary structure

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Gluten is a plant protein. It provides elasticity, shape and chewy texture of pastas and other products made of plants containing gluten such as wheat, barley and ray. Prolamin and gluten are main wheat proteins (constitute 80% of total protein content). Plant uses those proteins as energy source during germination. They are equally good energy source for people. Wheat is a staple food for 20% of the people around the world. Gluten is especially important for vegetarians because plant proteins are only source of proteins for them. Besides being consumed directly, plant proteins are used as additives for numerous dietary products: to improve physical characteristic of the food, its consistency, texture, quantity…. Product labels usually contain information about gluten content. This protein is also used in cosmetic industry (hair and dermatology products) and in pet food production.

Gluten is important nutritional ingredient, but it is associated with couple of disorders that affect a lot of people around the globe. Those are wheat allergy, celiac disease and gluten sensitivity. Wheat allergy results from increased sensitivity toward some of the wheat proteins; it is manifested by nausea, urticaria, atopy… as a consequence of increased level of IgE and mast cells. Both prolamin and gluten might trigger allergy reaction, but gluten induced wheat allergy is more common. Gluten molecule is composed of gliadin and glutinen fractions. There are 9 subunits of low molecular weight glutinen that are known triggers of allergy reaction. When gluten sensitivity exists, body reacts to gliadin fraction by producing large amount of anti-gliadin antibodies (IgA and IgG). Symptoms of gluten sensitivity are bloating, diarrhea, stomach discomfort and pain. Gluten sensitivity is a less severe than celiac disease - severe autoimmune disorder of the small intestine. Celiac disorder can be confirmed through biopsy and blood analysis. Typical manifestations of celiac disease are fatigue, nausea and diarrhea, result of intestinal microvillus shortening. Disorder can develop at any time during the lifetime and so far, only solution for people diagnosed with celiac disease is strict gluten free diet. Between 0.5 and 1% of people in the USA and 22.4 million of people around the world are diagnosed with celiac disorder.

Gluten can be found everywhere, both in products that normally contain gluten (wheat and its products) and products that are boosted with gluten during industrial processing (yogurt, ice cream…). Due to increased rate of celiac disease in modern society, a lot of food companies oriented toward gluten free food production. While waiting for gluten free industry to develop, scientists are looking for a solution through genetic engineering of the plants. Team of international scientists recently published article on the latest achievement in this field, revealing that gluten free wheat is successfully created.

To obtain gluten free plant, scientists first had to identify mechanism of gluten production. This protein is essential nutrient during embryonal development. Gluten is produced after couple of genes are expressed. Enzyme that triggers expression of gluten associated genes is called DEMETER (DME). DME encodes 5-methylcytosine DNA glycosylase, enzyme responsible for transcriptional activation of gliadins and low molecular weight glutenins (via demethylation of their promoter site). When DME was suppressed by 85.6%, gluten production in the endosperm was decreased by 76.4%.

Study focused on DME homeologs sequences, their evolutionary changes, similarity between different plant species and potential silencing methods... Result was first gluten free plant. In the phylogenetic analysis, when DME sequences were compared between rice, Arabidopsis, barley, wheat and sorgum, it was shown that they are highly (evolutionary) conserved and homology between examined species proved to be high. DME homeologs are cytogenetically mapped in the barley and wheat (located on chromosome 5 in both species) and cloned. They are responsible for complex transcriptional regulation of gliadins and low molecular weight glutenins. Inverted repeats (known as hair pins) were used to “disable” DME expression. Result was decreased level of alpha, beta and gamma glutenins and glutadins in developing endosperm. Depending on the type of hair pin used and DME homeologs transformed, expression of different glutenins and glutadins family members were suppressed. Ideal plant would be one with completely knockout DME homeologs sequences, resulting in gluten 100% free seed. This is a goal for some future experiments.

After first gluten (almost) free plant is created, next step is assessment of its safety in transgenic mice, gluten sensitivity apes and finally in patients diagnosed with celiac disease.

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how predict which aminoacid form secondary structure

November 29, 2012, 6:48 am

≫ Next: How to accelerate cellulosic biofuel production?

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Hi all,
How do predict what types of secondary structure (left alpha helices, right alpha helices, parallel beta sheet, antiparallel beta sheet) from amino acid sequence?
Reply as soon as possible

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How to accelerate cellulosic biofuel production?

November 29, 2012, 7:55 am

≫ Next: Innovations in the biorobotics field

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Plants could be useful source of biofuel. Ethanol can be derived from lignocelluloses (structural element of the cell wall in plants), from inedible part of the plants, wood or grass. Cellulosic ethanol undergoes longer processing than starch ethanol derived from corn or cane sugar. Advantage of this type of biofuel is mainly in the availability of biomass used and its type; plants used for cellulosic ethanol production are more diverse and have greater productivity compared to ones used in conventional biofuel production. Switchgrass (Panicum virgatum) and Miscanthus (Miscanthus x giganteus) are mostly used due to high productivity rate. Also, cellulosic ethanol decreases green house emission by 85% compared to reformulated gasoline and it is more eco-friendly than starch ethanol (doesn’t affect green house emission at all).

Main obstacle in cellulosic ethanol production lays in complicated extraction procedure. Two mechanisms are applied today: enzymatically triggered cellulolysis (by degrading the cellulose to glucose that will be fermented to ethanol later) and gasification (converting the lignocellulose to carbon monoxide and hydrogen that will be transformed to ethanol via fermentation or chemical catalysis). Due to large size and rigid structure, biomass used for cellulosic ethanol production needs to be processed physically first. This procedure will reduce biomass size. Lignin and cellulose are tightly bound with one another and chemical pretreatment that will release cellulose is essential to provide successful hydrolysis and further processing. By removing chemical barrier, enzymes could digest cellulose maximally and this process is called cellulose liberalization. Hydrolysis can be achieved chemically (using acids) or enzymatically (usually fungi derived enzymes). Enzymes used in hydrolysis have been improved over the years and some companies are developing genetically modified fungi producing enzymes such as cellulose, hemicellulase, and xylanase. Saccharomyces cerevisiae (baking yeast) is mostly used in brewery industry for sugar fermentation. Yeast is often and widely used microorganism that could survive harsh environmental conditions (bacterial metabolites, low pH, and high ethanol level for example). Genetically improved, it can produce ethanol from xylose and arabinose (or from both sugars). Beside yeast, Escherichia coli and Zymomonas mobilis will probably be genetically modified to enhance their fermentation potential for future biofuel productions.

Cellulosic ethanol production could be accelerated thanks to group of scientists and their recent discoveries. Scientists wanted to explore complex structure of the cell and its structural element, and reveal weak points in the currently used method of cellulose ethanol production and finally eliminate them. Using special imagining techniques, cellular architecture was examined on the nanoscale. Enzymes are one of the most important factors in successful ethanol production as they degrade biomass and speed up chemical reactions. This study especially focused on the currently used enzymes to investigate their mechanisms of action and assess potential weak points. Fungus and bacterium derived enzymes were used for evaluation of the cell wall degradation and sugar intermediate production. Exact location of enzymes responsible for degradation and exact digestion spots were discovered. Bacterial enzymes used are organized in large scaffolds prior attacking the cell wall, while fungi derived enzymes attack cellular wall individually. In both approaches, non-sugar particle (lignin) prevents the enzyme from reaching the target (cellulose). Pretreatment that could remove lignin without disturbing established cellular structure would be the optimal for cellulosic ethanol production. Scientists compared the model with large house that needs to be remodeled. If all doors in the house would be removed or left open, workers would be able to reach each room (and desired wall) easily, without wasting time. That approach is opposite to currently used pretreatment method where all spongier carbohydrates are usually removed, resulting in the structure that could easily lose its stability and collapse. When cellular structure is disrupted, resulted half “demolished house” couldn't be easily approached or remodeled. Enzymes work perfectly if they are dealing with structures in their natural environment. By removing unwanted materials from the cellular wall (lignin) without disturbing its biochemical properties and main “skeleton”, enzymes would have optimal working surface and speed of work would be sufficiently increased.

This discovery could optimize biofuel production by changing the direction of the future experiments and operating procedures. Further experiments and even deeper analysis of cellular dynamic and structure will provide more valuable information that could be beneficial for the cellulosic ethanol production.

