soil

The word “soil,” like many common words, has several

meanings. In its traditional meaning, soil is the natural medium for the growth of land plants, whether or not it has discernible soil horizons. This meaning is still the common understanding of the word, and the greatest interest in soil is centred on this meaning. People consider soil important because it supports plants that supply food, fibres, drugs, and other wants of humans and because it filters water and recycles wastes. Soil covers the earth’s surface as a continuum, except on bare rock, in areas of perpetual frost or deep water, or on the bare ice of glaciers. In this sense, soil has a thickness that is determined by the rooting depth of plants.

Soil in this text is a natural body comprised of solids

(minerals and organic matter), liquid, and gases that occurs on the land surface, occupies space, and is characterised by one or both of the following: horizons, or layers, that are

distinguishable from the initial material as a result of additions,losses, transfers, and transformations of energy and matter or the ability to support rooted plants in a natural environment. This definition is expanded from the 1975 version of Soil Taxonomy to include soils in areas of Antarctica where parthenogenesis occurs but where the climate is too harsh to support the higher plant

forms.

The upper limit of soil is the boundary between soil and air,

shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 m) for the growth of rooted plants. The horizontal boundaries of soil are areas where the soil grades to deep water,barren areas, rock, or ice. In some places the separation between soil and non soil is so gradual that clear distinctions cannot be made.

The lower boundary that separates soil from the non soil

Underneath is most difficult to define. Soil consists of the

Horizons near the earth’s surface that, in contrast to the

Underlying parent material, have been altered by the interactions Of climate, relief, and living organisms over time. Commonly,

Soil grades at its lower boundary to hard rock or to earthy

Materials virtually devoid of animals, roots, or other marks of Biological activity. The lowest depth of biological activity, However, is difficult to discern and is often gradual. For Purposes of classification, the lower boundary of soil is

Arbitrarily set at 200 cm. In soils where either biological activity or current pedogenic processes extend to depths

greater than 200 cm, the lower limit of the soil for classification purposes is still 200 cm. In some instances the more weakly cemented bedrocks (paralithic materials, defined later) have been described and used to differentiate soil series (series control section, defined later), even though the paralithic materials below a paralithic contact are not considered soil in the true sense. In areas where soil has thin cemented horizons that are impermeable to roots, the soil extends as deep as the

deepest cemented horizon, but not below 200 cm. For certain

management goals, layers deeper than the lower boundary of the soil that is classified (200 cm) must also be described if they affect the content and movement of water and air or other interpretative concerns.

In the humid tropics, earthy materials may extend to a depth

of many meters with no obvious changes below the upper 1 or 2 m, except for an occasional stone line. In many wet soils, greyed soil material may begin a few centimetres below the surface and,in some areas, continue down for several meters apparently unchanged with increasing depth. The latter condition can arise

through the gradual filling of a wet basin in which the A horizon is gradually added to the surface and becomes gleyed beneath.Finally, the A horizon rests on a thick mass of gleyed material that may be relatively uniform. In both of these situations, there is no alternative but to set the lower limit of soil at the arbitrary

limit of 200 cm. Soil, as defined in this text, does not need to have discernible

horizons, although the presence or absence of horizons and their nature are of extreme importance in soil classification. Plants can be grown under glass in pots filled with earthy materials, such as peat or sand, or even in water. Under proper conditions all these media are productive for plants, but they are non soil here in the sense that they cannot be classified in the same system that is used for the soils of a survey area, county, or even nation. Plants even grow on trees, but trees are regarded as non soil.

Soil has many properties that fluctuate with the seasons. It

may be alternately cold and warm or dry and moist. Biological activity is slowed or stopped if the soil becomes too cold or too dry. The soil receives flushes of organic matter when leaves fall or grasses die. Soil is not static. The pH, soluble salts, amount of organic matter and carbon-nitrogen ratio, numbers of microorganisms,soil fauna, temperature, and moisture all change with the seasons as well as with more extended periods of time. Soil

must be viewed from both the short-term and long-term

perspective.

Buried Soils

A buried soil is covered with a surface mantle of new soil

material that either is 50 cm or more thick or is 30 to 50 cm

thick and has a thickness that equals at least half the total

thickness of the named diagnostic horizons that are preserved in

the buried soil. A surface mantle of new material that does not have the required thickness for buried soils can be used to establish a phase of the mantled soil or even another soil series if the mantle affects the use of the soil.

