In this paper, the authors define a genetic program for stem cells by comparing the transcriptional profiles of mouse embryonic, neural, hematopoietic stem cells and two differentiated cells, the lateral ventricles of the brain and the main cell population of the bone marrow.

The genetic program if defined as follows:

1. Isolate the samples of mouse stem cells and differentiated cells.
   
2. Amplified probes were prepared by in vitro transcription and then hybridized to DNA microarray. To identify the genes used while DNA transcription.
   
3. The array were analyzed by a combination of the Affymetrix Microarray Suite and dChip software.
   
4. The results were validated by public genes database searches and function annotation.
   

在本篇論文中，作者定義出一套尋找與幹細胞有關的基因的操作程序。在這個程序中，它比較了老鼠的胚胎幹細胞 (ESCs)、神經幹細胞 (NSCs)、造血幹細胞  (HSCs) 以及側腦室細胞 (lateral ventricles of the brain) 與骨髓細胞 (main cell population of the bone marrow) 這兩種對應的已分化細胞於 DNA 轉錄至 mRNA 過程中的所得到不同資訊。

此操作程序如下：

1. 將各個幹細胞以及已分化細胞分離出來。
   
2. 經由 mRNA 強化，以 Oligonucleotide arrays 測試它們分別有作用的基因為何。
   
3. 將 Oligonucleotide arrays 分別以 Affymetrix Microarray Suite 和 dChip 兩套軟體
   作分析，並將兩種的測試結果結果相互比較分析。
   
4. 將本次實驗的結果與網路上的基因資料庫相比對以及功能上的檢查，驗證實驗結果的正確性。

The authors summarize many results about the biological reactions, interactions and their relations among one another, and then they show these relations in a network-like or circuit-diagram-like way. How to check the correctness of these interactions or to collect such relations is far beyond our abilities. Howbeit there may be something that we can do, to formalize this into an algorithm problem. Such as given some interactions and draw an edge-length-minimum or edge-use-minimum graph. It seems easy, but how to define the input is difficult. The inputs are involved one another, some are using "and" gates, some are using "or" gates, and some are time concerned. It is so complicated to define a perfect input form, much less to solve such problems.

Though it may be a tough work to formalize the problem. In another way it is an interesting and practical topic to study. If the input form is out of the question, what to be optimized in the output graph (edge, area, vertex etc.) is worth to discuss, too. In fact this may be an NP-complete problem. That means this may be a good subject in algorithms.

作者們總結了許多既知的生化反應、交互作用及反應間彼此的關係並且使用網路似(或說電路圖似)的方式將其關係表現出來。如何証實這些反應關係的正確與否、或收集這些反應關係，已非我們這些演算法專長的能力所及。雖則如此，我們依舊可能可以將此正式定義成一演算法之問題。例如給定各物質間之交互作用，要求繪出使用最短邊線總和或使用邊數總和最少的方式之關係圖。這問題看來容易，然而如何定義其輸入(input)卻是極其困難。輸入的各物質間彼此皆有影響，有些需同時成立方會交互作用、有些則是一者成立即可作用、更有些事實上是與時間相關。光是定義出完美的輸入格式就已經如此麻煩，更遑論要解決這樣的問題了。

雖然正式地定義出這個問題也許是個困難的工作。但就另一方面而言，這也是個有趣且實用的課題。而即使定義出正式的輸入格式是不成問題的，繪出的圖形中要以什麼做為「最佳」的依據也是值得討論，(如使用最少最短的邊、使用最少的點、或使用最少的面積等等)。事實上，這個問題極有可能是NP-Complete的問題。這個意謂這問題在演算法上是個出paper的好材料。

所謂niche是指所指的是讓幹細胞往不同途徑發展的訊號。本篇所研究的是造血幹細胞（HCS）在分子生物層級上的特性。

The hematopoietic microenvironment provides a complex molecular milieu that regulates the self-renewal and differentiation activities of stem cells. We have characterized a stem cell supportive stromal cell line, AFT024, that was derived from murine fetal liver.

方法：
我們首先將從AFT024的CDNA library中取出一些DNA，而這一些library都是跟幹細胞相關的，做為我們正向training 用的data，再來我們由2018個與幹細胞無關的取出一些DNA，找出那一些在幹細胞相關的有出現，但是在幹細胞無關便沒有出現的DNA，做為我們的input，經過Expression Analysis, Bioinformatics, Array Analysis的分析，再放入Stromal Cell Database(StroCDB)中去做比對，來尋找ATF024對於間質細胞的影響（PS.因為間質細胞會影響幹細胞），進而證明ATF024對於見質細胞有明顯的影響。

The picture of hematopoietic stem cell regulation by the microenvironment that emerges from our studies is complex. We are identified a large number of interesting and previously undescribed gene products, suggesting that hematopoietic cell-fate choices will be controlled by multicomponent molecular network. As such, the balance of self-renewal and differentiation is not likely to be governed by single or few stem cell factors, but rather by the integration of many interacting signal inputs.

