A Nobody's Knowledge Bank

Bioinformatics

2006-05-22T18:50:00.000+08:00

Bioinformatics and computational biology involve the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.

The terms bioinformatics and computational biology are often used interchangeably, although the former typically focuses on algorithm development and specific computational methods, while the latter focuses more on hypothesis testing and discovery in the biological domain.

Fermentation - Wikipedia, the free encyclopedia

2006-04-24T02:00:00.000+08:00

"Fermentation typically refers to the conversion of sugar to alcohol using yeast. The process is often used to produce wine and beer, but fermentation is also employed in preservation to create lactic acid in sour foods such as pickled cucumbers, kimchi and yogurt. The science of fermentation is known as zymology.

In its strictest sense, fermentation (formerly called zymosis) is the anaerobic metabolic breakdown of a nutrient molecule, such as glucose, without net oxidation. Fermentation does not release all the available energy in a molecule; it merely allows glycolysis (a process that yields two ATP per glucose) to continue by replenishing reduced coenzymes. Depending on which organism it is taking place in, fermentation may yield lactate, acetic acid, ethanol, or other reduced metabolites. Yeast produces ethanol and CO2; human muscle (under anaerobic conditions) produces lactic acid.

Fermentation is also used much more broadly to refer to the bulk growth of microorganisms on a growth medium. No distinction is made between aerobic and anaerobic metabolism when the word is used in this sense.

Fermentation usually implies that the action of the microorganisms is desirable. Occasionally wines are enhanced through the process of cofermentation. When fermentation stops prior to complete conversion of sugar to alcohol, a stuck fermentation is said to have occurred."

zygomycota

2006-04-24T01:53:00.000+08:00

Thiobacillus ferrooxidans

2006-04-24T01:36:00.000+08:00

"Thiobacillus ferrooxidans is recognized as being responsible for the oxidation of iron and inorganic sulfur compounds in areas such a mine tailings and coal deposits where these compounds are abundant."

Thiobacillus ferrooxidans

2006-04-24T01:29:00.001+08:00

Thiobacillus ferrooxidans

2006-04-24T01:29:00.000+08:00

Thiobacillus ferrooxidans

2006-04-24T01:28:00.000+08:00

Listeria monocytogenes - Wikipedia, the free encyclopedia

2006-04-24T01:19:00.000+08:00

"Listeria monocytogenes is a Gram-positive bacterium, in the division Firmicutes, named for Joseph Lister. It is motile by means of flagella. It can also move within eukaryotic cells by polymerizing actin comet tails with a protein called ActA. Some studies suggest that 1 to 10% of humans may carry L. monocytogenes in their intestines.

Researchers have found L. monocytogenes in at least 37 mammalian species, both domesticated and feral, as well as in at least 17 species of birds and possibly in some species of fish and shellfish. Laboratories can isolate L. monocytogenes from soil, silage, and other environmental sources. L. monocytogenes is quite hardy and resists the deleterious effects of freezing, drying, and heat remarkably well for a bacterium that does not form spores. Most L. monocytogenes are pathogenic to some degree."

Bacillus thuringiensis

2006-04-24T01:11:00.000+08:00

"B. thuringiensis (commonly known as 'Bt') is an insecticidal bacterium, marketed worldwide for control of many important plant pests - mainly caterpillars of the Lepidoptera (butterflies and moths) but also mosquito larvae, and simuliid blackflies that vector river blindness in Africa. Bt products represent about 1% of the total ‘agrochemical’ market (fungicides, herbicides and insecticides) across the world. The commercial Bt products are powders containing a mixture of dried spores and toxin crystals. They are applied to leaves or other environments where the insect larvae feed. The toxin genes have also been genetically engineered into several crop plants (see Agrobacterium). The method of use, mode of action, and host range of this biocontrol agent differ markedly from those of Bacillus popilliae."

