B********e
发帖数: 19317 | 1 Evolution 101 Table of Contents
1. An introduction to evolution
Evolution briefly defined and explained
2. The history of life: looking at the patterns
How does evolution lead to the tree of life?
* The family tree
* Understanding phylogenies
* Building the tree
* Homologies and analogies
* Using the tree for classification
* Adding time to the tree
* How we know what happened when
* Important events in the history of life
3. Mechanisms: the processes |
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B********e
发帖数: 19317 | 2 http://evolution.berkeley.edu/evolibrary/article/side_0_0/usingparsimony_01
Using parsimony
After studying some major vertebrate lineages and limiting the data to
characters that are likely homologous, you might end up with the following
evidence (note that there are many vertebrate lineages and many characters
excluded from this example for the sake of simplicity):
From studying fossils and lineages closely related to the vertebrate clade,
we hypothesize that the ancestor of vertebrates had non |
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B********e
发帖数: 19317 | 3 http://evolution.berkeley.edu/evolibrary/article/side_0_0/hoxgenes_01
"General purpose" control genes are important elements in building
complicated organisms like flies. Some "control" genes are common to many
organisms (they are homologous — inherited from our common ancestor). For
example, Hox genes help lay out the basic body forms of many animals,
including humans, flies, and worms. They set up the head-to-tail
organization. You can think of them as directing instructions as an embryo
devel |
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q*****g
发帖数: 1568 | 4 【 以下文字转载自 Anthropology 讨论区 】
【 原文由 qiuxing 所发表 】
Diffusion
文化扩散被20世纪早期人类学家们认为是解释很多文化和社会的异同的最有力的工
具。相邻的文化是会互相影响的，比如说美国英语就有无数从别的文化中借来的单
词。
但是不能机械的看待文化扩散，不能机械的认为所有的文化扩散的速率都一样，导
致的结果都一样（比如说文化趋同）。否则的话北爱尔兰人就应该都信一个宗教，
墨西哥人也都该讲英语而不是西班牙语，犹太人也都该承认耶稣是基督了。
另外一个必须注意的是如果拿生物进化来类比，diffusion是不可能在两个不同种
的生物中出现的，因为按照定义，不同种的生物不能交配，所以不可能发生基因的
扩散。所以生物进化是不能回头的，一旦两个基因pool的距离大到一定程度，它们
就分头走向各自的方向，以后可能会出现形式上的相似（homology），但不会有基
因层面上的交流。所以用一个树状结构来描述生物进化是再合适不过了，但对于文
化进化我们就不能这样说。理论上完全可以出现两条分支又融合成为一条的情况，
事实上也有一些（尽管远非主流）这样的例子。
这 |
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D****N
发帖数: 430 | 5 【 以下文字转载自 Anthropology 讨论区,原文如下 】
发信人: qiuxing (球星), 信区: Anthropology
标 题: 读书随笔 -- 18
发信站: Unknown Space - 未名空间 (Wed Nov 5 22:53:25 2003), 站内信件
Diffusion
文化扩散被20世纪早期人类学家们认为是解释很多文化和社会的异同的最有力的工
具。相邻的文化是会互相影响的，比如说美国英语就有无数从别的文化中借来的单
词。
但是不能机械的看待文化扩散，不能机械的认为所有的文化扩散的速率都一样，导
致的结果都一样（比如说文化趋同）。否则的话北爱尔兰人就应该都信一个宗教，
墨西哥人也都该讲英语而不是西班牙语，犹太人也都该承认耶稣是基督了。
另外一个必须注意的是如果拿生物进化来类比，diffusion是不可能在两个不同种
的生物中出现的，因为按照定义，不同种的生物不能交配，所以不可能发生基因的
扩散。所以生物进化是不能回头的，一旦两个基因pool的距离大到一定程度，它们
就分头走向各自的方向，以后可能会出现形式上的相似（homology），但不会有基 |
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E*****m
发帖数: 25615 | 6 公元前4004年， 十月末，生日剛過。
In the beginning — specifically on October 23, 4004 B.C., at noon — out of
quantum foam fluctuation God created the Big Bang. The bang was followed by
cosmological inflation. God saw that the Big Bang was very big, too big for
creatures that could worship him, so He created the earth. And darkness was
upon the face of the deep, so He commanded hydrogen atoms (which He created
out of Quarks and other subatomic goodies) to fuse and become helium atoms
and in the process release... 阅读全帖 |
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a******e
发帖数: 982 | 7 In the beginning — specifically on October 23, 4004 B.C., at noon — out of
quantum foam fluctuation God created the Big Bang. The bang was followed by
cosmological inflation. God saw that the Big Bang was very big, too big for
creatures that could worship him, so He created the earth. And darkness was
upon the face of the deep, so He commanded hydrogen atoms (which He created
out of Quarks and other subatomic goodies) to fuse and become helium atoms
and in the process release energy in the form ... 阅读全帖 |
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D*****r
发帖数: 6791 | 8 I support evolution because of the evidences in gene homology, fossil
records and comparative anatomy. The strength of proof supporting evolution
is far more rigorous than creationism.