Any horizons or layers underlying a plaggen epipedon are

considered to be buried.

A surface mantle of new material, as defined here, is largely

unaltered, at least in the lower part. It may have a diagnostic

surface horizon (epipedon) and/or a cambic horizon, but it has no other diagnostic subsurface horizons, all defined later.

However, there remains a layer 7.5 cm or more thick that fails the requirements for all diagnostic horizons, as defined later, overlying a horizon sequence that can be clearly identified as the solum of a buried soil in at least half of each pedon. The recognition of a surface mantle should not be based only on studies of associated soils.

plant biotechnology

Biotechnology is a scientific discipline with focus on the exploitation of

Metabolic properties of living organisms for the production of valuable products

of a very different structural and organizational level for the benefit of

Men. The products can be the organisms themselves (i.e., biomass or parts

of the organism body), products of cellular or organismic metabolism (i.e.,

enzymes, metabolites), or products formed from endogenous or exogenous

substrates with the help of single enzymes or complex metabolic routes. The

organisms under question vary from microbes (bacteria, fungi) to animals

and plants. In addition to intact organisms, isolated cells or enzyme preparations

are employed in biotechnology. The possibility to submit the producing

organisms or the cellular systems to technical and even industrial

procedures has led to highly productive processes. The products of biotechnology

are of importance for medicine, pharmaceutical sciences, agriculture,

food production, chemistry, and numerous other disciplines.

Biotechnology receives the necessary scientific and technical information

from a considerable number of disciplines. Cell biology, morphology

of the employed organisms, biochemistry, physiology, genetics, and various technical fields are major sources. In the last two decades, molecular biology

and gene technology have substantially contributed to the spectrum of scientific

disciplines forming biotechnology. As is always true for progress in

natural sciences, it is especially true for biotechnology that more rapid development

and gain of higher standards depend on the improvement of

methods.

In the historical development of biotechnology, microbes have been

used preferentially. They still offer an extremely rich potential for biotechnological

application. Animal systems and their cells are also valuable

systems, especially in view of the very costly products (i.e., antibodies,

vaccines). Although much later in the chronological process, plant biotechnology

has made an impressive development in gaining basic and applicable

knowledge as well as in establishing production processes. It is therefore

justified to speak of an emerging field.

A LONG HISTORY TO REACH A HIGH STANDARD

In each ecosystem plants and other photosynthetically active organisms are

responsible for primary production, which provides the energetic and nutritional

basis for all subsequent trophic levels. The extremely high ability of

plants to adapt to all kinds of environmental conditions and ecosystems has

led to an extremely wide and differentiated spectrum of plants. Since ancient

times higher plants have formed the main source of food for men, and

therefore, concomitant with early phases of settlements and agriculture, men

started to establish and improve crop plants. Archeological evidence has

clearly shown how long well-known crop species (i.e., maize, cereals, legumes)

have been grown, modified by selection, and thus improved in quality

and yield. Plant breeding is indeed an old art that has been continuously

developed in efficiency and scope. Quite typical for quality breeding of, for

instance, cereals is the long procedure required (sometimes decades) to reach

particular genotypes and to cross in specific genes or traits.

An interesting achievement in breeding of wheat is characterized by

the term green revolution, in which (around 1950-1960) wheat genotypes

from many different countries were used successfully on a very large scale

to breed high-yielding and durable lines. For many countries such new varieties

were a very great improvement for their agriculture.

Another important goal in breeding improved crop plants is the often

achieved adaptation to unfavorable environmental conditions (i.e., heat,

drought, salt, and other cues). Although good results have been obtained,

such efforts will undoubtedly remain in the focus of future efforts. Better

insight into the physiology, biochemistry, and chemical reactions as well as the gene regulation of the endogenous adaptation and defense mechanisms

that plants can express will contribute to these objectives. Gene technology

will be an essential component in these efforts.

Another characteristic feature of the long-term breeding of cereals,

potatoes, or vegetables is the fact that during the long periods the shape and

the outer appearance of the plants have changed so much that the original

wild types were either lost or no longer easily identified as starting material.