Biotech Basics - How Biotechnology Works

2006-04-23T23:58:00.000+08:00

Agrobacterium method

The left side of this diagram shows how Agrobacterium is used in broad-leafed (dicots) crops such as tomatoes, potatoes, cotton and canola to introduce a new gene into a plant. Agrobacterium tumefaciens is a soil microorganism that acts as a natural genetic engineer. It can insert a piece of its DNA into the chromosome of a plant cell. Monsanto researchers discovered that for some kinds of plants, Agrobacterium was the perfect method for introducing new traits into the plant. When pieces of plant tissue were added to culture with the Agrobacterium containing the new gene, the gene could be transferred into the plant cells. These cells grow into plants with the new trait.

Biotech Basics - How Biotechnology Works

2006-04-23T23:56:00.000+08:00

"Agrobacterium method

The left side of this diagram shows how Agrobacterium is used in broad-leafed (dicots) crops such as tomatoes, potatoes, cotton and canola to introduce a new gene into a plant. Agrobacterium tumefaciens is a soil microorganism that acts as a natural genetic engineer. It can insert a piece of its DNA into the chromosome of a plant cell. Monsanto researchers discovered that for some kinds of plants, Agrobacterium was the perfect method for introducing new traits into the plant. When pieces of plant tissue were added to culture with the Agrobacterium containing the new gene, the gene could be transferred into the plant cells. These cells grow into plants with the new trait."

Polymerase chain reaction - Wikipedia, the free encyclopedia

2006-04-23T23:53:00.000+08:00

"PCR is used to amplify a short, well-defined part of a DNA strand. This can be a single gene, or just a part of a gene. As opposed to living organisms, the PCR process can copy only short DNA fragments, usually up to 10 kb (kb stands for kilo base pairs). Certain methods can copy fragments up to 47 kb in size, which is still much less than the chromosomal DNA of a eukaryotic cell--for example, a human cell contains about three billion base pairs.

PCR, as currently practiced, requires several basic components. These components are:

* DNA template, or cDNA which contains the region of the DNA fragment to be amplified
* Two primers, which determine the beginning and end of the region to be amplified (see following section on primers)
* Taq polymerase, which copies the region to be amplified
* Deoxynucleotides-triphosphate, from which the DNA-Polymerase builds the new DNA
* Buffer, which provides a suitable chemical environment for the DNA-Polymerase

The PCR reaction is carried out in a thermal cycler. This is a machine that heats and cools the reaction tubes within it to the precise temperature required for each step of the reaction. To prevent evaporation of the reaction mixture (typically volumes between 15-100µl per tube), a heated lid is placed on top of the reaction tubes or a layer of oil is put on the surface of the reaction mixture. These machines cost more than USD 2,500 in 2004."

紅麴中的黴菌毒素——Citrinin

2006-04-23T23:13:00.000+08:00

明朝宋應星於「天工開物」，即隱喻了紅麴菌具有抑菌的功效。1977年Wong與Bau學者發現粗萃取的紅麴色素具有抗菌的活性。而後發現此抗菌物質monascidin A和Penicillium citrinum 所產生的citrinin在吸收光譜、NMR、MS等分析具有相同的特性，證實了兩者是同種物質。

Citrinin是一種典型的黴菌毒素，最早是由Penicillium citrinum菌中發現。之後於黴菌Aspergillum 及紅麴菌Monascus 中陸續發現。Citrinin是一種檸檬黃的結晶物，可溶於醇及稀鹼，對小鼠及大鼠LD₅₀ 值為35、67mg/kg。Citrinin除了是一種黴菌毒素外，亦具有其他生理活性，例如antimicrobial、phytotoxic、 cytotoxic、hypocholesterolemic及酵素抑制效應。

Citrinin對gram-positive細菌如Bacillus、Streptococcus及Pseudomonas等食品腐敗菌具有抑制作用。此外；citrinin也是一種肝腎毒素。目前亦有研究指出citrinin具有致畸形毒性，當citrinin注射量越高則致畸形的比率就越高，Ciegler等人曾指出注射citrinin於雞胚胎中會造成雞胚胎畸形，如腦畸形、腳變形、眼球凸出、形成交叉喙及頭頸扭曲方向不正常等。

