2013 年 11 月 – AP Biology

Stray Animals Not Safe In Winter

“Winter gives us the opportunity to stay inside and look outside. Snuggle up in thesofa, put a blanket over you,have a cup of hot cocoa, and enjoy the observations on this precious season.

“Winter is the time for comfort, for good food and warmth, for the touch of a friendly hand and for a talk beside the fire: It is the time for home. (the warmth in winter)

BUT what about those who don’t have a home? For them, winter is definitely not a time for comfort, but a time for freezing and hunger.

Homeless people could die of coldness, so could stray animals.

We see the homeless sleep in the subway stations or the underground, where it’s relatively warmer and free of the chilly wind. I don’t see many stray animals stay in the underground for night; perhaps they are afraid of humans. Most often they hide in trash cans, car engine compartment or inside the wheels or the tail pipes where it’s warmer, and to them, safer.

But the truth is it’s not safe at all sleeping inside any of the places above. Especially the latter three. In China every year countless cats are critically injured, even killed inside their “warm spots”. In the morning most people go downstairs, directly get in their cars, start the engine, and head for office. Chances are, a poor kitty was soundly sleeping under the hood of the car and didn’t get a chance to wake up and escape before the car moved and hurt her.

SO next time before starting your car, please take time to check inside the engine compartment, the wheels and the trail tube, see if any small animal is inside. Not just cats, rats, little yellow weasels, which are common here in Hefei are all possible.If you’ve checked and don’t see any of them but still aren’t sure, it’s also a very good idea to sound your horn for a few times and wait for seconds, as my mom always does. Hearing the noise, the small animals are alarmed and would come out and escape.

IF you forget to “release”the little thing and hurt it, please contact the veterinary hospital and get the animal medical treatment as soon as possible. Don’t try moving the animal if he/she is stuck in the wheel or the engine compartment. Don’t move your car, either.

Most of the homeless animals are homeless because some of us bought them and then abandoned them. Most of the wild animals would “break into” our city because we took their homes. Now they are just trying to survive in a strange place without sofa, fireplace or warm woods.Is there any reason why we shouldn’t at least give them a safer spot for overnight?

Mendel’s Genetics [7]: handling problems

In college, while learning genetics, you may be faced with data obtained from F1 and F2 generations of the crosses. And you are required to be able to recognize ratios in order to decide how many genes are involved, and whether or not epistasis (which we talked about last section) is taking place.

Example(1)

A cross between two pure-breeding white-fruited tomato plants produced and F1 generation which all plants had purple fruit. In the subsequent F2 generation 160 plants were obtained; of these 94 had purple fuit, and the rest had white fruit.

As we know nothing about the genes controlling fruit color in tomato, we must first ask ourselves a question: “DOES THE DATA FIT ANY OF THE KNOWN MENDELIAN RATIOS?”

Since only two phenotypes are involved, it can’t be 9:3:3:1, or 9:3:4 or any mendelian ratios with more than 2 numbers included.

On examination of ratios with 2 phenotypes, 9:7 looks like a possible candidate, but 3:1 may also fit.

In this case, to decide which is the best to fit the data, we introduce a new approach to this problem: the Chi-square test.

Chi-square( test)=
sum[(obseved expected)ˆ2/expected]

(Xˆ2 is always calculated from original data, never from percentages, frequencies or proportions.)

If Xˆ2 is large, the data doesn’t fit. A perfect fit gives Xˆ2 a zero. BUT HOW LARGE IS LARGE?

In addition to the result of Xˆ2, we need another piece of info to determine “how large is large”. We need to know the degrees of freedom.

Degrees of freedom are one less than the number of classes. They tell us something about the number of independent numbers we have, which relates to the usefulness of our data.

In this example, we have two phenotypic classes, purple, and white. It means when we have counted the purple ones, the number of the white ones is fixed so we have only one degree of freedom.

If we had three classes, we would have two degrees of freedom: when the two classes have been counted, the number of the third is fixed.

As the degrees of freedom gets bigger, Xˆ2 gets bigger. So the answer of HOW LARGE IS LARGE depends on different degrees of freedom.

