GEN-BIO

Genetic engineering - is a process of making changes on the genetic code of an organism. Its goal is to add one or more new traits that are not normally found in that organism. Through advanced studies in the structure of DNA and its chemical properties, scientists have been able to employ different techniques to extract, cut, and make unlimited copies of DNA.

DNA recombination - is a process of modifying the genes of organisms for practical purposes. It is done when a piece of DNA is combined with another DNA from another source. The resulting genetic product is called recombinant DNA. With this process, organisms get to have traits that are not normally found in their species.

Transformation Using a Vector - Recombinant DNA may be created through transformation with the help of a vector, such as bacterial cells.

Vectors - are organisms that are normally harmless but may help spread infection by transferring the genetic material from one host to another.

plasmid - circular DNA molecule

genetic marker - which makes it possible to distinguish bacteria that carry the plasmid-containing foreign DNA. Some of these genetic markers code for antibiotic resistance

restriction endonuclease enzyme - is used to cut the piece of the donor DNA. This enzyme cleaves the DNA at the phosphate-sugar bond, and thus sticky ends are created.

Sticky ends - are areas in the DNA where the bases are ready to be paired.

DNA ligase - an enzyme used to insert the donor DNA into the vector. It seals the sticky ends by joining the phosphate and the sugar bonds in the DNA.

Vectorless Gene Transfer - This process is similar to transformation, but it does not involve vectors.

electroporation - In this process, temporary holes are formed in the plasma membrane of the host cell by applying a significant amount of electricity in the culture medium. This enables the entry of foreign DNA via the pores.

protoplast fusion - In this process, cells are treated with chemicals to initiate recombination. In this process, bacterial cell walls are digested, turning the cells into protoplasts. These protoplasts are treated with polyethylene glycol to allow them to fuse, creating a random recombination of genes. The resulting recombinant cell will now grow a new cell wall.

microinjection - In this process, the host cell is immobilized by applying a mild suction with a blunt pipette. The foreign gene is then injected with a microinjection needle, thus creating recombinant DNA.

particle gun - In using this for recombination, the host cell is bombarded with tungsten particles coated with foreign DNA. This process is used in the field of agriculture. Many farmers use this method to genetically modify plants to make them highly resistant to insects and other pests. Some also use this method to develop crops that can survive extreme weather conditions.

Transduction - is the process wherein genetically engineered bacteriophages- viruses that parasitize bacteria- are introduced into the cell to create the desired recombinant DNA.

Agriculture - Transgenic plants, or plants that contain genes from other organisms, are now an important part in the field of agriculture. By using recombinant DNA technology, plants can now be grown with genes responsible for producing natural insecticides. This technology reduces the need for synthetic or artificial insecticides and pesticides.

Pseudomonas syriangae - The recombinant variant of this bacterium is called the ice-minus bacterium, which lacks the gene responsible for ice formation. The ice-minus bacteria prevent frost crystals from forming in plants.

Pseudomonas fluorescens - This is a nonpathogenic bacterium that has the ability to produce proteins rapidly. This characteristic is advantageous in developing biotherapeutics and vaccines.

Agrobacterium tumefaciens - In its natural state, this bacterium has a tumor-inducing (Ti) plasmid that causes crown gall disease in plants. The said Ti plasmid in the bacterium can be removed and replaced with a recombinant plasmid. This enables the now-modified bacterium to introduce beneficial genes to plants.

Genetically Engineered Traits: The Big Six

1. Herbicide Resistance
2. Insect Resistance
3. Virus Resistance
4. Altered Oil Content
5. Delayed Fruit Ripening
6. Pollen Control

Medicine - An important contribution of recombinant DNA technology in the field of medicine is the use of bacteria to create substances that our body needs whether to maintain good health or to treat a disease. For example, human insulin is created using recombinant DNA to help diabetics.

Food Industry - Recombinant technology has also improved the food industry. Some of the crops that we eat are now resistant to pests, diseases, and environmental stress. As a result, crop yields have increased and production costs have been kept lowered. Recombinant crops are also beneficial because of their improved nutritional quality and longer shelf life.

Special Creation/Divine Creation - Life forms may have been placed on earth by supernatural or divine forces. The hypothesis that a divine God created life is at the core of most major religions

Extraterrestrial Origin - This hypothesis, also referred as panspermia, proposes that meteors or cosmic dusts may have carried significant amounts of complex organic molecules to earth, kicking off the evolution of life. It is hypothesized that an early source of carbonaceous material is extraterrestrial, although not yet proven.

Spontaneous Origin - Most scientists accept the hypothesis of spontaneous origin – that life evolved from inanimate matter as associations among molecules became more and more complex. As changes in molecules increased their stability and caused them to persist longer, these molecules could initiate more and more complex associations, culminating in the evolution of cells.

At the ocean’s edge - Life may arise from the constantly forming bubbles at the edge of the ocean as suggested by some scientists.

Under frozen oceans - Just like Jupiter’s moon, Europa, it is hypothesized that life originated under a frozen ocean.