紅麴是我國傳統產品，藥用或作為食品添加劑或用於釀酒等在我國及日本等國家都已有規範。但在西方國家使用卻有些爭議，其中以紅麴中所含有的citrinin意見最多。

1999年荷蘭學者Monica等人從市售的紅麴產品中分析citrinin的含量約在0.2-17.1ppm，並進行Ames Salmonella-microsome assay及Salmonella- hepatocyte assay之微生物誘變試驗，結果並未發現紅麴產品有致變異性。作者同時指出紅麴發酵產物應用於食品已經好幾個世紀，但也從未有危害事件發生，這可歸於食品加工技術或發酵方法已減低citrinin 濃度，但對於紅麴中citrinin之污染仍應盡量避免。

國內對citrinin含量仍未定出最低含量標準，國外目前可查到者，一般以1 ppm（百萬分之一）為允許存在最低標準。

紅麴為中國幾千年來使用歷史悠久之傳統食品，其保健功效不斷被發現，相關研究應是方興未艾，前途看好。筆者以為紅麴既然是中國傳統食用之保健食品，其保健功效應繼續研究，有害成分亦應研發新產品使其符合安全標準。如此具有多功效、且安全的紅麴保健食品之上市，將指日可待。

Bugs in the News - What the Heck is an E. coli?

2006-04-23T22:56:00.000+08:00

What does E.coli mean?

E. coli is the abbreviated name of the bacterium in the Family Enterobacteriaceae named Escherichia (Genus) coli (Species). Dave Graham in the Department of Microbiology, University of Illinois at Urbana/Champaign, recently pointed me to information gleaned from G.W. Tannock's book, Normal Microflora,1995, Chapman & Hall, which reveals that approximately 0.1% of the total bacteria within an adult's intestines (on a Western diet) is represented by E. coli. Although, in a newborn infant's intestines E. coli, along with lactobacilli and enterococci represent the most abundant bacterial flora.

In fact, it is for this reason that the organisms which happily inhabit the intestinal tract as normal flora are named enteric bacteria. The Family to which E. coli belongs (Enterobacteriaceae, is named what it is - because of the Greek word enterikos - which pertains to the intestine. The name Escherichia comes from the name of the person Escherich, who in 1885 first isolated and characterized this bacterium...

: : 農業生技產業資訊網 : :

2006-04-23T22:55:00.000+08:00

: : 農業生技產業資訊網 : :

Axiom of Choice

2006-04-11T00:04:00.000+08:00

The Axiom of Choice (AC) was formulated about a century ago, and it was controversial for a few of decades after that; it may be considered the last great controversy of mathematics. It is now a basic assumption used in many parts of mathematics. In fact, assuming AC is equivalent to assuming any of these principles (and many others):

Given any two sets, one set has cardinality less than or equal to that of the other set -- i.e., one set is in one-to-one correspondence with some subset of the other. (Historical remark: It was questions like this that led to Zermelo's formulation of AC.)
Any vector space over a field F has a basis -- i.e., a maximal linearly independent subset -- over that field. (Remark: If we only consider the case where F is the real line, we obtain a slightly weaker statement; it is not yet known whether this statement is also equivalent to AC.)
Any product of compact topological spaces is compact. (This is now known as Tychonoff's Theorem, though Tychonoff himself only had in mind a much more specialized result that is not equivalent to the Axiom of Choice.)

Strong connectivity algorithm

2006-04-02T12:33:00.000+08:00

Define the DFS numbering dfsnum(v) to be the number of vertices visited before v in the DFS. Then if there is a back or cross edge out of the subtree of v, it's to something visited before v and therefore with a smaller dfsnum. We use this by defining the low value low(v) to be the smallest dfsnum of a vertex reachable by a back or cross edge from the subtree of v. If there is no such edge, low(v)=dfsnum(v). Then rephrasing what we've seen so far, v is a head of a component exactly when low(v)=dfsnum(v). The advantage of using these definitions is that dfsnum(v) is trivial to calculate as we perform the DFS, and low(v) is easily computed by combining the low values from the children of v with the values coming from back or cross edges out of v itself.