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Innovations in the biorobotics field

November 30, 2012, 4:14 am

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Idea of fully developed and functional robots that will look and act like humans is not new. People are fascinated by the idea of having their own electronic replica that could perform each task they normally do. According to a lot of Sci-Fi movies, our life would be much easier with robots. Creation of humanoid robot may look like an easy thing to do, but so far - only robots able to perform simple tasks are developed. Those robots don’t contain living parts, they are 100% made of electronics. They are very helpful, especially in medical field. For example, medical snake robot is used for minimally invasive cardiac surgery; it is under the full control of the surgeon during operative procedure.

Fully humanoid robots are still waiting to be developed due to complex human physiology, anatomy and functionality, based on perfectly balanced interaction between millions of cells. Robot that contains both electronic and living part is biorobot. Discipline dealing with biorobots is called biorobotics and it could be described as collective effort of cybernetics, bionics and cellular (genetic) engineering to create artificial organism. Synthetic biology and bionanotechnology are also tightly associated and helpful in the field of biorobotics. While creating artificial organism, scientists work on incorporating natural (biochemical) processes and living cells into electronic device.

Signal transduction propagates the body, affects cell communication, metabolism and all biochemical processes. It is essential for normal functioning of all living organisms. Different type of molecules could act like signal transducers: hormones, neurotransmitters, proteins... Cellular response is triggered when signaling molecule binds directly to the cellular receptor or when enters the cell and induce physiological response inside. Molecules that induce cellular response directly by entering the cell are called second messengers. Nitric oxide (NO) is typical representative of that group. It remains in gaseous form in each cellular environment and enters the cell via diffusion. It is synthesized from arginine and oxygen thanks to nitric oxide synthase enzyme. Once NO enters the cell, it triggers another second messenger - cGMP through the activation of the soluble guanylyl cyclase. List of cascade events and biological processes associated with NO is long; some of the most important are apoptosis, erections, vasodilation, muscle relaxation…

NO is selected as signal transduction molecule for the following biorobotics study due to diversity of roles that plays in living organisms. This is the first time that electronic part wasn’t designed to fit biologic system (cellular part of the robot) -quite opposite thing was performed - cellular component was modified to fit electronic part of the robot. Nitric oxide synthase (eNOS enzyme) was genetically altered. Using the plasmid, light–oxygen–voltage domain was inserted in eNOS gene, resulting in photoactive enzyme formation. Genetically altered cells were attached to platinum electrode. Light triggered enzymatic activity and resulted in NO production. Electrode used in the study was modified by covering the surface with NO sensitive layer that will allow transformation of the generated chemical signals into electric signals. Chinese ovary cells cell line (CHO-K1) was used, simply because these cells express high protein level. Proportion between produced NO and generated electric impulses was easily calculated. This is the first biorobotic model showing successfully established signaling transduction: optical signals trigger chemical signals that are converted in electric signals at the end. Another important characteristic of this model is the ability to self-replicate (since it is formed out of living cells) and to combine incoming signals and calculate overall signal. Described experiment is part of a larger study dealing with bio-hybrid robot called “Cyberplasm”. That robot will be first robot able to swim. Modulated (photosensitive) cells will act like eyes and guide robot in different directions according to the provided light. Scientists are hoping that this robot would be of great help with contaminated water and harsh chemicals. Goal will be to swim, collect needed data and deliver them back. “Cyberplasm” project is still not finished. For now, this robot assembles piece by piece and hopefully, it will not pass much time before it become fully developed.

Next step in biorobotics is establishment of the cellular communication. Besides technical improvements, list of biorobotic associated purposes will probably expand in the near future.

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Genes associated with cancer pathogenesis

November 30, 2012, 8:56 am

≫ Next: Ancient DNA could tell a lot of different stories

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All biochemical processes in the human body are tightly associated with gene expression. When some elements in this complex machinery doesn’t work properly, whole cascade of events will be disturbed, resulting in some kind of pathology. Mutated genes (carrying altered information) could be inherited. List of inherited conditions is long and well studied. Besides classical inherited disorders, a lot of pathologies arise during life. Mechanisms and/or triggers for a lot of different disorders are still waiting to be discovered. Most experiments are focused on DNA material and factors (both intrinsic and extrinsic) that are disturbing various processes on the molecular level. Mostly used model organisms for genetic experiments are fruit fly (Drosophila melanogaster). They are small, have a short and well known life cycle, and could be easily cultivated in the laboratory. Although it may look that insects don’t have much in common with humans, same ancestor and highly conserved genetic sequences allow scientists to analyze wide range of human disorders using Drosophila's genetic material. Latest set of valuable information derived from fruit fly experiment could help scientists in the future fight against cancer.

There are more than 200 different cancer types. With 13% of all registered cases, this is the leading cause of death worldwide (one out of 4 deaths in USA is cancer related). Cancer could affect all body parts, and most commonly affected organs are liver, lungs, stomach, colon, rectum, cervics. Some people have high predisposition to develop certain type of carcinoma (genetically inherited). External factors could greatly accelerate cancer development. Aggressive and toxic chemicals, UV radiation, radioactive elements, injuries, viruses… are usual cancerogenesis triggers. Removal of the cancerous tissue, chemotherapy and immune system boosting are only solutions for people diagnosed with cancer, but chances of winning the battle against the cancer are still small. Metastases are main reason of death because vital organs became affected when cancer start to spread. According to current statistics, number of diagnosed cases will continue rising and it is estimated that number of cancer related deaths will reach 13.1 million by 2030 (in 2008, “just” 7.6 million deaths were cancer related).

Scientists of the Stowers Institute for Medical Research investigate molecular mechanism behind human disease. They recently discovered and published unknown facts associated with cancer pathogenesis. Fruit fly was used as a model organism. Prior genetic expression, DNA needs to be uncoiled so that the transcriptional factors and other proteins could easily approach gene of interest. Methylation and demethylation will determine if “path” to the DNA molecule will be passable. These processes are associated with certain amino acids in histones. Histone complexes are responsible for DNA condensation. Usually, demethylation of histone amino acid residues result in activation of the genetic expression, while methylation prevents genetic expression (repression). Exception from this rule is seen with methylation of the lysine and arginine amino acid residues. When lysine 4 on the histone 3 (H3K4) is methylated - expression is allowed. Same could be applied with arginine residue on histone 3 (H3) and 4 (H4). Protein named Set1/COMPASS induces methylation of the H3K4 complex. It can be mono-, di- or trimethylated, which will determine the potential of genetic enhancer to approach DNA molecule. Trimethylation is associated with transcriptionally active genes. H3K4 monomethylation is associated with genetic expression in the tissue specific manner. Yeast genome has one COMPASS methylase, human genome contains 6 different families while drosophila genome contains 3 COMPASS families. Scientists from the Stowers Institute tested importance of each family by silencing their activity and observing further genetic expression patterns. When Trr complex (short version of Trithorax-related) was silenced, H3K4 methylation was decreased in the whole genome. Silencing the remaining two families didn’t provide the same effect. Further analysis of the Trr complex showed that it is closely associated with the enhancer (activator) of the genetic expression. Without Trr complex, enhancer couldn’t be activated and genetic expression will be suppressed. Two mutated forms of the genes MLL3 and MLL4 are often present in numerous cancer types (lymphomas, colorectal cancer, medulloblastoma, breast cancer) and they structurally highly resemble Trr complex. Using mouse fibroblast lacking MLL3, scientists wanted to examine changes in the methylation. They noticed decreased H3K4 monomethylation (in the enhancer region) when MLL3 was absent. This experiment showed for the first time that MLL3 and MLL4 could be important factors in cancer pathogenesis through activation and deactivation of the specific enhancers.

Precise role and mechanism of action during suppression/activation processes still need to be discovered.

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Ancient DNA could tell a lot of different stories

December 1, 2012, 3:12 am

≫ Next: Insect transmitted diseases could be prevented by symbiotic bacteria

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Information or “recipe” for every living organism is contained in DNA material (or RNA, in some viral species). DNA is composed of nucleotides aligned in two chains that bond together through complementary base pairing. Result is typical double helix shaped molecule. Every living creature should be proud of his uniqueness - there aren’t two individuals (except identical twins) that have the same DNA. Thanks to that fact, molecular fingerprinting is used for identification of the single individual, forensics can identify suspects, and paternity test could be performed … Growing number of experiments use DNA for gathering different kind of information. Since DNA material is able to survive long period of times, excavation of the various plant or animal remains could tell us a lot of different stories about past on the Earth.