所謂niche是指所指的是讓幹細胞往不同途徑發展的訊號。本篇所研究的是造血幹細胞（HCS）在分子生物層級上的特性。

在造血微環境中提供了一個複雜的分子背景，使的幹細胞可以自我更新（將原本所應該做的功能抹除）及差異化（指的是一種幹細胞可以分化成不同種類細胞的能力）。我們本篇便是將一個名為ATF024的間質細胞的一些特徵（作用）標示出來，而ATF024是由鼠類胎兒的肝中所粹取出來的。

方法：
我們首先將從AFT024的CDNA library中取出一些DNA，而這一些library都是跟幹細胞相關的，做為我們正向training 用的data，再來我們由2018個與幹細胞無關的取出一些DNA，找出那一些在幹細胞相關的有出現，但是在幹細胞無關便沒有出現的DNA，做為我們的input，經過Expression Analysis, Bioinformatics, Array Analysis的分析，再放入Stromal Cell Database(StroCDB)中去做比對，來尋找ATF024對於間質細胞的影響（PS.因為間質細胞會影響幹細胞），進而證明ATF024對於見質細胞有明顯的影響。

造血幹細胞在微環境中的調控是非常複雜的。我們已經證實許多中間的基因產物是由許多調控網路所產生的，而這一些東西又是由微環境所控制。所以我們知道，幹細胞的自我更新與差異化並不是僅僅由訊號，或是少數的幹細胞分子所控制。

The most characterized stem cells are those responsible for hematopoiesis in the mouse and in the human. Over last four decades, there are some properties found about hematopoiesis. First, stem cells can control the balance between self-renewal and commitment/differentiation. Second, stem cells are multipotent, which means that single stem cell can produce multiple lineage of mature blood cells. Third, stem cells offer a robust proliferative potential for normal blood cell production. Fourth, stem cells are rare. Finally, stem cells are quiescent or slowly cycling in adult hematopoiesis system.

Traditionally, the stem cell follows three central common dogmas. First, it has been assumed that stem cell mainly present in adult tissues. Second, it has been assumed that the stem cells can limit to the mature cells to compose the same tissue. Third, the process of stem cell differentiation is unidirectional and irreversible. However, recently researches denote that there exist some exception of the central dogmas. Therefore, the question that if the central dogmas should be revived arises. Genomics approaches to stem cell biology have a goal that is to apply genomic technologies to unravel the genetic programs of different somatic stem cell population. The presently available technologies allow us to explore the pattern of gene expression in cells at different levels of differentiation. A key aspect of all high-throughout gene expression studies is the ability to mine the dataset using computational approaches.

被研究最透徹的幹細胞是在老鼠跟人類的造血細胞，在過去四十年來，對於造血幹細胞有部份的發現。第一，幹細胞有控制自我更新跟分化的平衡的能力；第二，單一幹細胞可製造出多種的成熟細胞；第三，幹細胞提供足夠的造血(細胞)來源；最後，幹細胞在一般的成熟細胞中是處於不活動或低活動量的狀態。

在傳統的研究中，對於幹細胞的研究遵循著三個中央法則的假設。第一個假設是幹細胞主要會出現在成熟的組織中，第二個假設是幹細胞有限制成熟細胞組成相同組織的能力，第三個假設是幹細胞的分化是單一方向且不可逆的。然而，最近的研究指出，過去遵循的三個假設可能有例外的情況，因此，便有是否要重新定義對於幹細胞假設的疑問。而在基因體有關幹細胞的研究目標便是提出可以提供對於不同情況的幹細胞的解答，最近的研究提供我們在不同階段的分化中尋找基因有表現片段的技術，對於基因表現最主要的部份是以電腦計算的方法找出在資料中資訊的方法。

This paper identifies numerous individual candidate regulatory molecules, but they also pave the way for more global approaches to stem cell biology. A genome-wide gene expression analysis was performed in order to define regulatory pathways in stem cells. Subtracted complementary DNA libraries form highly purified murine fetal liver stem cells were analyzed with bioinformatic and array hybridization strategies. The production of stem cell microarrays will permit the analysis of fluctuations in the genetic program as a function of permutations in self-renewal, commitment, or other stem cell properties. A large percentage of the several thousand gene products that have been characterized correspond to previously undescribed molecules with properties suggestive of regulatory functions. The large collection of gene products will also facilitate proteomic strategies to uncover protein interaction networks. The SCDb will be a resource for the stem cell community and will foster the collaborative and consortial interactions necessary for global approaches to important biological questions.