In this example, we determine which ratio is the best fit by comparing the value of Xˆ2

Observed result: 94 purple 66 white

Result predicted by 9:7 ratio 160×9/16 =90 160×7/16 =70

Xˆ2=[(94-90)ˆ2/90]+[(66-70)ˆ2/70]=0.41,with one degree of freedom

Result predicted by 3:1 ratio 160×3/4=120 160×1/4=40

Xˆ2=[(94-120)ˆ2/120]+[(66-40)ˆ2/40]=22.5,with one degree of freedom

Using Xˆ2 probability tables can help quickly get to the value of Xˆ2.

the x2 ditribution table — X2 PROBABILITY TABLE, from “Instant Notes in Genetics”

How to use it?

Follow the line for the one degree of freedom(top line) to find the nearest values of xˆ2 above and below our value.

We can see that the value of 0.41 is between the probability of 0.975 and 0.050 with an affinity to 0.975, which means that if we repeated the experiment 1000 times, we have a probability close to 97.5% that the observed ratio would fit 9:7. The value of 22.5 is way beyond way exceeded with the probability of 0.001, which suggests that 3:1 ratio doesn’t fit the data.

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Data analysis after class:

A cross between pure-breeding white-fruited and purple-fruited tomato plants produced and F1 generation which all plants had purple fruit. In the subsequent F2 generation 160 plants were obtained; of these 99 had purple fuit, 25 had red fruit, and 36 had white fruit.

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卡方检验是以χ2分布为基础的一种常用假设检验方法，它的无效假设H0是：观察频数与期望频数没有差别。

该检验的基本思想是：首先假设H0成立，基于此前提计算出χ2值，它表示观察值与理论值之间的偏离程度。根据χ2分布及自由度可以确定在H0假设成立的情况下获得当前统计量及更极端情况的概率P。如果P值很小，说明观察值与理论值偏离程度太大，应当拒绝无效假设，表示比较资料之间有显著差异；否则就不能拒绝无效假设，尚不能认为样本所代表的实际情况和理论假设有差别。

the blueprint of life [7]: prokaryotic chromosome structure of DNA

First, let’s make sure the anatomy of prokaryotes are familiar to us:

Prokaryotes are the simplest living cells, typically 1~10μm in diameter, and are found in all environmental niches from the guts of the animals to acidic hot springs.

They are bounded by a cell (plasma)membrane comprising a lipid bilayer, in which are embeded proteins that allow the exit and entry of small molecules.
Most prokaryotes also have a rigid cell wall outside the plasma membrane, which prevents the cell from swelling or shrinking in environments where osmolarity differs significantly from that inside the cell.
Sometimes the cell wall is surrounded by an (often) polysaccharide envelope called capsule.
The cell interior (cytoplasm or cytosol) usually contains a single, circular chromosome compacted into a nucleoid and attached to the membrane.
There are no distinct subcelluar organelles in prokaryotes as in eukaryotes(except for the ribosomes核糖体).
The surface of a prokaryote may carry pili, which allow the prokaryote to attach to other cells and surfaces. Some prokaryotes also carry flagella, whose rotating motion allows the cell to swim.

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To talk about prokaryotic chromosome structure, we use E. coli (大肠杆菌)as the example.

E. coli chromosome contains a single supercoiled circular DNA molecule of length 4.6 million bp.
E. coli chromosome is highly folded: 1500 µm of DNA length versus ~1 µm of cell size, forming a structure called the nucleoid.
The nucleoid has a very high DNA concentration, perhaps 30~50 mg/ml, as well as containing all the proteins associated with DNA, such as polyerases, repressors(a protein that is determined by a regulatory gene, binds to a genetic operator, and inhibits the initiation of transcription of messenger RNA), etc.

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DNA domains (loops)

Remember this famous electron micrograph of an E. coli cell we showed before? The cell was carefully lysed, all the proteins removed and then, it was spread on an EM grid to reveal all of its DNA.

Several of such experiments revealed one level of organization of the nucleoid.

The DNA consists of 50~100 domains or loops, about 50~100 kb in size (kb: kilobase, a unit of measure of the length of a nucleic-acid chain that equals one thousand base pairs).
The ends of the loops are constrained by binding to a structure which probably consists of proteins attached to part of the cell membrane.
Not known whether the loops are static or dynamic, but one model suggests that the DNA may spool(wind) through sites of polyerase or other enzymic action at the base of the loops.