Ancient DNA represents DNA material extracted from old biological samples. Unlike classical DNA analysis, these specimens are of less quality. Archeological discoveries of different animal and plant materials precede DNA analysis. Even though DNA is present in each cell of the living organism, decomposition of the body after death limits the sources that could provide sufficient DNA for the further analysis. In the rare situations when body is entrapped in the ice or amber, high quality and quantity DNA is available. Various insects, plants and bacterial species were successfully investigated after DNA was extracted from amber entrapped specimens. For animal species, usual source of DNA are bones and teeth. Weather conditions (especially temperature and moisture) greatly affect the speed of DNA decay. At temperature of -5 Celsius, mitochondrial DNA is degraded to 1 base pair after 6.830.000 years. Degradation of the nuclear DNA is two times faster than mitochondrial. Using PCR method, scientists were able to multiply and investigate some very old samples dating back from Cretaceous period (145-66 million years ago). Not all ancient DNA samples are million years old. Some ancient DNA analysis investigates remains of much younger origin.

One recently published article investigates climate changes based on analysis of the ancient urine. Rock hyrax is cute little creature that looks like a rodent but is actually more closely related to the elephant. They inhabit rocky environment in Sub-Saharan Africa and Middle East. These social animals have specially designated area serving as mutual (communal) toilets. They are used for years, containing urine samples of a lot of hyrax generations. Urine crystallizes in time, forming stratified accumulations known as middens. Scientists found well preserved 10 thousands year old African middens that could provide more insight in climate changes associated with the hyrax habitat. Collected samples were investigated for organic molecules, metabolites and plant derived molecules. Forensic DNA analysis provided more information on the type of diet they have in the past revealing what plants were available 30.000 years ago. Since plant species are typical representatives of the each climate zone, list of available species on the hyrax menu precisely inform scientist which climate type existed 30.000 years ago. Middens were used for pollen analysis as well. That analysis increased the accuracy of predicted climate type. Given results showed that southern African climate underwent series of complex climate changes after last ice age (~20 000 years ago). Future experiments will investigate changes middens undergo when exposed to computerized simulations of past climate changes. Scientists are hoping that provided information would be helpful in revealing mysteries behind fast and unpredicted weather changes in this dynamic environment.

Another location and another set of animal excrements also provided evidence on previously lived flora and fauna. North West area of Australian continent is arid and any kind of old DNA is hard to find. However, scientists managed to found 700 - 30.000 years old samples of urine, fecal matter, hair, bones and eggshells cemented together in three locations. Different species (now extinct common brushtail possum and various arid grasses) that inhabited Western Australia were easily detected thanks to genetic analysis. Previous investigations focused on carbon dating, macrofossils and pollen identification; DNA analysis expanded previous data and helped in creating final image of the environment from the past.

Analyses of this kind are especially important for endangered species. Future conservation plans and efforts will work better if scientists become fully familiar with extinct species and be able to compare existing environmental data with the ones from the past.

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Insect transmitted diseases could be prevented by symbiotic bacteria

December 1, 2012, 8:11 am

≫ Next: New mRNA Influenza Vaccine - New Scientist

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Symbiosis is tight, mutualistic (cooperative), relationship between two or more biological species. Most symbiotic relationships last for a life time. Lichen is typical examples of symbiotic organism. It looks like a single species, but is actually composed of fungus and algae that are living in a tight relationship. Algae provide food through photosynthesis, and fungus provides water and mineral material from the ground. This community is obligatory; neither one species would survive without the other one. When symbiosis is facultative, two organisms could live separately, but they prefer symbiosis because their well being will be improved after they join forces. Humans form symbiotic relationships also. Intestinal bacteria are important part of immune system serving as significant defense line against pathogenic microorganisms; other gut bacteria could produce certain vitamins or accelerate digestion…. Symbiotic relationships are old probably as nature itself. Today, using the advantages of modern technology, man is able to directly affect and improve different symbiotic organisms to meet his own needs.

Recently published story describes a man who injured himself while cutting the old crab apple tree (branch impaled between his fingers). Although he properly cleaned the wound, it became infected and painful. He visited a doctor who sampled a liquid from the formed cyst for the bacteriological analysis. That analysis couldn’t determine the strain of infected agent. There were similarities with the already known bacteria but perfect match was missing. Bacterial species living in the gut of the insects, named Sodalis, proved to be its closest relative. Sodalis was discovered in 1999 as simbiont in 17 different insect species (most significant are tsetse fly, weevils, bird lice…). Newly discovered bacterial strain was named HS (shorter version of Human Sodalis). When genomes of Sodalis species living in tsetse fly and grain weevils were compared with the genome of the newly discovered species, it was obvious they are related but some interesting difference were noted. Almost half of the genes of the two well known bacterial species were lost or inactivated compared to genome of the HS species. HS provided new insight in the way symbiotic relationships between insects and bacterial species arise. Pathogenic bacteria species could be collected from the environment and domesticated inside certain insect species. Initially it was believed that spreading of the symbiotic bacteria from one insect species to another is possible via mites and other insects that contain symbiotic bacteria in their guts. Observed changes in the genome of the investigated bacteria offered another theory. Plants and animals derived pathogenic bacteria could be easily collected by the insects from their environment. Their further evolution from pathogenic to symbiotic partner is unique and insect specific. Both species need to find a way to adjust to a newly created community. Bacteria will lose virulent genes and this change will guarantee successful spreading of the future bacteria generation to the insect's offspring (instead from one species to another). They will be well fed thanks to food provided by the insect. In return, bacteria produce vitamin K and amino acids that are beneficial for insect nutrition. Also, bacteria could produce toxins to prevent parasitic wasp to lay eggs or fungi to colonize the insect. Loss of large number of bacterial genes resulted from the change in the lifestyle - genes essential for the classic environmental survival became unimportant. These modifications are beneficial for both species.

Close genetic link between Sodalis species and newly discovered HS species inspired scientists to design new solution against insect transmitted diseases. Tsetse fly is carrying a protozoan, well known inducer of the sleeping sickness. Sodalis species live inside the tsetse fly and can’t be grown in the laboratory, but HS species can. HS species could be genetically modified to fit tsetse fly and at the same time be able to induce killing of the protozoan after they are brought back in tsetse fly. By introducing modified bacteria back to the tsetse fly, insect will still be “equipped” with its valuable simbiont and disease transmission will be prevented through protozoan elimination. Same is planned for aphids that transmit viruses responsible for crop sickness (soybeans, alfalfa, peanuts…).

If this method proves to be successful, completely new chapter in treating insect transmitted diseases will open.

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New mRNA Influenza Vaccine - New Scientist

December 2, 2012, 4:17 am

≫ Next: Nanotech and starch based material could improve fruit ripening

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Influenza (flu) is infectious disorder induced by RNA viruses that belong to Orthomyxoviridae family. Three genera are associated with influenza disease in humans: Influenzavirus A, B and C. Flu is seasonal disorder, it reaches a peak in the winter. Being easily and highly spreadable, it often results in epidemics. Each year 3 to 5 million people get infected with influenza virus and between 250.000 and 500.000 cases end up fatally. Virus transmits trough bodily fluids, usually via coughing and sneezing (aerosol containing viral particles). People that are living or working in highly crowded spaces are at higher risk of developing disease due to close and often contacts with other individuals. Typical symptoms include chills, fever, muscle pain, sore throat, fatigue… It can lead to more severe disorder such as pneumonia. Worst case scenario is influenza pandemic: global spread of the virus ends up in mass infections. Several pandemic events were noted in 20th century. Most famous are Spanish flu in 1918 (with 50 million fatal cases), Asian flu in 1957 (between 1.5-2 million fatal cases) and Hong Kong flu in 1968 (1 million fatalities). In 2009, Swine flu triggered mass hysteria, but in reality, number of Swine flu fatalities didn't overcome typical seasonal flu mortality (~ 18.000 fatal cases).