Your applying "rigorous proof-checking" for evolution and then blindly
believing in creationism is the evidence of bigotry. |
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l**********t
发帖数: 5754 | 9
"he evidences in gene homology, fossil records and comparative anatomy" |
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d******2
发帖数: 107 | 10 1) We might be able to analyze littletshirts' refutation of evolution for
this "random" assumption by reviewing the anthropic principle(人择原理). I
think it can be applied here. Certain mutations have to happen for the Homo
sapiens to evolve. But that doesn't mean mutations have a guidance or
are intervened by divine objects.
Say you are playing cards. Cards are shuffled and randomly distributed to
players. When we see the cards played by a player, we can get an idea of
what cards the player has. W... 阅读全帖 |
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d******2
发帖数: 107 | 11 Sorry, I am tired, so I'll just try to give a temperary short answer.
The appearance of homo sapiens in evolution is to some extent random and to
some extent deterministic. It is to some extent deterministic because of the
non-random improved chance of survival and reproduction that those mutated
genes confer on individuals who possess them.
I cannot agree to reduce those deterministic side of evolution to randomness
. That would ignore the mechanisms explained by biologists and the multiple
sou... 阅读全帖 |
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D*****r
发帖数: 6791 | 12
Christian
基督教也没明确说自己是建立在“一个万能的人形神存在”的假设基础上啊。你要说地
球生命自然产生可能性很小，那一个万能神自然产生的可能性更小了。这就是为什么人
们用自然原理来解释世界，而不用”万能神“假设。如果这个万能神存在的话，它一定
是忍受了巨大的痛苦，千方百计地隐藏自己和自己创造的过程留下的证据。
演化是非随机的，在不断和周围环境的接触中探索有效利用能源的方式。植物跟叶绿体
联盟转化太阳能，动物跟线粒体联盟掠夺能量储备。
说一个最近的研究吧：蚤状蚤的基因多重复，这些基因的复制件的维护是受环境影响的。
引申一些，生物群体里的基因复制是海量存在的，就算现在随机突变完全停止，现在群
体里已经存在的基因变型的不同组合已经可以维持自然选择所需的多样性了，进化照常
进行，得千年以上才能注意到随机突变停止了。
The Ecoresponsive Genome of Daphnia pulex
http://www.sciencemag.org/content/331/6017/555.abstract?sid=ae7
摘要：
We describe the draft gen... 阅读全帖 |
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l**********t
发帖数: 5754 | 13
sequential in time. God creates the universe and living creatures in steps.
IMHO, the tree structure represents the closeness of difference species,
measured base on certain criteria (phenotpye or gene homology) -- these are
based on scientific evidences as you cited before. So "common ancestor" in
the tree simply represent their level of closeness (as in a cluster analysis
).