E coli DNA instant notes

image above is from”Instant Notes in Molecular Biology”

Supercoiling of the genome

The E. coli chromosome as a whole is negatively supercoiled, although there is some evidence that indicates individual domains may be supercoiled independently. Electron micrographs indicate that some domains may not be supercoiled, perhaps because the DNA has become broken in one strand, where other domains clearly do contain supercoils.

The domains may be topologically independent. There is, however, no real biochemical evidence for major differences in the level of supercoiling in different regions of the chromosome in vivo

DNA-binding proteins

The looped DNA domains of the chromosome are constrained further by inter-action with a number of DNA-binding proteins.

The most abundant of these are protein HU, a small basic (+charged) dimeric protein, which binds DNA non-specifically by the wrapping of the DNA aorund the protein.

And H-NS (formerly known as the protein H1), a monomeric neutral protein, which also binds DNA non-specifically in terms of sequence, but seems to have a preference for regions of DNA which are intrinsically bent.

These proteins are sometimes known as histone-like proteins, and have the effect of compacting the DNA, which is essential for the packaging of the DNA into the nucleoid, and of stabilizing and constraining the supercoiling of the chromosome.

Illustrations of wild animals [insect 8 Diptera]

双翅目DIPTERA

Diptera

True Flies / Mosquitoes / Gnats / Midges

The name Diptera, derived from the Greek words “di”meaning two and “ptera” meaning wings, refers to the fact that true flies have only a single pair of wings.

Classification & Distribution

Holometabola

complete development (egg, larva, pupa, adult)

The Diptera have traditionally been divided into three suborders:

Nematocera (flies with multisegmented antennae)
Brachycera (flies with stylate antennae)
Cyclorrhapha (flies with aristate antennae)

In some newer classifications, Brachycera includes the Cyclorrhapha.

Distribution: Abundant worldwide. Larvae are found in all fresh water, semi-aquatic, and moist terrestrial environments.

	North America	Worldwide
Number of Families	108	130
Number of Species	16,914	~98,500

Life History & Ecology

The order Diptera includes all true flies. These insects are distinctive because their hind wings are reduced to small, club-shaped structures called halteres – only the membranous front wings serve as aerodynamic surfaces. The halteres vibrate during flight and work much like a gyroscope to help the insect maintain balance.

All Dipteran larvae are legless. They live in aquatic (fresh water), semi-aquatic, or moist terrestrial environments. They are commonly found in the soil, in plant or animal tissues, and in carrion or dung — almost always where there is little danger of desiccation. Some species are herbivores, but most feed on dead organic matter or parasitize other animals, especially vertebrates, molluscs, and other arthropods. In the more primitive families (suborder Nematocera), fly larvae have well-developed head capsules with mandibulate mouthparts. These structures are reduced or absent in the more advanced suborders (Brachycera and Cyclorrhapha) where the larvae, known as maggots, have worm-like bodies and only a pair of mouth hooks for feeding.

Adult flies live in a wide range of habitats and display enormous variation in appearance and life style. Although most species have haustellate mouthparts and collect food in liquid form, their mouthparts are so diverse that some entomologists suspect the feeding adaptations may have arisen from more than a single evolutionary origin. In many families, the proboscis (rostrum) is adapted for sponging and/or lapping. These flies survive on honeydew, nectar, or the exudates of various plants and animals (dead or alive). In other families, the proboscis is adapted for cutting or piercing the tissues of a host. Some of these flies are predators of other arthropods (e.g., robber flies), but most of them are external parasites (e.g., mosquitoes and deer flies) that feed on the blood of their vertebrate hosts, including humans and most wild and domestic animals.