A typical example is corn. Modern agricultural crop plants are also bred for

very uniform physical appearance, time of flowering, and maturity so that

harvest by machines in an industrial manner is possible (examples are cotton,

maize, and cereals). It is a feature of our high-yielding agriculture that all

possible mechanical techniques are being employed.

Very precious treasures for future agriculture and for plant biotechnology

are the gene banks and the International Breeding Centers, where

great numbers of genotypes of crop plants are multiplied and carefully preserved

for long periods of time. Such "pools of genes" represent the basis

for sustainable development and allow future programs for improved adaptation

of plants to human needs. Fortunately, the understanding has gained

ground in recent years that in addition to crop plants all types of wild plants,

in every ecosystem, must be preserved because of the genetic resources to

be possibly exploited in the future.

An interesting development in itself, with a long history and remarkable

contributions to culture and art, is the numerous and sometimes highly

sophisticated ornamental plants produced in many countries. Beauty of color

and flower shape were the guidelines in their breeding and selection. Rather

early in this development the value of mutagenetic reagents was learned,

and these ornamentals also served to shape the term of a mutant. Recent

biochemical studies with, for example, snapdragon, tulip, chrysanthemum,

or petunia and their flavonoid constituents clearly presented evidence that

the various flower colors can contribute to identifing biosynthetic pathways.

In connection with flower pigments, which are secondary metabolites,

it should be remembered that numerous other secondary constitutents of very

different chemical structures are valuable Pharmaceuticals. In many countries

knowledge of plants as sources of drugs has been cherished for long

times. Modern pharmacological and chemical studies have helped in the

identification of the relevant compounds. Such investigations are still considered

important objectives of plant biotechnology. In some cases extensive

breeding programs have already achieved the selection and mass cultivation

of high-yielding lines. In modern pharmacy, about 25% of drugs still contain

active compounds from natural sources, which are primarily isolated from

plants.

For a good number of years in the period from 1950 to 1980, plant

biochemistry and plant biophysics concentrated on elucidation of the photosynthetic

processes. The pathways of CO2 assimilation as well as structure,

energy transfer reactions, and membrane organization of chloroplasts and

their thylakoids were objectives of primary interest. Chloroplast organization

and molecular function of this organelle can be regarded as well-understood

fields in plant biochemistry and physiology.

The last three decades of the 20th century were characterized by very

comprehensive molecular analyses of chemical reactions, metabolic pathways,

cellular organization, and adaptative responses to unfavorable environmental

conditions in numerous plant systems. A very broad set of data

has been accumulated so that plant biochemistry and closely related fields

can now offer a good understanding of plants as multicellular organisms and

highly adaptative systems. From a molecular point of view, the construction

and the functioning of the different tissues and organs have become clear.

Numerous experimental techniques have contributed to this development and

some are typical plant-specific methods (i.e., cell culture techniques) with a

very broad scope of application.

A fascinating field of modern plant biochemistry concerns the elucidation

of the function and the molecular mechanisms of the various photoreceptor

systems of higher plants. Red/far red receptors, blue light-absorbing

cryptochromes, and ultraviolet (UV) light photoreceptors are essential

components of plant development (1). These systems translate a light signal

into physiological responses via gene activation. Quite remarkable, phosphorylated/

unphosphorylated proteins are the essential components of the

signal transduction system (1,2). Biotechnology will gain from this knowledge,

and highly sensitive sensor systems could possibly be constructed.

In the history of plant sciences and biotechnology, the recent development

of molecular biology and the introduction of gene technology deserve

emphasis. Isolation, characterization, and functional determination of

genes have become possible. Many plant genes were rather rapidly identified,

and the number is increasing at enormous speed. Promoter analyses

and identification of promoter binding proteins have decisively contributed

to an understanding of the organization and function of plants as organisms

consisting of multiple tissues and different organs. The phenomena of multigenes

and multiple enzymes in one protein family were further revealed.

Many different techniques in molecular biology and gene technology turned

out to be extremely valuable. Recognition of the biology of Agrobacterium

tumefaciens and application of its transferred DNA (T-DNA) system represented

giant leaps forward. In general, because of these modern gene technological

methods, plant biotechnology has grown into a new dimension

with putative future possibilities that can hardly be overestimated.