Deep in the earth’s crust - Life may have formed as a by-product of volcanic activity where sulfuric minerals, iron and nickel recombine. It is suggested by Gunter Wachtershauser in 1988 and works of fellow scientists’ shows that these chemical combinations are able to form precursors of amino acids which can be later linked to peptides.

Within clay - The silicate surface chemistry was hypothesized by some researchers, emphasizing the positive charges of clay surface that may attract organic molecules and providing potential catalytic surface where life’s early chemistry may have occurred.

At deep sea vents - Another hypothesis is that life originated at deep sea vents where the necessary prebiotic molecules are synthesized by metal sulfides in the vents. The positive charge of sulfides may have attract the negative charge of biological molecules.

THE MILLER URREY EXPERIMENT - An early attempt to see what kinds of organic molecules might have been produced on the early earth was carried out by Stanley L. Miller and Harold C. Urey in 1953.

Eon - is the largest division of geologic time scale, it spans hundreds of thousands of million years.

Phanerozoic - represents a relatively brief period of half a billion years that constitutes the age of multicellular life on earth.

Proterozoic - also known as “age of hidden life”, is a geological eon spanning the time from the appearance of oxygen in Earth’s atmosphere to just before the proliferation of life.

Archeaen era - When earth’s crust had cooled down, allowing the formation of continents and the beginning of life on earth.

Hadean era - The last era is amed after the mythological Hades, it is when the earth is still forming.

Period - is the basic unit of the geologic time scale; during these spans of time, specific system of rocks were formed.

Epoch - is a subdivision of a geological period during which a rock series is deposited.

ancient cyanobacteria - The oldest among our organisms today, said to be 3.5 billion years old and found in a stromalite in Western Australia. This organism came from Archean era and has a huge role in shaping the change of course of our ecology, the oxygen present in air is generated by numerous of these organisms during this era.

Coronacollina acula - 560 million years old and characterized by hard body parts and spicules that extended 20 -40 cm from the main body which is 5 cm long. It came from Ediacaran epoch.

Trilobites - are arthropods and the soft part of their bodies were covered with exoskeleton, they uses their spine for support. Some live in mud or at great depths of the ocean.

Paleozoic era - this era’s periods are Cambrian, Ordovician, Carboniferous and Permian. During this era, the organisms vary from amphibians, vascular plants and reptiles. However, 90% of all marine animals went extinct at the end of this era.

Myosaurus grailis - a dicynodont from early Triassic epoch.

Dicynodonts - were toothless herbivores, they had caniniform tusk instead, and they vary from small to large burrowers.

Tyranosaurus rex - also known as the “king of the tyrant lizards” belonging to the genus of Coelurosaurian threpod dinosaur. It belongs to Jurassic epoch. These dinosaurs survive through scavenging and hunting.

Tyrannosaurides - a family of predatory dinosaurs

Mosasaurus - an extinct aquatic squamate reptile from Cretaceous epoch. They were apex predators, 12.4 meters long and called the “Lizard of the Meuse River”. These predators’ habitat preference is pelagic lifestyle, they love to reside in the surface of open seas where they can exploit rich marine life in its locality. Its fossils were found in the deposits of Atlantic Ocean.

Mesozoic era - also known as the “middle life” started around 245 million years ago and lasted for 180 million years. Also is known as the era of dinosaurs

Cenozoic era - or “recent life” is also known as the Age of mammals is divided into three periods: Paleogene, Neogene and Quaternary. This era started 65 million years ago and continues up to the present time.

Plesiadapiforms - are archaic members of the order of Primates, they originated from the Paleogene period. They are the first mammals to have finger nails instead of claws, they spent most of their times in trees and are fed on soft plant materials and insects. This lower evolutionary ancestors of Primates lives around 55 – 65 million years ago.

Ardipithecus ramidus - is the oldest species that possesses features that can be related to the hominid lineage. They are also the first organisms that exhibit bipedalism. They came from Neogene periods.

Mutation - Very occasionally, little copying alteration or change occurs during the process of DNA replication. This may because by a number of factors, which include but not limited to radiation, viruses, or carcinogens. Since the blueprint of any cell function is dictated by its genotype, even a minute mutation might mean that the cells fail work properly.

carcinogens - cancer causing materials

Gene Flow - A result of migrating individuals that breed in a new location is gene flow. Genes coming from the immigrants may add new alleles to the existing gene pool of the population, or they may modify the allele frequencies already present if they come from a population with different allele frequencies. Some events that lead to this may be in pollen or spores being disperse by air in a new location, animals hibernating and transferring to a new locale due to changes in temperatures, or humans moving to new cities or countries.

Recombination - Because of sexual reproduction, new gene combination are introduced into a population; thus, it can be an important source of genetic variation. As what you might already know, even siblings are not genetically identical to their parents or even to each other because when organism reproduce sexually, some genetic ___________ on homologous chromosomes occur during meiosis, bringing together new combinations of genes.

Genetic drift - Any change in the allele frequencies in a population due to random sampling is called genetic drift. In every new generation, some species, just by chance, may leave behind a few more descendants than other individual. The genes of these next generations will be genes of the “luckier” individuals, but not necessarily mean the healthier or “better” individuals. When a few “original” individual settle in a new region, the resulting population will not have all the alleles found among the members of the populations.

founder effect - The resulting patterns of genetic variation.