Physical Features

Immatures:

Culiciform
- Head capsule present with chewing mouthparts
- Legs absent
Vermiform (maggots)
- Without legs or a distinct head capsule
- Mouthparts reduced; only present as mouth hooks

Adults:

Antennae filiform, stylate, or aristate
Mouthparts suctorial (haustellate)
Mesothorax larger than pro- or metathorax
One pair of wings (front); hind wings reduced (halteres)
Tarsi 5-segmented

Major Families

Biting flies: In most cases, only the adult females take blood meals.♦
Herbivores: larvae feed on plant tissues.
Scavengers: larvae feed in dung, carrion, garbage, or other organic matter.
Predators: adults and/or larvae attack other insects as prey.:
Parasites: larvae are parasites or parasitoids of other animals.
Bug Bytes ♣
- Although they have only two wings, flies are among the best aerialists in the insect world – they can hover, fly backwards, turn in place, and even fly upside down to land on a ceiling.
- Flies have the highest wing-beat frequency of any animal. In some tiny midges, it may be as high as 1000 beats per second. Male mosquitoes are attracted by the wing-beat frequency of a virgin female.
- Larvae of some shore flies (family Ephydridae) live in unusual habitats that would kill other insects. For example, Ephydra brucei lives in hot springs and geysers where the water temperature exceeds 112 degrees Fahrenheit; Helaeomyia petrolei develop in pools of crude oil; and the brine fly, Ephydra cinera, can survive very high concentrations of salt.
- The arista in the antenna of higher flies is an air speed indicator. It allows the insect to sense how fast it is moving.
- As they mature, black fly pupae become inflated with air. Upon emergence, the pupal skin pops open and the adult fly floats to the water surface inside a bubble of air. It never even gets its feet wet!
- The little scuttle fly, Megaselia scataris (Phoridae), is truly an omnivore. It has been reared from decaying vegetation, shoe polish, paint emulsions, human cadavers pickled in formalin, and even lung tissue from living people.

====================================================↑Quoted from the General Entomology course at North Carolina State University >Resource Library > Compendium > diptera (© 2009 by John R. Meyer; Last Updated: 8 April 2009)

>Learn more about homoptera (www.insectsexplained.com)

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虻科Tabanidae(horse flies / deer flies, biting flies)

虻Tabanus sp.

大蚊科Tipulidae (crane flies, scavengers )

1. 大蚊 Tipua sp.

2. 斑大蚊 Nephrotoma appendiculata

3. 亮大蚊 Limonia sp

4. 雅大蚊Tipula sp.

5. 双色丽大蚊Tipula sp.

6. 短柄大蚊 Nephrotoma sp.

寄蝇科Tachinidae(parasites of other insects)

1. 绒寄蝇Tachina sp.

2.长须寄蝇Peletina sp.

3. 灰等腿寄蝇 Isomera cinerascens

4. 柞蚕饰腹寄蝇 Blepharipa tibialis

食蚜蝇科Syrphidae

1. 双色小蚜蝇Paragus bicolor

2. 亮黑斑眼蚜蝇Eristalinus tarsalis

3. 三带蜂蚜蝇Volucella trifasciata

4. 凹带蚜蝇Metasyrphus nitens

5. 紫额异巴蚜蝇Allobacha apicalis

6.切黑狭口蚜蝇 Asarkina ericetorum

7. 宽带细腹蚜蝇Sphaerophoria macrogaster

8. 宽盾蚜蝇Phytomia sp.

the blueprint of life [6]: Chromosomal Structure of DNA 1

vocabulary

•Nucleus: 细胞核; Nucleolus: 核仁; Nucleoid: 类核

• Mitosis: 有丝分裂; Meiosis: 减数分裂

Interphase: 分裂间期; Prophase: 分裂前期; Metaphase: 分裂中期; Anaphase: 分裂后期; Telophase: 分裂末期

• Histone: 组蛋白

• Nucleosome: 核小体

•Chromosome: 染色体; Chromatin: 染色质; eu- 真染色质; hetero- 异染色质

• Centromere: 中心粒; Telomere: 端粒

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WHAT is chromosome:

Structure containing the genes of a cell and made of a single DNA molecule and its associated proteins.

CHROMOSOMES OF EUKARYOTES, shown by prof. Dong

HOW long is DNA in an chromosome
HOW LONG IS DNA, shown by prof. Dong.

→A chromosome is too long to fit into a cell without compaction.

WHY is DNA packed into chromosomes

Chromosome is a compact form of the DNA that readily fits inside the cell
To protect DNA from damage
DNA in a chromosome can be transmitted efficiently to both daughter cells during cell division
Chromosome confers an overall organization to each molecule of DNA, which regulates gene expression as well as recombination

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Diversity of chromosomes

in terms of:

Shape: circular or linear
Number: species-specific

eg. -fruitfly 8; -human 46; -horse 64; -dog 78; -chicken 78

-maize 20; -rice 24; -wheat 42

Copy number: haploid单倍体, diploid双倍体, polyploid 多倍体

Overall structure: highly different between prokaryotes 原核生物and eukaryotes真核生物

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Next section we will first talk about prokaryotic chromosome structure of DNA.