Vaccination against flu is usual practice in most parts of the world and its popularity is growing each year. Idea behind flu vaccination is development of the "herd immunity": when 80% of people become immune against the virus - chances for further spreading are dropping down significantly. Vaccines are especially recommended for the sensitive group of people: children and elderly, immune-compromised and people with asthma, diabetes… Why flu and vaccinations against it are so important? Disease that spreads quickly and infects all age groups, result in less people available for work and hospitals full of elderly people that are treated longer than healthier (younger) groups of people. If 600.000 people die, 3 million people end up hospitalized and 30 million patients came to a hospital for a short visit, medical industry will have direct lost of ~10 billion dollars. Other institutions are affected by the seasonal flu also. Center for Disease Control and Prevention calculated that children in the USA missed 38.000 days in schools due to influenza. Influenza associated annual costs overcome 80 billion dollars. All this reasons accelerate vaccine industry and stimulate various experiments that could ensure novel, more efficient vaccination methods.

Influenza viruses are highly variable and each year new vaccine needs to develop. Typically, vaccine preparation will be guided by the seasonal viral strains (H1N1, H3N2, and B strain) recommended by WHO (World Health Organization). Most commonly, virus will be grown in the hen's egg. It takes around six months for vaccine to “mature”. Later, it will be mixed with other ingredients resulting in final vaccine. Cells in a culture could be used instead of an egg, but this is a long lasting process (several months). Latest improvement in the field of vaccine manufacturing could result in safer (egg allergy is prevented) and faster vaccines production (6 weeks in total).

mRNA is small molecule essential for genetic expression. It carries information about building protein from DNA to ribosome. If mRNA molecule is reprogrammed to induce synthesis of specific immune protein, desired immune response could be achieved. mRNA based vaccines are already used in carcinoma immunotherapy. They are applied intradermally; balanced immune response is achieved by targeted expression of immunoproteins that provide strong anti-tumor effect. Vaccination can be scheduled to fit the clinical situation. For the first time, mRNA vaccine for influenza treatment is designed. mRNA vaccine elicit predictive (B and T-cell dependent) immune response against influenza virus. Scientific team tested newly created mRNA vaccine against H1N1pdm09, swine flu and the H5N1 bird flu and so far - it proved to be effective against all of them. Vaccine could be manufactured easily in just a couple of weeks. It doesn’t have to be stored in refrigerator and tests in animals showed that is equally effective in old and young animals (tested in mice). Besides test on mice, vaccine proved to be safe and effective in ferrets and pigs.

Next step will be testing of safety/efficacy in humans. If it proves to be effective, mRNA vaccine could easily become a standard in future influenza vaccination programs. Personally, I believe that much better and safer way to boost immune system could be accomplished through regular sport and healthy diet and that is my favorite "vaccine". :-)

Reference: Lothar Stitz, Friedrich-Loeffler Institute in Riems Island, Germany

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Nanotech and starch based material could improve fruit ripening

December 2, 2012, 8:17 am

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Transformation of the fruit from green to fully mature, desirable for eating, is called ripening. Process is induced by gaseous plant hormone called ethylene. Its production is associated with outer temperature, surface wounds, and diseases. Ethylene triggers enzymatic activity that will convert complex polysaccharides (starch) to simple sugars, degrade chlorophyll and produce other pigments. Enzyme pectinase will degrade pectin and result in softer surface layer of the plant. Each fruit species demand certain weather conditions and climate to develop normally. During the past couple of years (thanks to improved shipping methods) fruit is traveling faster and people all over the globe can eat different types of fruit all year long. Ripened fruit can’t be safely transported because it is too soft and decay prone. Besides applying delay ripening methods, fruit is normally collected while still green. Artificial ripening (using different chemicals) will provide expected color and taste when fruit reach its final destination. Methods used in fruit ripening can provide fast and effective results but they are not necessarily 100% safe for humans. Also, if they are not administered properly, fruit might overripe and decay completely.

Calcium carbide is used as ripening agent in some countries. When combined with water, it turns in acetylene which induces fruit ripening. Calcium carbide can contain traces of arsenic and phosphorus that are known toxicants in humans. Mostly used ripening agent is ethylene. Specially designed facilities used for fruit ripening release previously determined amount of ethylene. Iodine is used to check ripening status of the fruit. Interaction between iodine and fruit sugar will indicate whether fruit is still green, in the ripening phase or fully ripe. Reaction between starch and iodine result in dark blue colored complex. Since starch turn in more simple sugar during ripening, green fruit will color dark when sprayed with iodine, while ripe fruit will produce bright color.

List of fruits that is collected while still green is long: bananas, papayas, mangos, tomatoes… are typical examples of fruit that will be harvested during “commercial maturity” stage and ripen prior being delivered to the desired location. Each species demand specific amount of ethylene to ripen properly. Although ethylene is safe artificial ripening agent, his storage and release could be a problem. Explosive accidents associated with tanks containing ethylene were reported in the past. Compressed gas is not just unsafe, but hard to accomplish and expensive to maintain. Scientists from the University of Queensland recently discovered another biological material that might offer solution for this issue. Starch derived material have crystalline structure and cavities that could safely encapsulate ethylene in couple of powder forms. Rise of temperature and humidity will induce ethylene release (from the powder complexes). This system is much cheaper and safer than previously used storage facilities and it could even be incorporated in the trucks that are delivering the fruit to the market. As a result, customers will be able to buy a fruit that have just ripened.

Another group of scientist (from the Massachusetts Institute of Technology) discovered the way to detect amount of ethylene using the newly developed nanotech device. Ethylene is small non-polar hard to detect molecule. Conventional methods applied in ethylene measurement are expensive. Newly developed device is portable, safe and easily produced. Sensor consists of two gold electrodes. Single walled carbon nanotubes and specially designed complex copper mixture lies in between electrodes. Bond between copper and nanotubes is very strong. When sensor is exposed to ethylene atmosphere, copper will bind ethylene and loosen its connection with nanotubes. Sensor is highly sensitive: electronic properties of the nanotube will register the slightest change in connectivity between copper mixture and nanotubes. Change in electronic resistance is proportional to the level of ethylene. Device was used to establish amount of ethylene released during ripening phase (amount of released ethylene is species specific) and to determine the peak of ripening for each species (when fruit ripen, it doesn’t demand ethylene anymore and it will slowly decrease its production). This little device could help prevent fruit from overripe and assist manufacturers while determining the proper amount of ethylene during ripening phase.

Newly applied method could greatly improve fruit ripening industry. Potential ethylene associated accidents could be prevented, timing associated with harvest and fruit ripening could be improved, and decay could be avoided.

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Factors That Increase Chances of Cancer Development in a Person

December 2, 2012, 8:19 pm

≫ Next: Botulinum Toxin: Medical Applications

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Among the most dreaded diseases, cancer is one of them and affects different organs or tissues within the body. In the present times, many types of cancers affecting different parts of the body with varied consequences have been unveiled, although the list may not be exhaustive. The different types of cancers affecting different organs or tissues are usually specific to that particular organ or tissue and may not affect any other remote organ or tissue, even though some rare cases may be observed, where a specific type of cancer affects a number of tissues and organs. A number of factors make some people predisposed and susceptible to the development of cancer within their body. Hence, like many other diseases, cancer may be regarded as a multi-factorial disease dependent on a number of factors that are summarized as follows:

a) Age makes some people predisposed to cancer. The advance in age leads to higher probability of development of genetic mistakes, which turns a normal cell into a cancerous one. The continuous exposure to carcinogens or other factors makes a cell prone to genetic changes during cell division that may result in cancerous growths.

b) Genetic makeup of some individuals increases the risk for development of cancer. Cancer results from a number of mutations in the genes of the individuals. These mutations may be inborn or may develop due to environmental factors like long-term exposure to carcinogens, etc. Although, the individuals inborn with genetic mutations may not develop cancer in all the cases, the chances of developing cancer is high among them, the phenomena being known as genetic predisposition. For e.g. the presence of one of the faulty genes BRCA1 and BRCA2 in the some women makes them predisposed to the development of breast cancer. However, the presence of genetic mutations is not always noticed in breast cancer patients that initiates the studies related to the viability of other factors in the cancer development.

c) The immunological system of the individuals has a promising role in the development of different types of cancers. The HIV positive individuals or AIDS patients have higher probability of developing cancer. Some individuals with history of organ transplantation with intake of immune system suppressing drugs for prevention of organ rejection or the individuals with inborn rare medical syndromes affecting immunity are predisposed to cancer development. Cervical cancer, cancers of genital areas, lymphomas, liver cancer, and stomach cancer may develop due to the overlapping of the mentioned conditions. The transplanted cells have the property of continuous cell division that makes them predisposed to develop genetic mistakes resulting in formation of cancerous cells.