這篇論文辨識很多獨特的候選調控分子，不過它們也為更總體的接近幹細胞生物學鋪路。

為了定義幹細胞的 regulatory pathways，genome-wide 的基因表現分析被執行. 從高純化鼠類胎兒肝臟幹細胞取出 complementary DNA 用生物資訊及 array hybridization 策略分析。幹細胞微陣列的產物將允許 the analysis of fluctuations in the genetic program as a function of permutations in self-renewal, commitment, or other stem cell properties. 幾千基因生成物中有大量比率它們的特徵符合先前沒有被描述且具有調控功能的分子。大量的收集基因生成物將也促進 proteomic strategies 去發現 protein interaction networks。SCDb (the Stem Cell Batabase) 將是一個資源為了幹細胞社群而且將培養合作和聯盟互動需求為了整體的著手重要的生物問題。

Hematopoietic stem cells (HSC) are defined by self-renewal and multilineage differentiation potentials. We utilized high-density arrays to compare gene expression in highly purified mouse HSC and their mature progeny. One molecule specifically expressed in immature cells is CD27. The CD27 protein is expressed by about 90% of cells in a purified HSC population. Interestingly, the CD27pos cells are enriched for cells with short-term hematopoietic activities ( colony forming potential in vivo and in vitro ), while the minority CD27neg population is more effective in clonal long-term transplantation.

造血幹細胞(Hematopoietic stem cells，HSC) 具有自我更新和分化成各種血液細胞的能力。我們利用高密度陣列( high-density arrays )來比較高度純化的鼠類HSC以及他們成熟後代的基因表現。在未成熟的細胞中，CD27是一個表現特別明確的分子，在高度純化的HSC族群中約有90%的細胞會表現出CD27蛋白質。有趣的是，CD27pos細胞在短期的造血活動中會被強化(在試管或生物體中形成聚落的能力)。相對少數的CD27neg族群則是在移植的長期持續上較為有效。

This paper is about identifying and characterizing the stem cell antigen AA4. This molecule is a type I transmembrane protein whose overall structure suggests a role in cell adhesion. During fetal ontogeny (days 9-14 of development), AA4 is expressed in three major cell types: vascular endothelial cells, aorta-associated hematopoietic clusters, and primitive fetal liver hematopoietic progenitors. In the adult, AA4 is abundant in lung, heart, and whole bone marrow. The observations suggest that AA4 plays a role in cell-cell interactions during hematopoietic and vascular development.

這篇paper主要是在做辨識幹細胞抗原AA4 的特徵。其分子是一種type I 透膜蛋白。這種透膜蛋白的整體結構可能在細胞附著時有重要的功能。在老鼠胎兒發展期間(9~14天)，AA4主要會在三種細胞表現：內皮血管細胞，動脈相關的造血細胞群，以及原始的胎兒肝造血祖細胞；而在成年期AA4則充斥在成年老鼠的心肺和骨髓。觀察結果顯示AA4可能在造血和血管發展期間細胞與細胞交互作用時扮演著重要的角色。

此外，根據網路查詢的資料，實驗用老鼠的平均懷孕天數是19~21天(三週，其他種類的老鼠最快有兩週的)，底下附上一些網址
http://las.nhri.org.tw/pregnant%20mice.htm
http://www.nvri.gov.tw/veter-info/08/08-001.htm

Mammalian blood formation originates in a small population of hematopoietic stem cells. However, currently, the only reliable functional assay system for the most primitive stem cell compartment is long-term in vivo transplantation. A major challenge in stem cell research is the establishment of culture systems that facilitate in vitro maintenance of long-term transplantable stem cell activity. A major challenge in stem cell research is the establishment of culture systems that facilitate in vitro maintenance of long-term transplantable stem cell activity.

We describe a long-term in vitro culture system using a single stromal cell clone (AFT024) that qualitatively and quantitatively supports transplantable stem cell activity present in highly purified. Accordingly, we established and characterized a large panel of conditionally immortalized, cloned stromal cell lines from midgestation fetal liver. This organ was chosen because during development it is where the stem cell compartment undergoes self-renewal expansion in addition to differentiationThe levels of stem cell activity present after 5 weeks of coculture with AFT024 far exceed those present in short-term cytokine-supported cultures. The stem/progenitor cell population is actively proliferating in culture and that the AFT024 cell line.