Flight Behavior: What Is The Use of Saving A Planet That Has No Soul Left In It?

World consumption of paper has grown 400 percent in the last 40 years. Now nearly 4 billion trees or 35 percent of the total trees cut around the world are used in paper industries on every continent.(source)

For the trees’ sake, please please please please use e-books!

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Flight Behavior by Barbara Kingsolver
Pages: 448
Release Date: November 6, 2012
Publisher: Harper
Genre: Literary Fiction

A novel you wouldn’t put down once opening the first page.

Barbara wrote with close attention to language and intelligent arrangement of plot. Only having read the first chapter, you would never get right what the novel is really about.

Generally, the 2012 novel focuses on the interactions between humans and the natural environmental they are living in, which leads to a core topic of today’s environmental situation:climate change. But not like what we read in Science, where climate change is drawn in a scientific way. No logical reasoning, non data analysis, climate change in Flight Behavior is lyrically written, tragic, sad, forcing innocent monarch butterflies abandon their hometown (also original wintering habitat) and flew all the way to a small town in southern U.S for survival.

Family matters, communities, scientists, butterflies, climate change, meanings of life, faith…

No more spoilers, hope you enjoy this book and after reading it, would see more respects in environmental conservation.

Illustrations of wild animals [insect 7 Homoptera 2]

同翅目 HOMOPTERA

角蝉科 Membracidae

1. 黑圆角蝉Gargara genistae

2. 小截角蝉 Truncatocornum parvum

沫蝉科 Cercopidae

1. 斑带丽沫蝉Cosmoscarta bispecularis

2. 东方丽沫蝉 Cosmoscarta heros

3. 紫胸丽沫蝉Cosmoscarta exultans

4. 象沫蝉 Philagra sp.

白纹象沫蝉Philagra aibinotata

6. 尖胸沫蝉Aphrophora sp.

蜡蝉科 Fulgoridae

1. 斑衣蜡蝉Lycirma delicatula

2. 雪白粒脉蜡蝉 Nisia atrovenosa

Mendel’s Genetics [6]: Examples of epistasis

In Mendel’s dihybrid cross, each gene locus(the position of a gene along a chromosome, often used to refer to the gene itself.) had an independent effect on a single phenotype. Thus, the R and r alleles affected only the shape of the seed and had no influence on seed color, while the Y and y alleles affected only seed color and had no influence on seed shape. In this case, there were two separate genes that coded for two separate characteristics.

But what happens when two different loci affect the same characteristic? For instance, what if both of the loci in Mendel’s experiment affected seed color?

Let’s begin with a relatively simple example.

example (1) 9:3:3:1→9:7

enzyme A serves to convert white substrate in an unnamed plant to white product; enzyme B synthesizes purple pigment and converts the white product to purple product.

In this case, If BOTH A & B exist, purple product is yielded;

If ONLY A OR B exists, synthesis of purple pigment cannot be completed, and purple product won’t be produced;

If NEITHER ENZYME exist, purple pigment, surely, cannot be synthesized, and purple product won’t be produced.

Based on the info above, the dihybrid F2 generation looks like this:

When the situation gets a little bit more complicated:

example (2) 9:3:3:1→9:3:4

enzyme A serves in the synthesis of red pigment and converts white substrate in an unnamed plant to red product; enzyme B synthesizes purple pigment and converts the red product to purple product.

In this case, If BOTH A & B exist, purple product is yielded;

If ONLY A exists, synthesis of red pigment can be completed but synthesis of purple pigment cannot, and red product will be produced;

If NEITHER ENZYME exist or ONLY B exists, surely, neither red or purple pigment, can be synthesized, and the the yield will be white.

Based on the info above, the dihybrid F2 generation looks like this:

A more complex situation:

example (3): 9:3:3:1→12:3:1

Here two enzymes compete for the same substrate. Enzyme A converts the substrate to a purple product, and enzyme B to a red product. BUT enzyme A has much higher affinity for the substrate than enzyme B. The difference in affinity is so marked that enzyme B can only work effectively without the presence of enzyme A

SO as long as enzyme A is present, the yield is be purple; only when enzyme B exists without enzyme A would the yield be red; and only when neither B or A exists would the yield be white.