We use one more simple data structure, a stack L (represented as a list) which we use to identify the subtree rooted at a vertex. We simply push each new vertex onto L as we visit it; then when we have finished visiting a vertex, its subtree will be everything pushed after it onto L. If v is a head, and we've already deleted the other heads in that subtree, the remaining vertices left on L will be exactly the component [v].

We are now ready to describe the actual algorithm. It simply performs a DFS, keeping track of the low and dfsnum values defined above, using them to identify heads of components, and when finding a head deleting the whole component from the graph, using L to find the vertices of the component.

    DFS(G)
   {
   make a new vertex x with edges x->v for all v
   initialize a counter N to zero
   initialize list L to empty
   build directed tree T, initially a single vertex {x}
   visit(x)
   }

   visit(p)
   {
   add p to L
   dfsnum(p) = N
   increment N
   low(p) = dfsnum(p)
   for each edge p->q
       if q is not already in T
       {
       add p->q to T
       visit(q)
       low(p) = min(low(p), low(q))
       } else low(p) = min(low(p), dfsnum(q))

   if low(p)=dfsnum(p)
   {
       output "component:"
       repeat
       remove last element v from L
       output v
       remove v from G
       until v=p
   }
   }

1.4.1 Connected Components

2006-03-27T18:46:00.000+08:00

Strongly Connected Component Implementation
Related Course: Introduction to Algorithm

Beta Integral -- From MathWorld

2006-03-21T21:50:00.000+08:00

Beta Integral
Beta Function

Related Course: Calculus, Statistics

Oligopoly - Wikipedia, the free encyclopedia

2006-03-14T14:48:00.000+08:00

market form in which a market is dominated by a small number of sellers (oligopolists). The word is derived from the Greek for few sellers. Because there are few participants in this type of market, each oligopolist is aware of the actions of the others. Oligopolistic markets are characterised by interactivity. The decisions of one firm influence, and are influenced by, the decisions of other firms. Strategic planning by oligopolists always involves taking into account the likely responses of the other market participants. An oligopy is a form of economy. As a quantitative description of oligopoly, the four-firm concentration ratio is often utilized. This measure expresses the market share of the four largest firms in an industry as a percentage. Using this measure, an oligopoly is defined as a market in which the four-firm concentration ratio is above 40%. An example would be the supermarket industry in the United Kingdom, with a four-firm concentration ratio of over 70% and the brewery industry also in the U.K has a four firm concentration ratio of a staggering 85%.

What's a number?

2006-03-14T13:41:00.000+08:00

Rational and Irrational numbers

Lemma 1

Between any two different rational numbers a and b there is at least one other rational number.
Between any two different irrational numbers a and b there is at least one other rational number.
Between any two different rational numbers a and b there is at least one other irrational number.
Between any two different irrational numbers a and b there is at least one other irrational number.

Corollary

In all four statements assertion of existence of a single number can be replaced with the assertion of existence of infinitely many numbers.

Lemma 5

The set I of all irrational numbers is not countable.

Lemma 6

The set of all algebraic numbers is countable.

Probability Paradox

2006-03-14T13:31:00.000+08:00

Probability is often taken too seriously. When someone hears that the probability of a given event occurring is zero, the usual interpretation is that the event will never occure. In other words, it is commonly thought that an event with a probability of zero is impossible.

However, take, for instance, the set of all integers. What is the probabilty of choosing a given integer at random? Since there are an infinite number of integers and we are choosing only one, we would the calculate the probability as being 1/infinity = 0.* But this means that we have zero probability of choosing any given number. That's perplexing, because if we choose a random number from the set of integers we will have just accomplished something that has a probability of zero!

Even more perplexing, the rational numbers are a countable subset of the uncountable set of real number. (The uncountably infinite set of irrational numbers are what makes the real numbers uncountable.) In other words, there are infinitely more irrational numbers than rational numbers. That means the probabiliy of choosing a rational number at random out of the set of real numbers is zero!

.....