d) The exposure to various environmental hazards in the daily life may also lead to cancer development. Different types of pollution, which may be man-made or natural consisting of harmful radiation, tobacco smoke, the ultra-violet rays of the sun, the hazards of work-place, effects of exposure to asbestos, etc are some of the possible reasons related to environment for the development of cancer.

e) Unhealthy lifestyle may also make people predisposed to cancer development. Smoking is one of the main reasons for the development of lung cancer. The intake of red and processed meat with alcohol accompanied with lack of physical activity also lead to predisposition to cancer development. In some cases, unhealthy lifestyle accompanied with eating junk food that may be laden with food additives may also lead to cancer.

f) In the daily life, people are exposed to a number of carcinogens or different cancer causing substances in different forms that may result in the development of cancer in one form or other. However, although everyone is exposed to carcinogens in one form or other, only some people are susceptible to cancer development. It is due to the extent of the influence of other factors.

g) In the development of most of the cancers, virus plays a major role by making genetic changes in the normal cells leading to the formation of cancerous cells e.g. cervical cancer, Lymphomas, T-cell Leukaemia, oro-pharyngeal cancer, etc are some of the cancers that are caused due to different types of viruses.

h) Infection resulting from different types of bacteria may in some cases lead to specific type of cancer for e.g. the stomach cancer results from the inflammation in the mucous lining of the stomach that is caused due to Helicobacter pylori. Different lymphomas of the stomach also result from the bacterial infections of the stomach.

In this way, it is seen that multiple factors play crucial roles in the development of cancer and the presence of some factors are closely linked with high risk making some people predisposed to the disease. Hence, to develop proper therapeutics for the disease, it is essential to consider the influence of all the factors and the possible roles played by them.

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Botulinum Toxin: Medical Applications

December 3, 2012, 4:14 am

≫ Next: Gene targeting induced selective loss of chromosome 21 in Down syndrome

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Botulinum toxin is a peptide produced by anaerobic bacteria Clostridium botulinum. This is one of the most potent neurotoxins in the world. Botulinum intoxication, characterized by severe paralysis that could end up fatally, is known as botulism. Large molecular mass prevents toxin to enter the brain, but it can interrupt synaptic connections in the peripheral nervous system and block acetylcholine (neurotransmitter) release. Despite numerous negative effects associated with botulinum toxin, it can be very useful in treating various medical conditions if applied properly.

Blepharospasm is medical condition characterized by uncontrolled eye blinking; it results from involuntary movement of the muscles around eyes. Disease could be triggered by impaired function of basal ganglia, fast life style and psychophysical stress, or due to dry eyes… Botulinum toxin provides relief by inducing the spasm of the muscles responsible for eye twitching. It needs to be applied every 3 months to maintain ocular muscle “under control”.

Strabismus is diagnosed when eyes are not properly aligned. Disorder results from extraocular muscles dysfunction or due to impaired brain - eyes coordination. Impaired binocular vision and depth perception are common disease attributes. Treatment options are limited to corrective glasses, lenses and patches that could correct the visual image created in the brain. Cosmetically, strabismus can be improved either by botulinum toxin injection or through surgery. Botulin toxin provokes muscle spasm and result in eye alignment. It needs to be injected every couple of months, since paralysis weakens in time.

Upper motor neuron syndrome results from lesion of the motor neurons (which innervate skeletal muscles). It is characterized by decreased muscle control, altered tonus, weakness, mioclonus, spasticity…. Severity of disease depends on the severity of motoneuron lesion and affected muscles. In the most cases, exercise combined with drug treatments could help restore muscle tonus and relief spasticity. Botulinum toxin is applied by direct injection in the muscle to alleviate muscle - neuron signals. There is a story about Australian that had a stroke 20 years ago and managed to leave the wheelchair recently thanks to botulinum applied for hypertonic muscles treatment.

Hyperchydrosis or excessive sweating results from increased activity of sympathetic nervous system; it could be triggered by some type of food, drink and smoking... Whether it is localized (palms, underarms, groins) or widely spread, surgical methods such as removal of the sweat glands or endoscopic thoracic sympathectomy could provide satisfying results. Less aggressive methods such as antiperspirant application could help also. Botulinum toxin can prevent perspiration by blocking neural control over sweat glands. Effects are visible during 3-9 months.

Cervical dystonia known as torticollis is medical condition associated with neck spasticity. Damaged sternocleidomastoid muscle can’t rotate and bend laterally resulting in abnormal head position (tilted in one side). Facial asymmetry can develop also. Disease can be congenital, induced by birth trauma or intrauterine malposition or can be acquired later in life (consequence of tumors, drugs, infectious diseases…). Typical treatments include muscle stretching and strengthening. When applied exercises doesn’t provide expected outcome, surgery could help release tensed muscle. Botulim toxin is often used in torticollis treatment; it effectively inhibits spastic contractions.

Chronic migraine is severe headache that affect one side of the head; it could last between 2 and 72 hours. Genetic predisposition (2/3 of all cases are inherited) and multiple environmental factors are implicated in migraine genesis. Nausea, vomiting, pain, sensitivity toward light and noise… are just few symptoms that typically occur during migraine. Analgesics and antiemetic are used for control of pain and nausea, respectively. Botulin injected in head and neck proved to be efficient in chronic migraine prophylaxis.

Achalasia or esophageal aperistalsis is disorder affecting smooth muscles of esophagus and lower esophageal sphincter. Food can’t pass esophagus normally due to low organ peristalsis and increased muscle tonus of the sphincter. Main symptoms are dysphagia (patients can’t swallow food normally), regurgitation and chest pain. Calcium channel blockers (decrease tonus of the sphincter) and surgical approach (Heller myotomy) are mostly used treatment options. Botulinum toxin induces sphincter paralysis. It can induce scarring of the muscle, so it’s avoided in patients who are planning surgical operation in the future. Botulinum is prescribed only to the patients that are not suitable for surgery.

Cosmetic industry exploits botulinum toxin very much. Most people consider that botulinum is used solely for wrinkle removal. Actually, list of disorders that could be treated with botulinum toxin is long. Unfortunately, effect is time limited and treatments need to be repeated every couple of months.

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Gene targeting induced selective loss of chromosome 21 in Down syndrome

December 3, 2012, 9:10 am

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Gene targeting uses homologues recombination techniques to change endogenous genes of interest by inserting new, or deleting and altering existing genes. Genetic recombination is facilitated by enzymes (usually of microbial origin) that cut and rejoin interrupted DNA strands during transformation of the genetic material. Size of the gene and its transcriptional activity are not limiting factors, allowing scientists to experiment with all kind of genes they want. Genes could be altered permanently, or just during certain development phase; they could be modified in specific tissue or in the whole organism. So far, gene targeting was applied in lot of different animal and plant species (from drosophila, human and mice to corn and tobacco). Methodology for each model organism is well known. Basically, genetic construct first need to be generated in the bacterial cell. It contains parts of the targeted gene, reporter gene and selectable marker. After genetic construct is inserted in embryonic stem cells, these cells will be injected to the embryo.

Targeting could be applied in numerous ways to provide different information on the investigated genes. Besides basic insight of gene functionalities, targeting could provide more information on gene related diseases and improve drug development project by guiding the process in the most suitable direction. That is the case with isogenic human disease models: selected cell are genetically altered to reflect exact genetic background of the disease. In vitro examination provides novel insight in the disease biology and allows scientists to test new therapeutic agents. Most cancers are investigated using this model. Although it is still new, it might become a standard in genetic disease investigation because it is less expensive and less complicated (in the technical sense) than conventional disease/drugs testing methodologies. Another way to apply targeting is in the field of protein engineering (novel proteins are designed).

Recently published article revealed that genetic targeting could be used for the elimination of the entire chromosome. Scientists from the University of Washington described targeted removal of the excess chromosome 21 in the fibroblast derived from the person with Down syndrome. Chromosome “free” cells were then transformed into induced pluripotent stem cells (iPS) for further investigation.