But this doesn't mean one species "evolve" into a different species -- the "
evolution" part is an assumption. You choo... 阅读全帖 |
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l**********t
发帖数: 5754 | 14
what evidence? the fossil records & the gene homology only show the RESULTS
of what happened, not the CAUSES for the variations. |
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l**********t
发帖数: 5754 | 15 I believe 不同物種 share common design patterns & building blocks as I
stated before, as shown by scientific research (gene homology, phenotypes
similarities, etc). The differences are deliberately/deterministically
introduced by God with increasing complexity and order. How God achieves
creation is for science to explore (this is not limited to "evolution theory
" of species). |
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q*****g
发帖数: 1568 | 16 Diffusion
文化扩散被20世纪早期人类学家们认为是解释很多文化和社会的异同的最有力的工
具。相邻的文化是会互相影响的，比如说美国英语就有无数从别的文化中借来的单
词。
但是不能机械的看待文化扩散，不能机械的认为所有的文化扩散的速率都一样，导
致的结果都一样（比如说文化趋同）。否则的话北爱尔兰人就应该都信一个宗教，
墨西哥人也都该讲英语而不是西班牙语，犹太人也都该承认耶稣是基督了。
另外一个必须注意的是如果拿生物进化来类比，diffusion是不可能在两个不同种
的生物中出现的，因为按照定义，不同种的生物不能交配，所以不可能发生基因的
扩散。所以生物进化是不能回头的，一旦两个基因pool的距离大到一定程度，它们
就分头走向各自的方向，以后可能会出现形式上的相似（homology），但不会有基
因层面上的交流。所以用一个树状结构来描述生物进化是再合适不过了，但对于文
化进化我们就不能这样说。理论上完全可以出现两条分支又融合成为一条的情况，
事实上也有一些（尽管远非主流）这样的例子。
这是我们拿生物进化来类比文明发展时一定要记住的一个相当本质的不同。 |
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c*******r
发帖数: 6 | 17 there are at least 12 caspases rigt now, they are all cystein proteases,
cut after asp (D) thus the name caspases. they are homologous to CED-3.
they can be divided into different groups, seems caspase-1 (ICE interleukin -1
converting enzyme) and some othe caspases are not very important in apoptosis,
but may play a role in immune responce. the other caspases are important in
apoptosis. they can be further divided into several groups by their role in
apoptosis, caspase 8 and 9 are thought to be |
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l*****k
发帖数: 587 | 18 chromosome problem leads to early death of the fetus, this is actually a good
mechanism for a species in that they don't invest too much on a bad starting
point.
the pairing of chromosome during meiosis will be totally screwed by the
chromosome translocation, so, the percentage can't be calculated accurately as
you stated, as the translocated portion of the chromosome will interfer with
the pairing between homologous chromosomes, the separation won't be like
in normal meiosis.
Thus the chance of |
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M****e
发帖数: 70 | 19 why mouse? mouse models have been used to understand the functions
of the orthologous human genes extensively. clinical investigations
of genes that are related to various diseases have been facilitated
using transgenic mice, such as studies on cystic fibrosis,
myotony dystrophy, obesity, diabetes mellitus. the recent publication
on Science 296:1661, "a comparison of whole-genome shotgun-
derived mouse chromosome 16 and the human genome", has highlighen
the homology shared between these two spec |
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M****e
发帖数: 70 | 20
analyze the homologous genes already known from AT genome to
see what people have done. get the most promising ones for
your project.
you have to verify the subcellular localization of these proteins
(in situ, western, IHC, IF, etc). establish developmental as
well as tissue-specific expression profiles for RNA/protein.
find out whether the expression or localization of these
proteins are induced, and by what kind of conditions. if so,
as you already suggested, investigate their functions under |
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M****e
发帖数: 70 | 21 one of them, a group in China different from the HuaDa Genome
Center, addressed the sequence of chr. 4 for O. sativa (i cannot
remember whethere this is the same subspecie as the draft seq.).
this work showed the 34.6Mb-long chr. 4 has the longest known
centromere in plants, harbors 4658 predicted proteins and 70
tRNAs. it domonstrates syntenies shared with other subspecies,
but little conservation to Arabido psis for gene orders (pay attn.
synteny but not homology).
Nature 420:316
the other gro |
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s*******e
发帖数: 23 | 22 (1)
fusiong protein with a enzyme digestion site. overexpress it and digest.
check media by western.
(2)
EGFP fused to N tel. microscopy
(3)
homology search of the N-ter from database.