Related course: Probability

An Introduction to Monte Carlo Methods

2006-03-10T11:07:00.001+08:00

The expression "Monte Carlo method" is actually very general. Monte Carlo (MC) methods are stochastic techniques--meaning they are based on the use of random numbers and probability statistics to investigate problems. You can find MC methods used in everything from economics to nuclear physics to regulating the flow of traffic. Of course the way they are applied varies widely from field to field, and there are dozens of subsets of MC even within chemistry. But, strictly speaking, to call something a "Monte Carlo" experiment, all you need to do is use random numbers to examine some problem.

The use of MC methods to model physical problems allows us to examine more complex systems than we otherwise can. Solving equations which describe the interactions between two atoms is fairly simple; solving the same equations for hundreds or thousands of atoms is impossible. With MC methods, a large system can be sampled in a number of random configurations, and that data can be used to describe the system as a whole.

"Hit and miss" integration is the simplest type of MC method to understand, and it is the type of experiment used in this lab to determine the HCl/DCl energy level population distribution. Before discussing the lab, however, we will begin with a simple geometric MC experiment which calculates the value of pi based on a "hit and miss" integration.

Related Courses: Digital Electronics, Probability, Statistics

An Introduction to Monte Carlo Methods

2006-03-10T11:07:00.000+08:00

Quorum sensing - Wikipedia, the free encyclopedia

2006-03-06T23:40:00.000+08:00

"The purpose of quorum sensing is to coordinate certain behaviour or actions between bacteria of the same kind, depending on their number. For example, opportunistic bacteria, such as Pseudomonas aeruginosa can grow within a host without harming it, until they reach a certain concentration. Then they become aggressive, their numbers sufficient to overcome the host's immune system and form a biofilm, leading to disease. It is hoped that the enzymatic degradation of the signalling molecules will prevent the formation of such biofilms and possibly weaken established biofilms. Distrupting the signalling process in this way is called quorum quenching."

Related Course: Introduction to Biotechnology

Deinococcus

2006-03-06T23:33:00.000+08:00

"Bacteria belonging to the family Deinococcaceae are some of the most radiation-resistant organisms yet discovered. Deinococcus (Micrococcus) radiodurans strain R1 (ATCC BAA-816) was first reported in 1956 by A. W. Anderson and coworkers of the Oregon Agricultural Experimental Station, Corvalis, Oregon. This obligate aerobic bacterium typically grows in rich medium as clusters of two cells (diplococci) in the early stages of growth, and as clusters of four cells (tetracocci) in the late stages of growth, is non-pathogenic, and best known for its ability to survive extremely high doses of acute ionizing radiation (10,000 Gy) without cell-killing. For comparison, 5 Gy is lethal to the average human, and 1,000 Gy can sterilize a culture of Escherichia coli. D. radiodurans is capable of growth under chronic radiation (60 Gy/hour) and resistant to other DNA damaging conditions including exposure to desiccation, UV light, and hydrogen peroxide. The genes and cellular pathways underlying the survival strategies of D. radiodurans are under investigation, and its resistance characteristics are being exploited in the development of bioremediation processes for cleanup of highly radioactive US Department of Energy waste sites."

Related Course: Introduction to Biotechnology

Pseudomonas

2006-03-06T23:30:00.000+08:00

"Pseudomonas aeruginosa is the epitome of an opportunistic pathogen of humans. The bacterium almost never infects uncompromised tissues, yet there is hardly any tissue that it cannot infect if the tissue defenses are compromised in some manner.

Pseudomonas aeruginosa is a Gram-negative, aerobic rod belonging to the bacterial family Pseudomonadaceae. The family includes other genera, which, together with certain other organisms, constitute the bacteria informally known as pseudomonads. These bacteria are common inhabitants of soil and water. They occur regularly on the surfaces of plants and occassionally on the surfaces of animals. The pseudomonads are well known to plant microbiologists because they are one of the few groups of bacteria that are true pathogens of plants. In fact, Pseudomonas aeruginosa is occasionally a pathogen of plants. But Pseudomonas aeruginosa and two former Pseudomonas species (now reclassified as Burkholderia) are pathogens of humans. A general treatment of the pseudomonads is presented in The Genus Pseudomonas . This chapter deals specifically with Pseudomonas aeruginosa as a pathogen of humans.