Adenoviral vector selectively inserted thymidine kinase neomycin phosphotransferase reporter gene (TKNEO) in the APP gene of the fibroblast DNA. APP gene encodes amyloid precursor protein that is integral part of cellular membranes in various tissues. Amyloid precursor protein is degraded via proteolysis to beta amyloid. Impaired version of beta amyloid can be easily recognized by its filamentous form. This protein is well studied due to tight association with Alzheimer’s disease: filamentous form of beta amyloid accumulates in the brain forming amyloid plaques, which are typical pathological finding in the brain of persons diagnosed with the disease. Reason why this specific gene is targeted is not clear, but TKNEO managed to be successfully incorporated in just one copy of the chromosome 21. When cells were selected against the TKNEO, the best way for them to survive was to eliminate extra chromosome which now pose a threat for their survival. Vast majority of the cells did exactly that. Most prominent survival method was spontaneous loss of extra chromosome during mitoses and the frequency observed indicated that selective pressure pushed the cells in this direction. Other survival methods: epigenetic mutation, silencing of the TKNEO gene, targeted deletion of the gene, and point mutation were noted at much lower rate. At the end, all Down syndrome derived cells that remain in trisomic state end up killed. Only cells that spontaneously reverted to their disomic state remained alive. Newly derived generation of the disomic cells were further transformed in iPS thanks to selective transcriptional and growth factors applied. These cells showed high proliferation rate.

This experiment showed for the first time that genetic targeting could affect the number of chromosomes beside certain genes and/or their parts and it certainly paved the path for the future clinical and research analysis. Treatment of Down syndrome using this method is still far from possible. Scientists are not sure if this method is 100% safe or associated with potential genotoxicity. For the moment, described technique will be used for gathering information about disease that could help scientists create better future therapeutics.

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New drugs could help combat obesity

December 4, 2012, 1:51 am

≫ Next: Drug for Fragile X syndrome and autism

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Food is source of energy for all biological functions in the living organisms. In the past, food wasn’t easily accessible as it is today. People had to pass long distances, cope with poor weather conditions and skip different environmental obstacles before catching a pray that could provide necessary dose of energy. Body learned to turn all excess amount of energy in fat to be used when regular food is not available. This mechanism is no longer needed because latest technologies simplify food production and its distribution on the global scale and offer a lot of edible materials that provide not just energy but pleasure in the modern society. Feeding is one of the primal instincts that need to be satisfied if we want to survive. Ironically, eating is what is killing thousands of people nowadays.

Obesity is medical condition diagnosed when body mass index exceeds 30 kg/m2 (BMI is calculated when number of kg is divided with height expressed in square meters). It usually results from excess calories intake and lack of physical activity. Genetic predisposition can play a role. Some type of diseases and medications (anti-psychotics, for example) could increase appetite and result in excess weight gain. Number of people diagnosed with obesity is increasing. Annually, between 111,909 and 365,000 people in USA and around 1 million people in Europe die due to obesity. Increased weight pose a great threat to the health. It is associated with cardiovascular disorders, diabetes type 2, metabolic syndrome, apnea, asthma…. People could treat obesity surgically by removing fat or by reducing gastric volume, but without changes in the lifestyle (including modified diet and regular exercise) most people will turn preoperative weight back. Most medications for obesity work as appetite suppressor. Some of those were pulled back from the market due severe side effects - fatal heart valve problems were noted. As from July 2012, two new drugs for obesity treatment are approved by the FDA.

Belviq (Lorcaserine) is selective serotonin agonist (binds to 5-HT2C receptor) that acts as appetite suppressor. After binding to receptor, proopiomelanocortin will be produced and patient will experience satiety. In time, that will result in weight loss. Since, its mechanism of action is similar to a previously mentioned drug, scientists paid special attention during Belviq development to create a drug that will avoid binding to the receptors in the heart valve.

Qsymia is combination of two previously marketed drugs: topiramate and phentermine. Topiramate is anti-seizure drug having weight loss as a side effect. Phentermine acts like appetite suppressor and a stimulant. This drug is more powerful than a Belviq.

If drugs work properly, patients will experience appetite reduction and will not feel hunger in between meals. Drugs will not boost the metabolism and patients are strongly advised to increase their everyday activities and move as much as possible. Both drugs showed promising effects; participants in the study managed to lose 4-8 percent of their body mass and reduce blood sugar level, which is another beneficial effect. Qsymia can reduce cholesterol level and blood pressure also. Both drugs will be available only via prescription. People that want to lose pound or two will not be able to get them. Just overweight and obese patients diagnosed with some of the typical obese related medical conditions (cardiac problems, diabetes type 2, increased cholesterol level…) will be able to use these medications.

Typical side effects may include dry mouth, constipation and tingling in the fingers. Qsymia is associated with severe heart side effects; it could increase heart rate and induce birth defects if taken during pregnancy. Women who are planning pregnancy should avoid this medication. Belviq may interfere with drugs that are usually prescribed for migraine and depression.

Increased body weight used to be a sign of wealth and good social-economic status in the past. Growing number of overweight people wasn’t recognized as a medical condition until 20th century. In 1997 WHO (World Health Organization) announced that obesity takes epidemic proportions with 9.8% obese people globally. Modern medicine provides a lot of evidence that excess amount of body fat leads to numerous serious disorders that could shorten life expectancy and prevent people from living healthy and happy life. Surgical procedures, novel drugs, and regular exercise combined with proper diet management… could reduce the number of diagnosed cases in the future.

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Drug for Fragile X syndrome and autism

December 4, 2012, 6:17 am

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Fragile X syndrome is inherited disorder associated mostly with males. Most prominent features of the disease are mental retardation, autistic and stereotypic (repetitive) behavior. It results from FMR1 (fragile X mental retardation 1) gene impairment. FMR1 gene is located on the X chromosome and it is essential for normal mental development. Since males have only one copy of the X chromosome, impaired version of the gene will inevitably result in disease. Number of CGG triplet repeats in the FMR1 gene indicates whether gene is healthy or mutated (fully mutated gene contains > 200 repeats) and serves as a marker in genetic testing for people who are at risk of getting offspring with disease. Fragile X is also known as single-gene cause of autism. Except drugs that are used to prevent hyperactivity, anxiety, aggressiveness (known symptoms of the disease), there is no single marketed drug that is specifically designed to treat social aspect of the fragile X syndrome.

Autism is neurodevelopmental disorder. It is characterized by impaired social and communication skills, and repetitive and restrictive behavior. Genetic background of disease is not fully revealed. Investigators are not certain if disease develops after rare genetic variants are combined (several genes are implicated) or as a consequence of rare genetic mutation. Sometimes, agents that induce birth defects (heavy metals, vaccines, toxins…) could trigger autism development. Estimated costs for an individual diagnosed with autism are ~3.99 million dollars for a lifetime. Disorder is “expensive” because autistic persons demand special medical care, special education and they rarely become capable to work and earn independent from their guardians. There is no known cure for autism. Children are usually treated with antipsychotics, anticonvulsants and antidepressants to alleviate some of the disease symptoms.

Recently published article announced that fragile X syndrome initially developed drug could be beneficial for the people diagnosed with autism. Researchers didn't have necessary data about dysfunctional brain pathways associated with altered behavior (typical for neurodevelopmental disorders), but recent experiment on genetically altered animals provided more information on potential biochemistry behind disease. Experiments on the mouse with fragile X showed lower level of gamma aminobutiryc acid (neurotransmitter) in various brain areas, including hippocampus (associated with memory, activity and orientation). Scientists hypothesized that lack of this neurotransmitter could trigger social anxiety and avoidance - typical fragile X associated behavior. Arbaclofen (or STX 209) acts like gamma aminobutyric acid type B agonist (synthetic imitator). It produces the same physiological effect as naturally (organism derived) substance and compensates the lack of gamma aminobutyric acid in the body. When tested in mice, drug showed great reduction of repetitive and anti-social behavior. Study in humans showed equally promising effects. It lasted for 2 years and comprised of mostly male fragile X sufferers aged 6 to 39. Drug was submitted in 2 doses per day during six weeks. After last dose was applied, 4 to 6 weeks long pause was made before participants were evaluated. Participants were monitored for: irritability, lethargy, repetitive behavior, hyperactivity… Social avoidance and parent-nominated problem behaviors showed improvement in all subjects. Arbaclofen could be of great help in treatment of autism due to high similarity of social and behavior problems with fragile X syndrome. Future trials will provide more information on drug safety and effectiveness in both disorders.