(4)
I don't know. :) |
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S*****l
发帖数: 1200 | 23 我知道的有一个Roche的database，应该还在develop过程中，
但现在已经有比较多的数据了。http://mousesnp.roche.com/
另外的还有很多group在做一些跟疾病相关的基因在老鼠中的
homolog的polymorphism，如果你能找到这些paper的话，他们
应该也会提供他们的polymorphism列表或database。 |
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M****e
发帖数: 70 | 24 your question does not provide enough information, at least
you should suggest its possible function, for example,
topology, intracellular domain, etc. this ligand could be
chemical compound, peptide hormone, or protein-protein
interaction activation, etc.
a couple of suggestions if it is an unknown gene:
search for homologous gene, function in model systems from
C elgans, fruit fly to mouse? what is already known?
protein motif analysis (post-translational modification?
proteolysis sites? possi |
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d********r
发帖数: 303 | 25 This is an interesting paper because it elucidated how much information the
comparative genomics can tell us. In this paper, the authors discovered ten
new mycobacteriaphages, sequenced their genome and compared their genomes with
each other. The conclusion is revealing.
1) It shows the mycobacteriaphage genomes are highly mosaic, which means in
some part of the genome the sequence is homologous, while in other area, it is
not. This result shows there is significant horizontal gene transfer am |
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f***j
发帖数: 2 | 26
(序列为MEKVQYLTRSAIRRASTIEMPQQARQKLQNLFINFCL
几次
You need to change default expect value (10) to a higher value. This is what I
got when blast against Arabidopsis proteins. But anyway, since the sequence is
too short, it's hard to find homologs from other species (confidence level is
low).
At1g26270.1 68414.m03205 phosphatidylinositol 3- and 4-kinase family
protein similar to phosphatidylinositol 4-kinase type-II
beta [Homo sapiens] GI:20159767; contains Pfam profile
|
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s*******e
发帖数: 740 | 27 哦，忘了提醒你一下
关于第三点，一般人们并不用target序列做probe，而要把probe选在target区域外
这是因为你的序列也可以randomly整合到genomic DNA中去，而你只想要homologous
recombinate的产物，所以不要用target序列做probe，否则有很多假的positve
Good luck! |
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h*********9
发帖数: 361 | 28 No, totally different. site/gene-specific insertion by homologous
recombination. |
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j*****q
发帖数: 82 | 29 大大们进来看看
两条homo arm一定要一模一样的序列吗？
如果其中一条（长的那条，大概6kbp）中间有大概100bp不到的不同序列，会影响
recombination的efficiency吗？
多谢 |
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n********k
发帖数: 2818 | 30 it depends on what you are doing, and how big the risk u like to take?
Nobody really knows in practice(I
asssume u are doing mice knockout?......for easy targeting locus, it is
likely fine but if you are unlucky, u
might get nothing...if it is easy to correct, I would just remake it,
otherwise go ahead with your targeting and
see what happens...If it were me, I'll definitely remake the construct, it
takes nothing to remake one:))
compare to the targeting,. one step is about a week work, isn't it |
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n********k
发帖数: 2818 | 31 BTw, there are several experts on this board on the topic, maybe they will
have different opinion.... |
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j*****q
发帖数: 82 | 32 多谢ls的。
这100bp不到的序列是一定要加的，类似一个mutation。HR的目的是knock in。因为就
100bp不到的sequences，我就直接做在一个homo arm里了。不知道可不可以。
继续等大大 |
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n********k
发帖数: 2818 | 34 it is a totally different question now...u are talking about two
recombination events or hope to have one non-
perfect recombination event so that u can get in both ur knockin arm and
another 100bp with ur long arm...I
don't know, it could be tricky..I have a friend who did similar things but
used double selections... don't really
have experience with this, so maybe someone else could help...BTW, u could
have asked question more
clearly...no biggie |
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n********k
发帖数: 2818 | 35 Finally u came:)))...I also have a question in this case, so will the
efficiency of desired targeting much lower, or
not really with your experience... Another question is what if the middle
fragment is like 10kb or even more....I
was thinking it would take two recombination events to get them in...then
the efficiency would be really low...