Pseudomonas aeruginosa is an opportunistic pathogen, meaning that it exploits some break in the host defenses to initiate an infection. It causes urinary tract infections, respiratory system infections, dermatitis, soft tissue infections, bacteremia, bone and joint infections, gastrointestinal infections and a variety of systemic infections, particularly in patients with severe burns and in cancer and AIDS patients who are immunosuppressed. Pseudomonas aeruginosa infection is a serious problem in patients hospitalized with cancer, cystic fibrosis, and burns. The case fatality rate in these patients is 50 percent."

Related Course: Introduction to Biotechnology

Epulopiscium

2006-03-06T23:23:00.000+08:00

Epulopiscium fishelsoni - a visible species of microbes
"Epulopiscium fishelsoni was first found in the gut of the brown surgeonfish Acanthurus nigrofuscus in the Red Sea in 1985. Since then, similar organisms have been found in surgeonfish in the Hawaiian Islands, French Polynesia, Tuvalu, Guam, southern Japan, Papua New Guinea, the Great Barrier Reef, and South Africa (Bresler et al. 1998). Due to the daily cycle of the E. fishelsoni, it affects the pH of the surgeonfish's gut fluids differently during the day and night which suggests that cyclic metabolic changes occur within the bacterium."

Related Course: Introduction to biotechnology

Countable and Uncountable Sets

2006-03-02T16:17:00.000+08:00

Countable set - Wikipedia
Uncountable Set - Wikipedia

Related Course: Discrete Mathematics & Probability

GNU tar 1.15.90

2006-03-01T21:57:00.000+08:00

Related Course: System Programming

Automating Program Compilation - Writing Makefiles

2006-03-01T21:37:00.000+08:00

Related Course: System Programming

GCC Manual

2006-03-01T21:24:00.000+08:00

General Programming Information

-Wall: All of the above `-W' options combined. This enables all the warnings about constructions that some users consider questionable, and that are easy to avoid (or modify to prevent the warning), even in conjunction with macros. This also enables some language-specific warnings described in C++ Dialect Options and Objective-C and Objective-C++ Dialect Options.

-c

Compile or assemble the source files, but do not link. The linking stage simply is not done. The ultimate output is in the form of an object file for each source file.

By default, the object file name for a source file is made by replacing the suffix `.c', `.i', `.s', etc., with `.o'.

Unrecognized input files, not requiring compilation or assembly, are ignored.

C++ string class

2006-02-28T23:27:00.001+08:00

C++ string class

General Programming Information

C++ Vectors

2006-02-28T23:27:00.000+08:00

C++ Vectors

General Programming Information

How to write a Makefile

2006-02-28T23:26:00.000+08:00

How to write a Makefile

Related Course: System Programming

A Nobody's Knowledge Bank

Bioinformatics

Fermentation - Wikipedia, the free encyclopedia

zygomycota

Thiobacillus ferrooxidans

Thiobacillus ferrooxidans

Thiobacillus ferrooxidans

Thiobacillus ferrooxidans

Listeria monocytogenes - Wikipedia, the free encyclopedia

Bacillus thuringiensis

Biotech Basics - How Biotechnology Works

Biotech Basics - How Biotechnology Works

Polymerase chain reaction - Wikipedia, the free encyclopedia

紅麴中的黴菌毒素——Citrinin

Bugs in the News - What the Heck is an E. coli?

What does E.coli mean?

: : 農業生技產業資訊網 : :

Axiom of Choice

Strong connectivity algorithm

1.4.1 Connected Components

Beta Integral -- From MathWorld

Oligopoly - Wikipedia, the free encyclopedia

What's a number?

Rational and Irrational numbers

Lemma 1

Corollary

Lemma 2

Lemma 3

Lemma 4

Lemma 5

Lemma 6

Probability Paradox

An Introduction to Monte Carlo Methods

An Introduction to Monte Carlo Methods

Quorum sensing - Wikipedia, the free encyclopedia

Deinococcus

Pseudomonas

Epulopiscium

Countable and Uncountable Sets

GNU tar 1.15.90

Automating Program Compilation - Writing Makefiles

GCC Manual

C++ string class

C++ Vectors

How to write a Makefile