DNA repair mechanism

Contents

Introduction

Sources of damage

Types of repair mechanisms

DNA repair and aging

DNA repair and cancer

References               

Introduction

          DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

Sources of damage

Endogenous damage:

Spontaneous mutation

Oxidative deamination

Exogenous damage:

Ultraviolet [UV 200-300nm] radiation

X-rays and Gamma rays

Plant toxins

Mutagenic chemicals

Chemotherapy and Radiotherapy

Types of repair

Preventative

Direct DNA repair

Post replication repair

Preventative repair

Eliminate superoxide free radicals

Direct DNA repair

Mainly three types:

Alkyltransferase

Photoreactivation

Excision repair

Alkyltransferases

A group of enzymes which remove alkyl group from the bases of DNA

The best studied of the alkyltransferase is O6 – methyl guanine methyl transferase (MGMT).

Photoreactivation

Restores dimerized pyrimidines to their original form

Excision Repair

Recognizes and excises damaged nucleotides and arrange them with the correct ones

Postreplication repair

There are mainly three types:

Recombination repair

Mismatch repair

SOS response

Recombination repair

Replaces a lesions with the addition of correct nucleotides using one strand as a template

Mismatch repair system

Replaces mismatched nucleotides with the correct one

SOS responses

Activate excision, recombination and other response mechanisms

DNA repair and aging

DNA repair and cancer

Inherited mutations that affect DNA repair genes are strongly associated with high cancer risks in humans.

Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway.

BRCA1 and BRCA2, two famous mutations conferring a hugely increased risk of breast cancer on carriers, are both associated with a large number of DNA repair pathways.

DNA bases may be modified by deamination OR alkylation.
The position of the modified (damaged) base is called the ‘abasic site’ or ‘AP site’
In the E.coli the DNA glycolsylase can recognize the AP site and remove its bases.

Then the AP endonuclease removes the AP site and neighbouring nucleotides.

The Gap is filled by DNA polymerase I and DNA ligase.


NUCLEOTIDE EXCISION REPAIR

In E.coli proteins UvrA, UvrB, UvrC are involved in removing the damaged nucleotides.
The gap is then filled by DNA polymerase I and DNA ligase.
Nucleotide excision repair is particularly important in recongnising thymine dimers that form as a result of exposure to UV radiation.

MISMATCH REPAIR

To repair mismatched bases the system has to know which base is the correct one.
In E.coli this is achieved by a special methylase called “Dam methylase”, which can methylate all adenines that occur within (5’) GATC sequence.
To distinguish old and new strand old strand is methylated while new is not.

CONCLUSION

DNA repair mechanisms promote genomic stability and prevent cancer.
Thus, DNA repair mechanisms provide a way of proofreading and repairing damaged DNA.

References

Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Biology of the Cell, p963. WH Freeman: New York, NY. 5th ed.

Toshihiro Ohta, Shin-ichi Tokishita, Kayo Mochizuki, Jun Kawase

Masahide Sakahira and Hideo Yamagata, UV Sensitivity and Mutagenesis of the Extremely Thermophilic Eubacterium Thermus thermophilus HB27, Genes and Environment Vol. 28 (2006) , No. 2 p.56-61.

Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene, ch. 9 and 10. Peason Benjamin Cummings; CSHL Press. 5th ed.

DNA FINGERPRINTING

DNA 101 - What is it?
  What is DNA Fingerprinting?
  How is DNA Fingerprinting done?
  What are the applications of DNA Fingerprinting?
  What are the problems with DNA Fingerprinting?
  Further reading
  Glossary

What is DNA Fingerprinting?

The chemical structure of everyone's DNA is the same. The only difference between people (or any animal) is the order of the base pairs. There are so many millions of base pairs in each person's DNA that every person has a different sequence.

Using these sequences, every person could be identified solely by the sequence of their base pairs. However, because there are so many millions of base pairs, the task would be very time-consuming. Instead, scientists are able to use a shorter method, because of repeating patterns in DNA.

These patterns do not, however, give an individual "fingerprint," but they are able to determine whether two DNA samples are from the same person, related people, or non-related people. Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain probability of a match.

Making DNA Fingerprints

DNA fingerprinting is a laboratory procedure that requires six steps:

1: Isolation of DNA.
DNA must be recovered from the cells or tissues of the body. Only a small amount of tissue - like blood, hair, or skin - is needed. For example, the amount of DNA found at the root of one hair is usually sufficient.