Natural Selection - It is Charles Darwin’s theory, it encompasses the phrase, “when the environment changes, natural selection often favors different traits in a species." Humans are significantly changing the environment in a number of ways; we therefore should not be flabbergasted to see biological species that try to adapt to these new conditions.

Artificial selection - is exactly the same mechanism as natural selection but it is sort of controlled by human purposes rather than natural forces. Even if we have been successful in shifting the frequency of alleles in various dog breeds, we have not created new species.

Hardy-Weinberg Equilibrium - it is also important to know the underlying principle when a population will have a stable genetic frequency.

Geographic or habitat isolation (Ecological) – potential mates occupy different areas or habitats thus, they never come in contact. Rivers change course, mountains rise, continents drift, organisms migrate, and what was once a continuous population is divided into two or more smaller populations.

Temporal or seasonal isolation (Allochronic) – different groups may not be reproductively mature at the same season, or month or year. Example are individuals that have bold behavioral types might be more likely to feed, or to mate, during times of high-predation risk than individuals with shy temperament types that are less likely to be active during risky periods.

Behavioral isolation (Ethological) – patterns of courtship are different. Example are some birds that construct elaborate bowers and decorate them with different colors in order to woo females. If two incipient species evolved differences in this mating ritual, it might permanently isolate them and complete the process of speciation

Mechanical isolation – differences in reproductive organs prevent successful interbreeding. Lack of "fit" between sexual organs: This is a big issue for insects with variably-shaped genitalia. These damselfly penises illustrate just how complex insect genitalia may be.

Gamete Viability isolation (Gametic) – incompatibilities between egg and sperm prevent fertilization. Example are foxes which cannot interbred with coyotes, wolves, and domestic dogs

Hybrid inviability – fertilized egg fails to develop past the early embryonic stages.

Hybrid sterility – hybrids are sterile because gonads develop abnormally or there is abnormal segregation of chromosomes during meiosis. The ability to participate in hybridization is not equally distributed in the populations and frequently is restricted to a small proportion of cross-compatible genotypes.

Hybrid breakdown - F1 hybrids are normal, vigorous and viable, but F2 contains many weak or sterile individuals. There are genes contributing to genetic incompatibilities, and therefore it results to the evolution of intrinsic reproductive isolation (hybrid sterility and inevitability).

Carl von Linnaeus - the Father of Taxonomy

George Louis Leclerc - known as Count Buffon, was a French naturalist who first described descent with modification such as environmental influences, migration, geographical isolation and the struggle for existence.

Georges Cuvier - a vertebrate zoologist and palaeontologist proposed the theory of catastrophism. He explained that there might have been violent and sudden natural catastrophes such as great floods, tectonic earthquakes, and rapid formation of mountain chains, which resulted to death and extinction of most plants and animals.

uniformitarianism – large geological changes occurred not in catastrophic events but by gradual accumulation of small geological changes over long period of time.

Jean Baptiste de Lamarck - was the first biologist to believe that life forms evolve. He proposed the Inheritance of Acquired Characteristics, which is also called Lamarckian Evolution.

Charles Darwin - develop a theory that would contradict the special creation of every organism and imply that all species evolve from common ancestors through a process called natural selection.

Creationism - is the idea that living things are created and remains unchanged since the beginning.

Catastrophism - is the idea that violent and sudden natural catastrophes have resulted to death and extinction of most plants and animals. After each catastrophe, God created new sets of life forms.

Fossils - are remains of ancient organisms trapped in rocks, tar pits, frozen in ice or embedded in amber.

HOMOLOGOUS STRUCTURES - are structures with the same set of bones that presumably evolved from a common ancestor. They appear different and may have varied functions.

ANALOGOUS STRUCTURES - are structures that perform the same function but have very different embryological development or set of structures like bones

VESTIGIAL STRUCTURES - are structures or attributes that have lost most of its ancestral function in more recent species.

Embryology - is the study of the development of an organism from an embryo to its adult form. Common structures are shared in the embryo stage and disappear by the time the embryo reaches the juvenile or adult form.

Biogeography - is the study of geographical distribution of fossils and living organisms.

Taxonomy - This is the field of study that organize living things into groups as they are identified, come from a Greek word ‘taxis’ that means Order or arrangement.

Taxonomist - They decide how to classify species, explore how they fit in their ecosystem and categorize relationship with others in their habitat before giving them names according to standardized system, the binomial naming. This is consists of the genus and specie.

hierarchical taxonomic classification - helps scientists understand and organize the diversity of life in our planet. Basically, it means groups are classified within larger groups. Each level of hierarchy is called the taxonomic level wherein the kingdom is the highest and specie the lowest. It means from general to specific.

taxonomic level - level of hierarchy

Specie - is the basic unit of classification. They are organisms that share many features and can breed with each other producing fertile offspring.

phylogeny - the history of the evolution of a species or group, especially in reference to lines of descent and relationships among broad groups of organisms.

Phylogenetics - is the study of evolutionary relationships among biological entities.

Morphology - The science of the form and structure of organisms