Since pharmacological treatment is still unavailable, another treatment option should be tested. Previous studies with horses and dolphins showed that autistic children manage to relax and socialize when they are near these animals. Latest study showed that almost any animal species (dogs, cats, rabbits, hamsters…) could produce similar healing effect. Autistic kids experience difficulties in recognizing other people’s emotions and needs and animals could learn them various important skills such as ability to share and provide comfort when needed. Trick is to introduce animal to a family later. If animal is already present when autistic children is born, animal will be considered as a part of normal environment and children wouldn’t change his own behavior to comfort the animal. Also, when animal is brought to the family, interaction between the family members will change and become more intense and warmer, which will significantly affect behavior of autistic children. You just need to decide which animal species suits you the best.

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Cytogenetic Technologist Job Description, Salary and Training Programs

December 6, 2012, 3:04 am

≫ Next: Ergonomist Job Description, Salary and Training Programs

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What is Cytogenetic technology?

Cytogenetics deals with the study of cell division along with the structure of chromosomes. The main application of this field is in the study of different congenital birth defects and genetic diseases involving the study of acquired abnormalities in the chromosomes that are usually found in different types of cancer. The Human Genome project has played a very important role in the development of the new field of cytogenetic technology. It has helped a great deal in the study related to relevant genes responsible for different diseases as well as in the development of knowledge regarding the location and sequence of the fatal genes. Recent studies have shown the involvement of genes in most of the fatal diseases affecting humans. Hence, targeting the genes responsible for the diseases is becoming increasingly important. Hence, cytogenetic technology has shown great advancement and is being applied clinically for diagnostic, prognostic, and monitoring purposes of various inherited and acquired abnormalities in the genes. The main application of cytogenetics is in the prenatal diagnosis of the amniotic fluid by amniocentesis and the sampling of the chorionic villus as well as in the peripheral blood studies for postnatal diagnosis. It has also found application in the diagnosis and treatments of different haematological diseases and fertility problems.

Career description and skills necessary for a Cytogenetic technologist

A good background in science is very essential for a cytogenetic technologist to carry out proper cytogenetic analysis of the different specimens collected such as amniotic fluid, blood, and bone marrow. A clinical cytogenetic technologist has many responsibilities. His responsibility starts with the evaluation of proper methods carried out for the handling of the different types of samples for cytogenetic analysis involving proper collection, transport, and storage of the collected samples. He must be well equipped with knowledge regarding the different cell culture and harvesting techniques with proper understanding of cell cycle mechanisms and the biochemistry behind the different procedures carried out in a cytogenetic analysis. Being knowledgeable in the different laboratory practices regarding genetics and its related nomenclature to be able to identify the presence of abnormalities in the chromosomes is required of a cytogenetic technologist. He must be able to perform the karyotyping of human chromosomes i.e. organization of chromosomes according to a standardized ideogram as well as chromosome preparation analysis, different staining procedures including slide preparation, microscopic and photomicroscopic analysis, computer imaging techniques and he must be up-to-date with the new developments in the field of molecular cytogenetics.

In addition to being equipped with good laboratory skills, he must be well aware of the safety protocols as well as the different quality assurance principles applicable in his area with knowledge about the different legal implications in his field. A good professional and ethical behaviour meeting the expected standards of a healthcare professional, is expected from a good cytogenetic technologist. Along with appropriate professional conduct, stress management, interpersonal communication skills are necessary for interaction with patients, other health-care personnel in his work place and public in general. In many cases, proper cytogenetic counselling becomes essential for the family members too, apart from the patient. Hence, the cytogenetic technologist must be well prepared in advance to meet the requirements, when essential with the maintenance of proper records of the patients and having detailed knowledge regarding the case.

Employment opportunities

The cytogenetic technologist has a wide range of opportunities in the medical field. Employment opportunities exist in hospitals, clinics, research laboratories, public health facilities, private medical laboratories, government facilities as well as in educational institutions as faculty.

Salary

The salary of a cytogenetic cytologist varies according to the employer and geographic location. The BLS projects job growth of 10 to 19 percent from 2010 to 2020. According to the survey conducted by the Dept. Of Academic affairs at MD Anderson Cancer Centre, the average starting salary for a staff cytogenetic technologist is $38,000 to $50,000. The median annual salary in 2011 was $57,000.

Educational background

The selection of a proper educational programme is very essential for a career in cytogenetic technology due to preferences of the prospective employers regarding the program accreditation. A bachelor’s degree in cytogenetic technology or cytogenetics from an accredited institution is essential. The prerequisites of the area of study are biology, chemistry, biochemistry or cellular biology, immunobiology, microbiology, genetics, cytogenetics, hematology, laboratory information systems, safety and quality control in laboratories. Pre-professional and professional course works are also included in the professional course. After meeting the academic and laboratory educational requirements, the students are certified by the Board of Registry of the American Society for Clinical Pathology. The National Accrediting Agency for Clinical Laboratory Sciences (NAACLS) also offers accreditation to the educational program of Cytogenetic technology.

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Ergonomist Job Description, Salary and Training Programs

December 6, 2012, 3:14 am

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Ergonomics

The Association of Canadian Ergonomists define Ergonomics as the scientific discipline concerned with interactions among humans and other elements of a system (e.g. the tools, equipment, products, tasks, organization, technology, and environment). The profession applies theory, principles, data, methods, and analysis to design in order to optimize human well-being and overall system performance. It is a multidisciplinary field that promotes both health and productivity in the working environment. The coming together of biological and life sciences with behavioural and social sciences topped with technical sciences is the basic idea of ergonomics.

Responsibilities of an Ergonomist

An ergonomist is an occupational health expert mainly involved in the designing of efficient and comfortable tools, equipments, and furniture for use in work place of different organizations by the application of scientific knowledge and problem-solving skills. Consideration of human anatomy along with safety to minimize physical strain is the working motto of an ergonomist, who uses a holistic approach to ensure the physical, social, cognitive, organizational, environmental, and other important factors for designing and modification of any system. The main responsibilities include the following:

a) Interpreting the interaction of humans with the equipments, to analyse the limitations of human body by careful observation and evaluation in the working environment.

b) Study system performance by developing experimental designs, using data collections instruments and procedures to analyse workplace risk assessments.

c) Assess the effect of working environment on the users and analyse the areas for improvement and optimization of existing practices and procedures.

d) Investigate the demands forced on the workers regarding their physical, postural, physiological, cognitive, job, work, and stress parameters.

e) With the help of different instruments, modelling and simulation studies, the physical environment is assessed.

f) Designing practical solutions to help the workers and analyse the suitability of these to meet the needs of the workers in terms of motor, cognitive, and sensory capabilities of workers.

g) Producing user manuals for the proper and efficient use of the new products.

h) Make reports of the findings and recommendations by writing proposals and presenting statistical data.

i) Employing creative methods to implement the new systems.

j) Teaching the workers about the dynamics of human body and proper work practices.

k) Investigating workplace accidents by visiting a wide range of working environments such as offices, factories, hospitals, etc. and to assess the health and safety standards.

l) Providing recommendations, training, and advice to the clients as well as colleagues regarding personnel management, and the specification, design, evaluation, operation and maintenance of the products and systems.

m) Acting as expert witness to industrial injury and understand the working pattern of specific systems and industries in short space of time.

n) Consulting and liaising with other professionals such as health specialists and designers to collect and integrate data from several scientific and professional points of view.

o) Identifying new opportunities for work.

Employment opportunities

The skills and knowledge of an ergonomist have application in different public and private sector organizations such as government bodies, computer consultancies, major manufacturing companies, defence and process companies, research institutes, safety/consumer laboratories, transport companies, hospitals, universities, utility companies, NHS. Ergonomists may also work on a self-employed consultancy based contracts.
Opportunities for ergonomists are advertised in different newspapers and publications such as The Ergonomist, The Psychologist, Applied Ergonomics and Ergonomics, etc.

Educational Background

There are basically two routes to qualify as a professional ergonomist.

1) A BSc in Ergonomics recognised by the Institute of Ergonomics and Human Factors with a post graduation degree in a relevant area such as MSc or PhD by course or research.

2) A Post-graduate degree in design, biology, psychology, kinesiology, biomechanics, medicine, sociology, anthropology, physics, occupational therapy, mathematics, operational research, physiology, sports science can be helpful in case of graduates without relevant first degree.