recombination
may
maximize
floxed |
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H****N
发帖数: 997 | 36 Hey how is it going? To your first question, the efficiency will be lower,
but not that much lower. Say if you have 3 kb on the side and 2kb in the
middle, you may have half the efficiency of what you would without the
insertion. As to the second question, if you have a 10kb fragment in the
middle, the chance of getting the desired recombination may be very low. It'
s just my gut feeling and I don't have any actual experience with a long
middle arm. If I were you, I would give it a try, if the |
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n********k
发帖数: 2818 | 37 thanks a lot, don't have anything like that in planning , just something I
thought i shall ask your opinion about
it in case I need to do in the future...so far everything is on track,
finished one study last year and trying to
wrap another one this year and then hope to have more freedom to think about
moving on...
,
It' |
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j*****q
发帖数: 82 | 38 hi, henben,
yes, the less than 100bp contains a loxp site. acutally i am also aware of
two HR event in it. but i dnt have any marker to select the 100bp events.
but it is quite easy to distinguish the insertion.
does it mean the second HR to integrate the 100bp will be very low
efficiency?
does it mean the introduction of 100bp will be just by chance? |
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j*****q
发帖数: 82 | 39 and Happy new year all guys. |
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j*****q
发帖数: 82 | 41 3k+5k的位置。
does it matter？ |
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H****N
发帖数: 997 | 42 Sorry I did not see this earlier. You don't need a selection marker for the
insertion, but you need a genotyping strategy to distinguish the two HR
events. |
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s******y
发帖数: 28562 | 43 For yeast, it will be alright.
For mammalian system...I don't know |
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f**********e
发帖数: 1994 | 44 我 2002 年进 protein structure prediction 这屁行当的时候就是这样想的。
这鸟问题大家已经日了 20+ 年了，结果唯一的结论是 homology modeling 有用。
这种 long-standing 的问题大家会审美疲劳的。不中。 |
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X***n
发帖数: 366 | 45 Try SLIC.
Nature Methods - 4, 251 - 256 (2007)
Published online: 11 February 2007; | doi:10.1038/nmeth1010
Harnessing homologous recombination in vitro to generate recombinant DNA via
SLIC
Mamie Z Li & Stephen J Elledge
4500 bp. Is it possible that I clone this big fragment all at once and get
the
. Many |
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s******y
发帖数: 28562 | 46 你是想问Homologous recombination?
这个很简单啊，就是序列相似的DNA片断在重组酶的作用下发生互换。
其中涉及相似片断的结合，和交叉点(Holliday junction)的切断，
新片断的连接三个步骤。 |
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s******y
发帖数: 28562 | 47
Yes, but will happen in a lower probability. When there is DNA damage,
several signal pathway will activate the recombinase system and increase the
recombination frequency.
What do you mean ? I cannot understand your question.
If you are wondering if we would put a homologous region in the designed
fragment in order to target it to a specific region, then the answer is
"YES, we do".
If you want to know the theory and practice of doing knockout, the easier
way to to look at wikipedia |
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s******y
发帖数: 28562 | 48 It is possible but it is very, very unlikely.
The homology between human are toooo high. A killing food for a particular
race will also have effect for other races, even though with different
extents. |
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s******r
发帖数: 2876 | 49 如果是转基因水稻的话，西方人不爱吃，
就可以实现目标。
It is possible but it is very, very unlikely.
The homology between human are toooo high. A killing food for a particular
race will also have effect for other races, even though with different
extents. |
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g***y
发帖数: 201 | 50 多年没做这个了，知识比较老化。
1.比较两个arm的sequence homology between 129 and B6.
一般的担忧是因为两个strain的序列有差别，可能影响同源重组的效率。但是如果幸运
的话也许你感兴趣的区域两者高度同源。
否则，几个OPTIONs
A。选用B6 derived ES CELL,有些service提供的。
B.让你的arm尽量长. 但是还是不能保证一定会有positive clone,要看运气，并且问题
是plasmid大到一定程度就不稳定了。比较safe的办法是用BAC recombineering做
BAC based construct.
C。 use long-range high fidelity DNA polymerase to PCR 129 genomic sequence.
这个对cloning要求有点高，并且要做sequencing确定没PCR error |
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