Based on the info above, the dihybrid F2 generation looks like this:

[F2] purple: red: white=12: 3: 1

The three examples above lead us to a new concept: Epistasis.

Sometimes genes can mask each other’s presence or combine to produce an entirely new trait. Epistasis describes how gene interactions can affect phenotypes.

In a strict sense, 12: 3: 1 is the only ratio which was originally referred to as epistasis, because the presence of enzyme A can completely make the genotype of the B gene. But the term is now used wherever genes interact to alter the expected ratios.

There are several other variations of the 9:3:3:1 ratio caused by interaction between the gene products, including 9:6:1, 15:1, and 13:3.

In every case the ratios are derived by summing together the four phenotype classes 9, 3, 3, or 1 of the basic ratio.

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For more examples and explanations of the Epistasis, see Epistasis and Its Effects on Phenotype | Learn Science at Scitable

The blueprint of life [5]: spectroscopic and thermal properties of DNA

UV absorption

DNA absorbs UV light due to the conjugated aromatic nature of the bases; the sugar-phosphate backbone does not contribute appreciably(perceptibly/measurably) to absorption.

The wavelength of maximum absorption of light by both DNA and RNA is 260 nm, which is conveniently distinct from the λmax of protein(280 nm).

The absorption properties of DNA can be used for detection, quantitation and assessment of property.

Hypochromicity

UV absorption at 260nm is greatest for isolated nucleotides, intermediate for single-stranded DNA(ssDNA) or RNA, and least for double-stranded DNA(dsDNA)

The classical term for the change in absorbance is hypochromicity. For example, dsDNA is hypochromic (from the Greek for ‘less colored‘) relative to ss DNA, which is hypochromic relative to isolated nucleotides.

Thermodynamics of DNA

Denaturation: the transition of macromolecule from the native state to the denatured state. For DNA, under denaturing conditions (heating or high pH), double helix is separated to generate single-stranded form.

Melting Temperature(Tm): the temperature at which the rise in A260(absorbance at 260nm) is half complete during denaturation.

Factors that affect the Tm

1. G+C content: the higher G+C content, the higher Tm.

2. Ionic strength: The Tm increases as the cation (+) concentration increases. like Na+, K+ or Mg2+.

3. High pH or Agents that disrupt H-bonds or interfere with base stacking: formamide (甲酰胺)or urea (尿素)will decrease the Tm.

4. The imperfect hybridization between related but not completely complementary strands will reduce the Tm, about 1 °C for each percent mismatch.

The process of denaturation can be observed conveniently by the increase in absorbance as double-stranded nucleic acids are converted to single strands

Renaturation: Process of a macromolecule returning to its native 3-D structure. For DNA this involves the two strands of denatured DNA basepairing to restore the nature form of dsDNA. Also known as reannealing (重退火).

Requirements for renaturation:

1. Proper salt concentration: neutralize electrostatic repulsion

2. Proper reannealing temperature: 20-25℃ below Tm

Determinants for renaturation efficiency

(DNA renatures on cooling, but will form fully double-stranded native DNA only if the cooling is sufficiently slow to allow the complementary strands to anneal.)

1. Extent of base matching and

2. copy of matching regions

Thus, repetitive DNA renatures faster than single copy DNA

RENATURATION CURVES FOR E.COLI &MOUSE DNA, shown by prof. Dong

Example(1)

双翅目DIPTERA

Life History & Ecology

Immatures:

Adults:

虻科Tabanidae(horse flies / deer flies, biting flies)

寄蝇科Tachinidae(parasites of other insects)

食蚜蝇科Syrphidae

vocabulary

Diversity of chromosomes

同翅目 HOMOPTERA

角蝉科 Membracidae

沫蝉科 Cercopidae

蜡蝉科 Fulgoridae

Let’s begin with a relatively simple example.

When the situation gets a little bit more complicated:

A more complex situation:

The three examples above lead us to a new concept: Epistasis.

UV absorption

Thermodynamics of DNA

Thermodynamics of DNA