哺乳動物血液的來源是由造血幹細胞增生.然而目前研究幹細胞可靠的方法是在活體內移植.在試管內的還沒有較可靠的方法.對於在試管內培養幹細胞的困難再於如何提供給幹細胞的一個增殖環境.

在這實驗當中我們使用了AFT024來刺激幹細胞,AFT024可以使幹細胞維持在高純度的狀態.我們選取懷孕中期的老鼠的胎兒肝臟.會選用這器官的目的是因為其在發展過程中,會經歷自我更新(self-renewal).最後實驗得知然而使用AFT024的培養環境下遠勝於組織素(cytokine-supported) .AFT024的確可以刺激幹細胞/祖細胞增殖.

Dlk is a transmembrane protein that possesses six epidermal growth factor-like(EGF-like) sequences at the extracellular domain, a single transmembrane domain and an intracellular tail. The extracellular EFG-like region of Dlk can be released by action of an unknown protease that cuts the extracellular region near the cell membrane. Dlk belongs to the EGF-like homeotic protein family and plays an important role in the differential process of cell. Some proteins like Serrate Delta and Notch are also blong to EGF-like homeotic protein family. Dlk has been involved in several differentiation processes, such as adipogenesis, hematopoiesis and neuroendocrine differentiation.

Hematopoiesis means the complex process that the bone marrow stem cells differentiate to mature corpuscles. In the process of hematopoiesis need many kinds of cytokines and stromal cells that provide support and interact with each other. This paper verified the fetal liver derived stromal cell line（AFT024）contain dlk protein. AFT024 have hematopoietic-supporting ability.

If the soluble protein consisted of the dlk extracellular domain and progenitor cells cocultured in semisolid media which lack for stromal cell, the progenitor cells would not differentiate to mature corpuscles. It means that dlk can`t promote the growth of progenitor cells single. The adipocytic stromal cell be considered the best hematopoietic supporter in general. When the adipocytic stromal cell differentiate to preadipocytes they would not have ability to support. Dlk can restrain the differentiation of adipocytic stromal cell, thus they can always assist hematopoiesis. This shows dlk protein plays an important role in the process of hematopoiesis.

Dlk (delta-like)本身是一種跨膜蛋白質(transmembrane protein)，構造上包含：細胞外區域(extracellular domain)、跨膜區域域(transmembrane domain) 和細胞內區域(intracellular domain)。dlk 的主要構造在於細胞外區域有六個重覆排列的類似表皮細胞生長因(EGF-like)。此外，在這段細胞外的構造上有一處可被酵素作用的切點(proteolytic processing site)，位置約接近細胞膜近側，在經不知名酵素作用後，會產生可溶片段並釋出細胞外去進行作用。dlk 屬於EGF-like homeotic superfamily 的成員之一，被認為在細胞分化過程中可能扮演重要角色。一些蛋白質如 Serrate、Delta 及Notch (Serrate 與Delta 的接受體) 與dlk 同屬EGF-like homeotic superfamily 的成員。dlk 的主要功能包括：抑制脂肪細胞形成、協助造血細胞分化成熟以及參與神經內分泌細胞的分化等。

造血(hematopoiesis)是指把骨髓幹細胞(bone marrow stem cells)分化為成熟的血球細胞，是一個複雜的分化過程。在造血過程中，除了要有多種細胞激素(cytokines)外，還需要一個支撐物(support)，一方面提供細胞附著固定的場所，另一方面可讓細胞和細胞之間進行交互作用。此篇paper證實了來自胎兒肝臟的基質細胞株(AFT024)具有dlk 蛋白質，而此細胞也是具有造血細胞支撐物的功能。

在沒有基質細胞的情況下，把dlk 可溶片段(soluble form)與前驅細胞(progenitor cells)共同培養在半固態(semisolid)培養基中，結果發現並不能讓這些前驅細胞分化成血球細胞，表示在缺乏基質細胞的狀況下，dlk 無法促進前驅細胞的生長。一般認為有能力分化成脂肪細胞（preadipocytes）的脂肪基質細胞（adipocytic stromal cell）是最好的造血支撐物，但是一旦分化成脂肪細胞，這些基質細胞便失去支撐物的功能。而dlk 可以抑制骨髓處的這些基質細胞，使其無法分化成脂肪細胞，如此便可不失去其支撐物的能力，持續著身體的造血功能。由此可知，在造血過程中，dlk 蛋白質扮演著重要的角色。