2: Cutting, sizing, and sorting.
Special enzymes called restriction enzymes are used to cut the DNA at specific places. For example, an enzyme called EcoR1, found in bacteria, will cut DNA only when the sequence GAATTC occurs. The DNA pieces are sorted according to size by a sieving technique called electrophoresis. The DNA pieces are passed through a gel made from seaweed agarose (a jelly-like product made from seaweed). This technique is the biotechnology equivalent of screening sand through progressively finer mesh screens to determine particle sizes.

3: Transfer of DNA to nylon.
The distribution of DNA pieces is transferred to a nylon sheet by placing the sheet on the gel and soaking them overnight.

4-5: Probing.
Adding radioactive or colored probes to the nylon sheet produces a pattern called the DNA fingerprint. Each probe typically sticks in only one or two specific places on the nylon sheet.

6: DNA fingerprint.
The final DNA fingerprint is built by using several probes (5-10 or more) simultaneously. It resembles the bar codes used by grocery store scanners.

Practical Applications of DNA Fingerprinting

1. Paternity and Maternity
Because a person inherits his or her VNTRs from his or her parents, VNTR patterns can be used to establish paternity and maternity. The patterns are so specific that a parental VNTR pattern can be reconstructed even if only the children's VNTR patterns are known (the more children produced, the more reliable the reconstruction). Parent-child VNTR pattern analysis has been used to solve standard father-identification cases as well as more complicated cases of confirming legal nationality and, in instances of adoption, biological parenthood.

2. Criminal Identification and Forensics
DNA isolated from blood, hair, skin cells, or other genetic evidence left at the scene of a crime can be compared, through VNTR patterns, with the DNA of a criminal suspect to determine guilt or innocence. VNTR patterns are also useful in establishing the identity of a homicide victim, either from DNA found as evidence or from the body itself.

3. Personal Identification
The notion of using DNA fingerprints as a sort of genetic bar code to identify individuals has been discussed, but this is not likely to happen anytime in the foreseeable future. The technology required to isolate, keep on file, and then analyze millions of very specified VNTR patterns is both expensive and impractical. Social security numbers, picture ID, and other more mundane methods are much more likely to remain the prevalent ways to establish personal identification.

Preparation of the Student Materials

•The supplies can best be provided to the class in groups of five students.

•The DNA samples should be refrigerated until class time.

•It is too expensive for the Office of Biotechnology to provide DNA for every student in a class. The office will provide enough DNA, restriction endonuclease, and reaction buffer for a minimum of two groups of five students or a maximum of one group of five students in every class section, whichever is greater.

DNA Fingerprinting
Preparation of the Student Materials
(cont.)

•For the other student groups, use distilled water to replace the DNA, restriction endonuclease, and reaction buffer.

•Every group of students should be provided with the blue migration dye.

DNA and Enzyme Prep

Step 1

•For each group of students label 7-1.5 ml tubes "C,1,2,3,4, N and D" with a permanent felt pen.

•Tube "N" will contain the enzyme mixture.

•Tube "D" will contain the migration dye.

DNA and Enzyme Prep
Step 2

•Pipette 17 µl of a 0.025 µg/µl concentration of pBR322 DNA into the tube labeled "C."

DNA and Enzyme Prep
Step 3

•In the tube labeled "1" pipette 17 µl of 0.15 µg/µl concentration of lambda DNA.

DNA and Enzyme Prep
Step 4

•In the tube labeled "2" pipette 17 µl of 0.075 µg/µl concentration of Ad-2 DNA.

DNA and Enzyme Prep
Step 5

•In the tube labeled "3" pipette 17 µl of 0.025 mg/ml concentration of pBR322 DNA.

DNA and Enzyme Prep
Step 6

•In the tube labeled "4" pipette 17 µl of  0.025 µg/µl concentration of pUC19 DNA.

DNA and Enzyme Prep

Step 7

•In the microcentrifuge tube (1.5 ml) labeled "N," pipette 15 µl of reaction buffer and 3 µl Bgl 1.

DNA and Enzyme Prep
Step 8

•In a microcentrifuge tube (1.5 ml) labeled "D,"  pipette 40 µl of blue migration dye.