However, experience in the relevant area is beneficial and can be gained by approaching the employers, or taking part in voluntary work, placements, vacation courses, job shadowing, and networking. Some courses include a year of practical experience and the choice of course may affect the specialisation area as a professional ergonomist. Sandwich options on degree courses are helpful as they offer a year of practical experience.

Membership in the Institute of Ergonomics and Human Factors helps a great deal in finding the right opportunities, which is open to all. The added advantage in the entry of qualified and experienced candidates in this institute is their listing in the professional register with their profile being sent to prospective employers offering more employment opportunities.

Potential Skills in an ergonomist

Good problem solving with numerical and analytical skills are an essential must in an ergonomist combined with good interpersonal communication and negotiation skills. Good grasping power of technical concepts with systematic approach to work and being up-to-date about latest developments in the field is an added advantage for a bright career. A good ergonomist must be creative and be willing to work independently as well as in a team.

Salary

Salaries vary according to the organizations. According to UK’s official career website, the range of typical salaries for new ergonomics graduate is £20,000-£25,000 while those with around five years experience may have £25,000-£40,000. The senior ergonomists may earn up to £60,000. According to BLS, the median annual ergonomist salary was just over $77,000 in 2011.

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Collection, Storage and Uses of Stem Cells

December 11, 2012, 10:38 am

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Stem cells are the basic cells of the human body, which are necessary for the development of all tissues. However, they have the ability to morph into specific tissues during the life. This means that they represent a kind of "backup cells" to restore damaged tissues.

Today, the majority of stem cell therapies is performed using adult stem cell, but stem cell therapies with umbilical cord blood have also given excellent results and are increasingly used. For now, the stem cells are used to treat blood diseases, metabolic diseases and immune system disorders.

Treatment implies regeneration of damaged tissues and organs using stem cells. Patient’s own stem cells have been successfully used in the treatment of cardiovascular disease.

Therefore, an entire medical discipline has been developed in order to use stem cells to treat a variety of diseases. Today, over 70 different diseases are successfully treated (different types of leukemia, genetic metabolic disorders, immune system disorders, anemia…).

Where can we take stem cells from?
- Stem cells exist in the human body from embryonic development to the end of life, in various tissues. In adults, the highest concentration is in the bone marrow and blood. But taking stem cells from the bone marrow is painful and difficult process. In some cases it is even necessary to prick femur more than a hundred times. Therefore, the last 15 years, the idea of keeping person’s own stem cells taken from umbilical cord blood after birth came to life. They are very young and vital, and the process of obtaining is completely safe and painless. The blood sample is taken from the umbilical cord after separating the child from the mother after birth. Stem cells are then isolated from the blood sample and frozen to minus 196 degrees in the gas phase of liquid nitrogen. This process is called cryopreservation, and that way saved stem cells can last indefinitely and, most importantly, they do not get old.

Where to store the samples taken?
- During the last decade, a considerable number of stem cell banks have been formed because more and more parents decide to keep the stem cells from the umbilical cord blood of their newborns. European leader among private-family stem cell banks is a Belgian-Dutch company, Cryo-Save (http://www.cryo-save.com ), with a central laboratory in Belgium. The bank keeps over 100,000 stem cell samples from around the world. For safety reasons, samples are stored in two locations – in Belgium and in the Netherlands.

Who takes the stem cells in the maternity ward?
- The process of taking a sample of blood for stem cells performs an obstetrician immediately after delivery and separation of the newborn. A sample is taken from the part of the umbilical cord that remains attached to placenta and it is placed in a special bag that is part of a set. The procedure is quick (one or two minutes) and painless for both mother and baby. The collected blood is than placed in transport containers. The sample is kept strictly at room temperature until the processing (15-25 degrees).

Do you need special training of the hospital personnel to perform this procedure? What is the success of this procedure?

- Maternity hospital where the samples are taken from umbilical cord blood, have trained personnel (doctors) to carry out these procedures. The amount of blood that can be collected, and the concentration and viability of stem cells in the sample are individual and vary on a case by case basis. The results of the procedures performed can be known after processing in the laboratory. Statistically, this procedure was successful in 95 percent of the cases.

Which family members can use stem cells?
- Stem cells taken at birth from the umbilical cord are the cells of the newborn. If applied in treatment of the child (autologous), they are completely identical. After that, it is most likely to be applicable in siblings and then in parents. Anyway, before allogenic transplantation, compatibility between donor and recipient must first be checked.

How many times can you use a sample? For example, is it possible to treat more family members with different diseases?

- The amount of stem cells that are obtained from a sample of the umbilical cord blood is individual and varies in significant ranges. For each case, quantity required to be used is specifically determined, and whether it is necessary to take additional samples or their multiplications.

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Commercial Use of the Plants Improved by Genetic Engineering

December 12, 2012, 3:16 pm

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Genetic engineering or recombinant DNA technology involves the whole specter of techniques for finding a specific gene in the genome of a species, isolating, cloning, determining the sequence of nucleotides, changing it, and installing it in genome of the same or different species. By selecting the proper regulatory regions (e.g. promoter), gene in the target organism can be activated according to desire of researchers in the specific conditions or in specific tissues. That technology is being applied successfully for almost 30 years in scientific research and has achieved useful properties of different types of organisms.

No matter whether the final aim of the application of genetic engineering is scientific research or achieving useful properties of commercially valuable organisms, the procedures are the same. Also, regardless of whether carried on prokaryotic organisms, plants or animals, the basic techniques are very similar and almost always involve insertion of the desired DNA fragments into bacterial plasmid, using restriction endonucleases and DNA ligase. Fragment (gene) that needs to be incorporated into the genome of the target organism is prepared, analyzed and multiplied using plasmids in Escherichia coli. Depending on the organism (bacteria, plant or animals), the procedures of inserting the desired gene into the genome may vary. In plants, for this purpose, the bacterium Agrobacterium tumefaciens is most commonly used, or the desired gene gets inserted into the cell by device called "gene gun". Once the desired gene is incorporated into the cell genome of certain plant, the whole plants regenerate from these cells, and those plants are commonly referred to as transgenic plants.

The Properties of Agrobacterium Tumefaciens and Interaction with Plants
A. tumefaciens lives in the soil almost everywhere in the world. Genetic Material of this bacteria is made of one large circular double-stranded DNA molecule (Bacterial chromosome) and one relatively large plasmid (plasmid Ti). The bacteria has developed unusual behavior during evolution - when the plant close to the ground is injured, bacteria move towards that place by chemotaxis, enter the intercellular spaces, and attach to the healthy plant cells, inserting into the plant genome a specific part of their plasmids (that part of the plasmid is called T-DNA). T-DNA contains two sets of genes: genes forgrowth regulators (plant hormones) and the genes for the substances that bacteria use as food (all the genes contain eukaryotic promoters so they are active in transcription in plant cells). Cells in which the genome of the bacterial T-DNA is incorporated are transformed cells. Growth regulators stimulate uncontrolled proliferation of transformed plant cells, and from such cells in a relatively short period of time a cluster of identical cells is developed (the tumor). Because of the different sets of genes in the T-DNA, tumor cells produce and secret into the intracellular space substances that bacteria use as food.

How is A. tumefaciens used in genetic engineering?
After the plasmid Ti is isolated from bacteria, the T-DNA genes are all cropped leaving only peripheral T-DNA sequences about 25 nucleotide pairs long (these edges of the T-DNA are essential for the transfer of T-DNA from the bacterium into the plant genome). Instead of the original gene in T-DNA, using restriction endonucleases and DNA ligaze, the desired gene, which was previously prepared and amplified by another plasmid in the bacterium E. coli, is incorporated. Such a recombinant plasmid is inserted into the bacterium A. tumefaciens and the bacteria are grown in a liquid medium. Then the cells of the plant we want to transform are added in the bacterial suspension. Since bacteria do not distinguish the original T-DNA from T-DNA in which desired genes are incorporated, it will incorporate desired genes into the genome of plant cells by the same mechanism by which it naturally does. From plant cells which have incorporated the desired gene, the plants are regenerated using appropriate nutrient medium. The new plants are then planted in the ground.

Recombinant DNA technology and genetic engineering provide almost incredible opportunities for improving the properties of organisms used for various purposes. Some properties that are the target for hundreds of years, it is possible to get in a very elegant way using the application of these technologies. Genetic engineering is currently the only technology used in breeding plants, and the most important thing is that by its application we know exactly what kind of changes in the genetic material caused the new properties.

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